title: PineappleDB: An online pineapple bioinformatics resource

authors: Moyle, Richard L.

abstract: Background: A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences.
Description: PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information.
Conclusion: The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

text: PineappleDB: An online pineapple bioinformatics resource Background: A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences.
Description: PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information.
Conclusion: The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

year: 2005-10

title: Modelling New Zealand dairy farm systems to design greenhouse gas mitigation strategies

authors: Adler, Alfredo A.

subjects: mitigaiton cost

abstract: Dairy cattle in New Zealand account for about 17% of the country’s total greenhouse gas (GHG) load. As the nation progresses in its efforts to reduce these emissions, is likely that the dairy industry will face physical constraints and/or financial costs associated with their mitigation. For this study, a non-linear optimization model was developed to analyse the cost-effectiveness of diverse mitigation strategies for reducing GHG loads between 10–30% within systems of different production intensity in the main dairy farming regions of New Zealand: Waikato and Canterbury. Pastoral dairy farms, as found in New Zealand, are complex farming systems with many interdependent management variables and any change in one of these variables in order to reduce GHG emissions will inevitably affect the system as a whole, generating changes in its physical and economic outputs. Computer modelling is thus highly suited to evaluate alternative strategies, given its capacity to represent and consider these interdependencies simultaneously.
De-intensification, by reducing any combination of stocking rate, nitrogen fertiliser and supplement use, was a key strategy in reducing GHG emissions in an economic manner across the whole range of farming systems and regions considered in this study, as well as for all levels of emissions constraints tested. The mean farm profit reduction found under this level of mitigation across all studied systems was 6%, when no other mitigation strategies were available. To achieve this, the mean reduction in stocking rate was 8.8% and the mean nitrogen fertilizer reduction was 36%. Nitrogen fertiliser usage increases GHG emissions by increasing the available mineral nitrogen in soil and thus increasing denitrification and also by increasing enteric methane emissions as more fibrous feed is available to be consumed. The mean profit reduction was 6.9% and 4.9% for the Waikato and Canterbury regions, respectively.
The Canterbury medium-input system had a lower cost of mitigation than the other systems, associated with the use of more supplements with high embedded GHG emissions in the baseline. Accordingly, the use of this kind of supplement was quickly reduced by the optimization model in the mitigation scenarios. At the other end, the Canterbury high input system had the highest cost of mitigation, arising from a combination of larger GHG-e reductions required in absolute terms and the low profitability of the baseline plan, given its high use of imported supplement. In contrast, the abatement cost in the Waikato systems was intermediate between these two extremes.
Improved reproductive performance and improved genetic merit of the herd were selected as optimal in all cases where specific mitigation strategies were available. Profit was reduced by 1.6%, on average, in this case when 10% GHG emissions reductions were imposed. To adapt to this constraint, stocking rate was reduced by 8.1%, while N fertilizer was reduced by 30.7%, on average. Thus, although the availability of specific mitigation strategies was valuable in reducing the profit losses arising from mitigation, these were not sufficient to reduce emissions without some degree of de-intensification. 
Other mitigation strategies, like removing cows from pasture or the use of denitrification inhibitors, were not always cost effective and only entered the optimal solution when higher levels of mitigation were imposed. This demonstrates that the high cost of adopting these specific mitigation strategies is only warranted when systems are exposed to larger profit reductions associated with higher levels of de-intensification. A quick calculation using average reduction in milksolids production found in this study shows that the loss of revenue of the dairy industry if 30% mitigation of GHG is imposed can represent as much as half the export earnings of the entire beef industry of the nation.

text: Modelling New Zealand dairy farm systems to design greenhouse gas mitigation strategies Dairy cattle in New Zealand account for about 17% of the country’s total greenhouse gas (GHG) load. As the nation progresses in its efforts to reduce these emissions, is likely that the dairy industry will face physical constraints and/or financial costs associated with their mitigation. For this study, a non-linear optimization model was developed to analyse the cost-effectiveness of diverse mitigation strategies for reducing GHG loads between 10–30% within systems of different production intensity in the main dairy farming regions of New Zealand: Waikato and Canterbury. Pastoral dairy farms, as found in New Zealand, are complex farming systems with many interdependent management variables and any change in one of these variables in order to reduce GHG emissions will inevitably affect the system as a whole, generating changes in its physical and economic outputs. Computer modelling is thus highly suited to evaluate alternative strategies, given its capacity to represent and consider these interdependencies simultaneously.
De-intensification, by reducing any combination of stocking rate, nitrogen fertiliser and supplement use, was a key strategy in reducing GHG emissions in an economic manner across the whole range of farming systems and regions considered in this study, as well as for all levels of emissions constraints tested. The mean farm profit reduction found under this level of mitigation across all studied systems was 6%, when no other mitigation strategies were available. To achieve this, the mean reduction in stocking rate was 8.8% and the mean nitrogen fertilizer reduction was 36%. Nitrogen fertiliser usage increases GHG emissions by increasing the available mineral nitrogen in soil and thus increasing denitrification and also by increasing enteric methane emissions as more fibrous feed is available to be consumed. The mean profit reduction was 6.9% and 4.9% for the Waikato and Canterbury regions, respectively.
The Canterbury medium-input system had a lower cost of mitigation than the other systems, associated with the use of more supplements with high embedded GHG emissions in the baseline. Accordingly, the use of this kind of supplement was quickly reduced by the optimization model in the mitigation scenarios. At the other end, the Canterbury high input system had the highest cost of mitigation, arising from a combination of larger GHG-e reductions required in absolute terms and the low profitability of the baseline plan, given its high use of imported supplement. In contrast, the abatement cost in the Waikato systems was intermediate between these two extremes.
Improved reproductive performance and improved genetic merit of the herd were selected as optimal in all cases where specific mitigation strategies were available. Profit was reduced by 1.6%, on average, in this case when 10% GHG emissions reductions were imposed. To adapt to this constraint, stocking rate was reduced by 8.1%, while N fertilizer was reduced by 30.7%, on average. Thus, although the availability of specific mitigation strategies was valuable in reducing the profit losses arising from mitigation, these were not sufficient to reduce emissions without some degree of de-intensification. 
Other mitigation strategies, like removing cows from pasture or the use of denitrification inhibitors, were not always cost effective and only entered the optimal solution when higher levels of mitigation were imposed. This demonstrates that the high cost of adopting these specific mitigation strategies is only warranted when systems are exposed to larger profit reductions associated with higher levels of de-intensification. A quick calculation using average reduction in milksolids production found in this study shows that the loss of revenue of the dairy industry if 30% mitigation of GHG is imposed can represent as much as half the export earnings of the entire beef industry of the nation.

year: 2014

title: An investigation into the commercial feasibility of Jasus edwardsii aquaculture in New Zealand

authors: Ruru, Ian Hector

subjects: New Zealand

abstract: In 1996 New Zealand introduced legislation to allow Jasus edwardsii pueruli to be collected as "seedstock" and ongrown in a commercial aquaculture trial. The aim of this thesis was to investigate the commercial feasibility of J. edwardsii aquaculture in New Zealand by working with an organisation involved in the trial.
The methodology involved a combination of experiments in the field, in laboratories, and within an ongrowing facility. This thesis examined five key areas and found the following:
1. Data obtained in the research indicates that New Zealand will continue to rely on harvesting pueruli from the wild since significant technical obstacles remain in the development of commercial scale pueruli hatcheries. Forecast data, obtained using the delphi technique and information about current research on larval rearing, indicates that commercial scale supply of pueruli from hatcheries may occur between 2017 and 2021.
2. Harvesting trials collected a low number of pueruli with the lowest unit cost for collection being $1.80. A greater collection rate could be achieved with a better understanding of seasonal and local settlement patterns.
3. Survival rates in pueruli transporting experiments were significantly affected by stocking density, time and temperature. The safest transit conditions were achieved with 15 pueruli per litre for less than 6 hours at 14°C.
4. A range of stocking densities, from 3 lobsters per tank to 12 per tank, were tested for their effect on growth of six-month old lobsters. The lobsters were reared in a total recirculation seawater system at a constant 16°C, and fed fresh mussels (Perna canaliculus). For the 121 day trial, no statistically significant effect was detected. However, there was a trend for growth rates to be highest at 3 and 6 lobsters per tank and for growth rates at stocking densities of 9 and 12 lobsters per tank to decrease after Day 50. Lobsters showed increased mortality at the highest stocking rate.
5. A bioeconomic model of a hypothetical farm was developed to assess economic benefits and risks and to determine overall profitability. The model showed an annual net cash position of $287,100 and cumulative cash position of $859,200 by the 10th year of operation based on annual sales of 10,837 kg at $65 per kg. The model indicates that the highest cost components in the first 10 years are processing and transport, and labour. Based on the model and the scenarios examined, profitability is very sensitive to factors such as the farm size, processing and transport costs, and sale price. Biological factors such as growth rates, survival, and feed requirements also influence overall profitability. Good returns will depend upon consistent exports of high quality lobsters.
The study concludes that commercial feasibility will be affected by these key areas. The potential of J. edwardsii aquaculture in New Zealand will continue to benefit from further research.

text: An investigation into the commercial feasibility of Jasus edwardsii aquaculture in New Zealand In 1996 New Zealand introduced legislation to allow Jasus edwardsii pueruli to be collected as "seedstock" and ongrown in a commercial aquaculture trial. The aim of this thesis was to investigate the commercial feasibility of J. edwardsii aquaculture in New Zealand by working with an organisation involved in the trial.
The methodology involved a combination of experiments in the field, in laboratories, and within an ongrowing facility. This thesis examined five key areas and found the following:
1. Data obtained in the research indicates that New Zealand will continue to rely on harvesting pueruli from the wild since significant technical obstacles remain in the development of commercial scale pueruli hatcheries. Forecast data, obtained using the delphi technique and information about current research on larval rearing, indicates that commercial scale supply of pueruli from hatcheries may occur between 2017 and 2021.
2. Harvesting trials collected a low number of pueruli with the lowest unit cost for collection being $1.80. A greater collection rate could be achieved with a better understanding of seasonal and local settlement patterns.
3. Survival rates in pueruli transporting experiments were significantly affected by stocking density, time and temperature. The safest transit conditions were achieved with 15 pueruli per litre for less than 6 hours at 14°C.
4. A range of stocking densities, from 3 lobsters per tank to 12 per tank, were tested for their effect on growth of six-month old lobsters. The lobsters were reared in a total recirculation seawater system at a constant 16°C, and fed fresh mussels (Perna canaliculus). For the 121 day trial, no statistically significant effect was detected. However, there was a trend for growth rates to be highest at 3 and 6 lobsters per tank and for growth rates at stocking densities of 9 and 12 lobsters per tank to decrease after Day 50. Lobsters showed increased mortality at the highest stocking rate.
5. A bioeconomic model of a hypothetical farm was developed to assess economic benefits and risks and to determine overall profitability. The model showed an annual net cash position of $287,100 and cumulative cash position of $859,200 by the 10th year of operation based on annual sales of 10,837 kg at $65 per kg. The model indicates that the highest cost components in the first 10 years are processing and transport, and labour. Based on the model and the scenarios examined, profitability is very sensitive to factors such as the farm size, processing and transport costs, and sale price. Biological factors such as growth rates, survival, and feed requirements also influence overall profitability. Good returns will depend upon consistent exports of high quality lobsters.
The study concludes that commercial feasibility will be affected by these key areas. The potential of J. edwardsii aquaculture in New Zealand will continue to benefit from further research.

year: 2000