Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, F-ST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program

Studies of braided non-Abelian anyons using anyonic tensor networks

The content of this thesis can be broadly summarised into two categories: first, I constructed modified numerical algorithms based on tensor networks to simulate systems of anyons in low dimensions, and second, I used those methods to study the topological phases the anyons form when they braid around one another. In the first phase of my thesis, I extended the anyonic tensor network algorithms, by incorporating U(1) symmetry to give a modified ansatz, Anyon-U(1) tensor networks, which are capable of simulating anyonic systems at any rational filling fraction. In the second phase, I used the numerical methods to study some models of non-Abelian anyons that naturally allows for exchange of anyons. I proposed a lattice model of anyons, which I dubbed anyonic Hubbard model, which is a pair of coupled chains of anyons (or simply called anyonic ladder). Each site of the ladder can either host a single anyonic charge, or it can be empty. The anyons are able to move around, interact with one another, and exchange positions with other anyons, when vacancies exist. Exchange of anyons is a non-trivial process which may influence the formation of different kinds of new phases of matter. I studied this model using the two prominent species of anyons: Fibonacci and Ising anyons, and made a number of interesting discoveries about their phase diagrams. I identified new phases of matter arising from both the interaction between these anyons and their exchange braid statistics.Comment: 150 pages, PhD thesis, Macquarie University, Sydney. Chapter 6 of this thesis titled "Phase transitions in braided non-Abelian anyonic system" contains results which are yet to be finalised and publishe

On Random Bubble Lattices

We study random bubble lattices which can be produced by processes such as first order phase transitions, and derive characteristics that are important for understanding the percolation of distinct varieties of bubbles. The results are relevant to the formation of topological defects as they show that infinite domain walls and strings will be produced during appropriate first order transitions, and that the most suitable regular lattice to study defect formation in three dimensions is a face centered cubic lattice. Another application of our work is to the distribution of voids in the large-scale structure of the universe. We argue that the present universe is more akin to a system undergoing a first-order phase transition than to one that is crystallizing, as is implicit in the Voronoi foam description. Based on the picture of a bubbly universe, we predict a mean coordination number for the voids of 13.4. The mean coordination number may also be used as a tool to distinguish between different scenarios for structure formation.Comment: several modifications including new abstract, comparison with froth models, asymptotics of coordination number distribution, further discussion of biased defects, and relevance to large-scale structur

Can a Higher Protein/Low Glycemic Index vs. a Conventional Diet Attenuate Changes in Appetite and Gut Hormones Following Weight Loss? : A 3-Year PREVIEW Sub-study

Background: Previous research showed that weight-reducing diets increase appetite sensations and/or circulating ghrelin concentrations for up to 36 months, with transient or enduring perturbations in circulating concentrations of the satiety hormone peptide YY. Objective: This study assessed whether a diet that is higher in protein and low in glycemic index (GI) may attenuate these changes. Methods: 136 adults with pre-diabetes and a body mass index of >= 25 kg/m(2) underwent a 2-month weight-reducing total meal replacement diet. Participants who lost >= 8% body weight were randomized to one of two 34-month weight-maintenance diets: a higher-protein and moderate-carbohydrate (CHO) diet with low GI, or a moderate-protein and higher-CHO diet with moderate GI. Both arms involved recommendations to increase physical activity. Fasting plasma concentrations of total ghrelin and total peptide YY, and appetite sensations, were measured at 0 months (pre-weight loss), at 2 months (immediately post-weight loss), and at 6, 12, 24, and 36 months. Results: There was a decrease in plasma peptide YY concentrations and an increase in ghrelin after the 2-month weight-reducing diet, and these values approached pre-weight-loss values by 6 and 24 months, respectively (P = 0.32 and P = 0.08, respectively, vs. 0 months). However, there were no differences between the two weight-maintenance diets. Subjective appetite sensations were not affected by the weight-reducing diet nor the weight-maintenance diets. While participants regained an average of similar to 50% of the weight they had lost by 36 months, the changes in ghrelin and peptide YY during the weight-reducing phase did not correlate with weight regain. Conclusion: A higher-protein, low-GI diet for weight maintenance does not attenuate changes in ghrelin or peptide YY compared with a moderate-protein, moderate-GI diet.Peer reviewe

Predicting global habitat suitability for stony corals on seamounts

Aim Globally, species distribution patterns in the deep sea are poorly resolved, with spatial coverage being sparse for most taxa and true absence data missing. Increasing human impacts on deep-sea ecosystems mean that reaching a better understanding of such patterns is becoming more urgent. Cold-water stony corals (Order Scleractinia) form structurally complex habitats (dense thickets or reefs) that can support a diversity of other associated fauna. Despite their widely accepted ecological importance, records of scleractinian corals on seamounts are patchy and simply not available for most of the global ocean. The objective of this paper is to model the global distribution of suitable habitat for stony corals on seamounts. Location Seamounts worldwide. Methods We compiled a database containing all accessible records of scleractinian corals on seamounts. Two modelling approaches developed for presence-only data were used to predict global habitat suitability for seamount scleractinians: maximum entropy modelling (Maxent) and environmental niche factor analysis (ENFA). We generated habitat-suitability maps and used a cross-validation process with a threshold-independent metric to evaluate the performance of the models. Results Both models performed well in cross-validation, although the Maxent method consistently outperformed ENFA. Highly suitable habitat for seamount stony corals was predicted to occur at most modelled depths in the North Atlantic, and in a circumglobal strip in the Southern Hemisphere between 20° and 50° S and shallower than around 1500 m. Seamount summits in most other regions appeared much less likely to provide suitable habitat, except for small near-surface patches. The patterns of habitat suitability largely reflect current biogeographical knowledge. Environmental variables positively associated with high predicted habitat suitability included the aragonite saturation state, and oxygen saturation and concentration. By contrast, low levels of dissolved inorganic carbon, nitrate, phosphate and silicate were associated with high predicted suitability. High correlation among variables made assessing individual drivers difficult. Main conclusions Our models predict environmental conditions likely to play a role in determining large-scale scleractinian coral distributions on seamounts, and provide a baseline scenario on a global scale. These results present a first-order hypothesis that can be tested by further sampling. Given the high vulnerability of cold-water corals to human impacts, such predictions are crucial tools in developing worldwide conservation and management strategies for seamount ecosystems. © 2009 Blackwell Publishing Ltd

Developing Successful Breeding Programs for New Zealand Aquaculture: A Perspective on Progress and Future Genomic Opportunities

Over the past 40 years New Zealand (NZ) aquaculture has grown into a significant primary industry. Tonnage is small on a global scale, but the industry has built an international reputation for the supply of high quality seafood to many overseas markets. Since the early 1990s the industry has recognized the potential gains from selective breeding and the challenge has been to develop programs that can overcome biological obstacles (such as larval rearing and mortality) and operate cost-effectively on a relatively small scale while still providing significant gains in multiple traits of economic value. This paper provides an overview of the current status, and a perspective on genomic technology implementation, for the family based genetic improvement programs established for the two main species farmed in NZ: Chinook (king) salmon (Oncorhynchus tshawytscha) and GreenshellTM mussel (Perna canaliculus). These programs have provided significant benefit to the industry in which we are now developing genomic resources based on genotyping-by-sequencing to complement the breeding programs, enable evaluation of the genetic diversity and identify the potential benefits of genomic selection. This represents an opportunity to increase genetic gain and more effectively utilize the potential for within family selection

Towards an integrated molecular model of plant-virus interactions

[EN] The application in recent years of network theory methods to the study of host-virus interactions is providing a new perspective to the way viruses manipulate the host to promote their own replication. An integrated molecular model of such pathosystems require three detailed maps describing, firstly, the interactions between viral elements, secondly, the interactions between host elements, and thirdly, the cross-interactions between viral and host elements. Here, we compile available information for Potyvirus infecting Arabidopsis thaliana. With an integrated model, it is possible to analyze the mode of virus action and how the perturbation of the virus targets propagates along the network. These studies suggest that viral pathogenicity results not only from the alteration of individual elements but it is a systemic property.This work was supported by the grant BFU2009-06993 from the Spanish Ministry of Science and Innovation to S.F.E. G.R. thanks an EMBO long-term fellowship co-funded by Marie Curie actions (ALTF-1177-2011).Elena Fito, SF.; Rodrigo Tarrega, G. (2012). Towards an integrated molecular model of plant-virus interactions. Current Opinion in Virology. 2(6):719-724. https://doi.org/10.1016/j.coviro.2012.09.004S7197242

Developing a matrix to identify and prioritise research recommendations in HIV Prevention

BACKGROUND: HIV prevention continues to be problematic in the UK, as it does globally. The UK Department of Health has a strategic direction with greater focus on prevention as part of its World Class Commissioning Programme. There is a need for targeted evidence-based prevention initiatives. This is an exploratory study to develop an evidence mapping tool in the form of a matrix: this will be used to identify important gaps in contemporary HIV prevention evidence relevant to the UK. It has the potential to aid prioritisation in future research.METHODS: Categories for prevention and risk groups were developed for HIV prevention in consultation with external experts. These were used as axes on a matrix tool to map evidence. Systematic searches for publications on HIV prevention were undertaken using electronic databases for primary and secondary research undertaken mainly in UK, USA, Canada, Australia and New Zealand, 2006-9. Each publication was screened for inclusion then coded. The risk groups and prevention areas in each paper were counted: several publications addressed multiple risk groups. The counts were exported to the matrix and clearly illustrate the concentrations and gaps of literature in HIV prevention.RESULTS: 716 systematic reviews, randomised control trials and other primary research met the inclusion criteria for HIV prevention. The matrix identified several under researched areas in HIV prevention.CONCLUSIONS: This is the first categorisation system for HIV prevention and the matrix is a novel tool for evidence mapping. Some important yet under-researched areas have been identified in HIV prevention evidence: identifying the undiagnosed population; international adaptation; education; intervention combinations; transgender; sex-workers; heterosexuals and older age groups.<br/