title: Induced reproduction in Pātiki (Rhombosolea leporina), a novel endemic aquaculture candidate

authors: Ellis-Smith, Brooke Georgia

subjects: Aquaculture

abstract: The rapid global population growth combined with the decline of wild-capture fisheries has resulted in the global expansion of aquaculture. New Zealand’s aquaculture industry remains largely underdeveloped and as such, industry growth would benefit from species diversification. The endemic yellowbelly flounder (Rhombosolea leporina) is a promising candidate species for New Zealand aquaculture due to its high market value, fast growth rate and the global demand for flatfishes. At present, very limited knowledge exists regarding the reproductive biology of this species, and notably the control of reproduction in captivity. Successful finfish aquaculture requires a robust understanding of reproduction for effective broodstock management. This thesis investigates induced ovulation in yellowbelly flounder using a gonadotropin releasing hormone analogue (GnRHa). The study pairs physiology and genetics to advance the current knowledge of reproduction in this species.
GnRHa was administrated to induce ovulation in yellowbelly flounder, over a 28-day period. One of three treatments were assigned to 27 female yellowbelly flounder (n=9): 50 µg/kg GnRHa, 100 µg/kg GnRHa, or a sham treatment of 50 µg/kg Ringer’s solution. Histological and fresh oocyte analyses were carried out and batch fecundity, fertilization and ovulation rates were assessed. Reproductive dysfunction experienced by yellowbelly flounder in this study was through incomplete germinal vesicle migration and a failure to enter hydration. Ovulation was only observed in GnRHa treated fish and the ovulatory periodicity appeared to be approximately 72 hours in fish that ovulated more than once. This study confirms that yellowbelly flounder are multiple group synchronous batch spawners. Although fewer fish than expected ovulated (four), significantly more GnRHa treated fish completed final oocyte maturation and entered hydration compared to the controls. Furthermore, fecundity, fertilization rates and egg viability were high, with fertilization >80% achieved in some initial ovulations. In contrast, eggs obtained from fish that had ovulated for a second time, were characterised by low fecundity and fertilization rates. Nonetheless, this data indicates GnRHa can successfully induce ovulation at dosages of at least 50 µg/kg without adversely affecting egg quality in at least the first batch. Further refinement is essential to optimize a protocol for the reliable induction of reproduction in this species. Low incidences of ovulation may be a factor of dosage or inappropriate ovarian maturity at the time of hormone administration. This highlights the need to confirm oocyte maturity immediately prior to GnRHa treatment. To aid future work, a classification index for the identification of ovarian developmental stage based on fresh oocyte morphology was developed for yellowbelly flounder. 
To further advance future research into yellowbelly flounder reproduction, brain, pituitary and gonad transcriptomic libraries were generated for female yellowbelly flounder using RNA-seq. Protein sequences of eight reproduction related genes were successfully identified and characterised, which were StAR, Gpr54, Lhβ, Fshβ, Fshr, Cyp19a1a, Cyp19a1b and Hsd17b1. Conserved functional regions, phylogenetic analysis and homology with sequences from other Pleuronectiformes confirmed the identities of these genes and indicated that their functional roles are likely conserved. Characterisation of these genes provides highly valuable information for future quantitative assessment of gene expression throughout the yellowbelly flounder reproductive axis. 
The results presented in this thesis will help to inform future work to control and optimize reproduction in captive yellowbelly flounder. In addition, the genetic data will enable molecular tools to be developed, including quantitative PCR primers as well as the potential for recombinant gonadotropins to develop enzyme-linked immunosorbent assays. These tools will be highly valuable to accurately assess the effects of GnRHa treatment on reproduction and gene expression under differing culture conditions. This study indicates that successful ovulation and good quality eggs may be achieved in yellowbelly flounder using GnRHa treatment.

text: Induced reproduction in Pātiki (Rhombosolea leporina), a novel endemic aquaculture candidate The rapid global population growth combined with the decline of wild-capture fisheries has resulted in the global expansion of aquaculture. New Zealand’s aquaculture industry remains largely underdeveloped and as such, industry growth would benefit from species diversification. The endemic yellowbelly flounder (Rhombosolea leporina) is a promising candidate species for New Zealand aquaculture due to its high market value, fast growth rate and the global demand for flatfishes. At present, very limited knowledge exists regarding the reproductive biology of this species, and notably the control of reproduction in captivity. Successful finfish aquaculture requires a robust understanding of reproduction for effective broodstock management. This thesis investigates induced ovulation in yellowbelly flounder using a gonadotropin releasing hormone analogue (GnRHa). The study pairs physiology and genetics to advance the current knowledge of reproduction in this species.
GnRHa was administrated to induce ovulation in yellowbelly flounder, over a 28-day period. One of three treatments were assigned to 27 female yellowbelly flounder (n=9): 50 µg/kg GnRHa, 100 µg/kg GnRHa, or a sham treatment of 50 µg/kg Ringer’s solution. Histological and fresh oocyte analyses were carried out and batch fecundity, fertilization and ovulation rates were assessed. Reproductive dysfunction experienced by yellowbelly flounder in this study was through incomplete germinal vesicle migration and a failure to enter hydration. Ovulation was only observed in GnRHa treated fish and the ovulatory periodicity appeared to be approximately 72 hours in fish that ovulated more than once. This study confirms that yellowbelly flounder are multiple group synchronous batch spawners. Although fewer fish than expected ovulated (four), significantly more GnRHa treated fish completed final oocyte maturation and entered hydration compared to the controls. Furthermore, fecundity, fertilization rates and egg viability were high, with fertilization >80% achieved in some initial ovulations. In contrast, eggs obtained from fish that had ovulated for a second time, were characterised by low fecundity and fertilization rates. Nonetheless, this data indicates GnRHa can successfully induce ovulation at dosages of at least 50 µg/kg without adversely affecting egg quality in at least the first batch. Further refinement is essential to optimize a protocol for the reliable induction of reproduction in this species. Low incidences of ovulation may be a factor of dosage or inappropriate ovarian maturity at the time of hormone administration. This highlights the need to confirm oocyte maturity immediately prior to GnRHa treatment. To aid future work, a classification index for the identification of ovarian developmental stage based on fresh oocyte morphology was developed for yellowbelly flounder. 
To further advance future research into yellowbelly flounder reproduction, brain, pituitary and gonad transcriptomic libraries were generated for female yellowbelly flounder using RNA-seq. Protein sequences of eight reproduction related genes were successfully identified and characterised, which were StAR, Gpr54, Lhβ, Fshβ, Fshr, Cyp19a1a, Cyp19a1b and Hsd17b1. Conserved functional regions, phylogenetic analysis and homology with sequences from other Pleuronectiformes confirmed the identities of these genes and indicated that their functional roles are likely conserved. Characterisation of these genes provides highly valuable information for future quantitative assessment of gene expression throughout the yellowbelly flounder reproductive axis. 
The results presented in this thesis will help to inform future work to control and optimize reproduction in captive yellowbelly flounder. In addition, the genetic data will enable molecular tools to be developed, including quantitative PCR primers as well as the potential for recombinant gonadotropins to develop enzyme-linked immunosorbent assays. These tools will be highly valuable to accurately assess the effects of GnRHa treatment on reproduction and gene expression under differing culture conditions. This study indicates that successful ovulation and good quality eggs may be achieved in yellowbelly flounder using GnRHa treatment.

year: 2022

title: An Adaptive Model-based Mutation Operator for the Wind Farm Layout Optimisation Problem

authors: Mayo, Michael

subjects: Machine learning

abstract: A novel mutation operator for the wind farm layout optimisation problem is proposed and tested. When a wind farm layout is simulated, statistics such as an individual turbine’s wake free ratio can be computed. These statistics are in addition to the global measure being optimised, for example the overall cost of energy extraction of the farm. We present algorithms that first of all build a predictive model of the wake free ratio across an entire wind farm. This model is then used inside a mutation operator to perturb turbines towards positions of high predicted wake free ratio. We evaluate our approach by comparing a 1+1 Evolutionary Strategy using this new mutation operator vs. the same algorithm with a more standard random mutation operator, and show that our new operator leads to the discovery of wind farm layouts having a statistically significantly lower cost of energy extraction.

text: An Adaptive Model-based Mutation Operator for the Wind Farm Layout Optimisation Problem A novel mutation operator for the wind farm layout optimisation problem is proposed and tested. When a wind farm layout is simulated, statistics such as an individual turbine’s wake free ratio can be computed. These statistics are in addition to the global measure being optimised, for example the overall cost of energy extraction of the farm. We present algorithms that first of all build a predictive model of the wake free ratio across an entire wind farm. This model is then used inside a mutation operator to perturb turbines towards positions of high predicted wake free ratio. We evaluate our approach by comparing a 1+1 Evolutionary Strategy using this new mutation operator vs. the same algorithm with a more standard random mutation operator, and show that our new operator leads to the discovery of wind farm layouts having a statistically significantly lower cost of energy extraction.

year: 2015

title: Management of patients with early stage lung cancer - why do some patients not receive treatment with curative intent?

authors: Lawrenson, Ross

subjects: Lung cancer

abstract: BACKGROUNDS: This study aims to understand the factors that influence whether patients receive potentially curative treatment for early stage lung cancer. A key question was whether indigenous Māori patients were less likely to receive treatment. 
METHODS: Patients included those diagnosed with early stage lung cancer in 2011-2018 and resident in the New Zealand Midland Cancer Network region. Logistic regression model was used to estimate the odds ratios of having curative surgery/ treatment. The Kaplan Meier method was used to examine the all-cause survival and Cox proportional hazard model was used to estimate the hazard ratio of death. 
RESULTS: In total 419/583 (71.9%) of patients with Stage I and II disease were treated with curative intent - 272 (46.7%) patients had curative surgery. Patients not receiving potentially curative treatment were older, were less likely to have non-small cell lung cancer (NSCLC), had poorer lung function and were more likely to have an ECOG performance status of 2+. Current smokers were less likely to be treated with surgery and more likely to receive treatment with radiotherapy and chemotherapy. Those who were treated with surgery had a 2-year survival of 87.8% (95% CI: 83.8-91.8%) and 5-year survival of 69.6% (95% CI: 63.2-76.0%). Stereotactic ablative body radiotherapy (SABR) has equivalent effect on survival compared to curative surgery (hazard ratio: 0.77, 95% CI: 0.37-1.61). After adjustment we could find no difference in treatment and survival between Māori and non-Māori. 
CONCLUSIONS: The majority of patients with stage I and II lung cancer are managed with potentially curative treatment - mainly surgery and increasingly with SABR. The outcomes of those being diagnosed with stage I and II disease and receiving treatment is positive with 70% surviving 5 years.

text: Management of patients with early stage lung cancer - why do some patients not receive treatment with curative intent? BACKGROUNDS: This study aims to understand the factors that influence whether patients receive potentially curative treatment for early stage lung cancer. A key question was whether indigenous Māori patients were less likely to receive treatment. 
METHODS: Patients included those diagnosed with early stage lung cancer in 2011-2018 and resident in the New Zealand Midland Cancer Network region. Logistic regression model was used to estimate the odds ratios of having curative surgery/ treatment. The Kaplan Meier method was used to examine the all-cause survival and Cox proportional hazard model was used to estimate the hazard ratio of death. 
RESULTS: In total 419/583 (71.9%) of patients with Stage I and II disease were treated with curative intent - 272 (46.7%) patients had curative surgery. Patients not receiving potentially curative treatment were older, were less likely to have non-small cell lung cancer (NSCLC), had poorer lung function and were more likely to have an ECOG performance status of 2+. Current smokers were less likely to be treated with surgery and more likely to receive treatment with radiotherapy and chemotherapy. Those who were treated with surgery had a 2-year survival of 87.8% (95% CI: 83.8-91.8%) and 5-year survival of 69.6% (95% CI: 63.2-76.0%). Stereotactic ablative body radiotherapy (SABR) has equivalent effect on survival compared to curative surgery (hazard ratio: 0.77, 95% CI: 0.37-1.61). After adjustment we could find no difference in treatment and survival between Māori and non-Māori. 
CONCLUSIONS: The majority of patients with stage I and II lung cancer are managed with potentially curative treatment - mainly surgery and increasingly with SABR. The outcomes of those being diagnosed with stage I and II disease and receiving treatment is positive with 70% surviving 5 years.

year: 2020