Bio-economic system-dynamics modelling to investigate strategic management options in New Zealand sheep farming enterprises : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Farm Management, School of Agriculture and Environment, Massey University, Manawatu, New Zealand

The average and range of production and profit levels achieved in New Zealand sheep farming enterprises indicate potential for improvement across many farms. Ewe wastage, use of terminal sires, and breed transition to produce higher value wool are issues currently pertinent to the profitability of farms on New Zealand North Island Hill Country with dual-purpose breeding ewe flocks. A bio-economic system-dynamics sheep farm model was identified as appropriate to model these profitability scenarios where changes in ewe flock structure were integral. The objectives of the current research were: to develop the model; validate output through examining ewe flock wastage (premature ewe losses) rates; and use the model to investigate use of terminal (meat breed) sires to increase income from lamb sales, and a gradual flock breed transition from purebred Romney to ¾ Merino ¼ Romney to increase income from wool sales. Component modules were flock dynamics (including sheep sales), sheep feed demand, feed supply from pasture, feed balance, wool production, and economics. Model output aligned with previously published industry data and was therefore considered a realistic representation of New Zealand North Island Hill Country sheep farming systems. Flock wastage rates ranging from 5% to 21% were studied, sheep enterprise cash operating surplus (COS) reduced by $1,069 per 1$101/ha compared with no use of terminal sires, due to higher survival and growth rates in crossbred lambs sold earlier for higher prices. Flock breed transition through crossbreeding a Romney flock with Merino sires demonstrated reductions in COS during the breed transition period and greater COS post-breed change. Net present value analysis showed whole farm COS with breed transition to be up to 26% greater than maintaining the purebred Romney flock. Breed transition scenarios with higher Merino-Romney crossbred ewe lamb selection intensity achieved lower average wool fibre diameter, with a longer breed transition period (i.e. ten years of transition) and greater economic benefit. Overall, the model was effective in investigating the selected scenarios and the results can be used to inform decision making of New Zealand farmers

Killer cell immunoglobulin-like receptor (KIR) genes and their HLA-C ligands in a Ugandan population.

Killer cell immunoglobulin-like receptor (KIR) genes are expressed by natural killer cells and encoded by a family of genes exhibiting considerable haplotypic and allelic variation. HLA-C molecules, the dominant ligands for KIR, are present in all individuals and are discriminated by two KIR epitopes, C1 and C2. We studied the frequencies of KIR genes and HLA-C1 and C2 groups in a large cohort (n = 492) from Kampala, Uganda, East Africa and compared our findings with published data from other populations in sub-Saharan Africa (SSA) and several European populations. We find considerably more KIR diversity and weaker linkage disequilibrium in SSA compared to the European populations and describe several novel KIR genotypes. C1 and C2 frequencies were similar to other SSA populations with a higher frequency of the C2 epitope (54.9 %) compared to Europe (average 39.7 %). Analysis of this large cohort from Uganda in the context of other African populations reveals variations in KIR and HLA-C1 and C2 that are consistent with migrations within Africa and potential selection pressures on these genes. Our results will help understand how KIR/HLA-C interactions contribute to resistance to pathogens and reproductive success

Tissue-Specific Education of Decidual NK Cells.

During human pregnancy, fetal trophoblast cells invade the decidua and remodel maternal spiral arteries to establish adequate nutrition during gestation. Tissue NK cells in the decidua (dNK) express inhibitory NK receptors (iNKR) that recognize allogeneic HLA-C molecules on trophoblast. Where this results in excessive dNK inhibition, the risk of pre-eclampsia or growth restriction is increased. However, the role of maternal, self-HLA-C in regulating dNK responsiveness is unknown. We investigated how the expression and function of five iNKR in dNK is influenced by maternal HLA-C. In dNK isolated from women who have HLA-C alleles that carry a C2 epitope, there is decreased expression frequency of the cognate receptor, KIR2DL1. In contrast, women with HLA-C alleles bearing a C1 epitope have increased frequency of the corresponding receptor, KIR2DL3. Maternal HLA-C had no significant effect on KIR2DL1 or KIR2DL3 in peripheral blood NK cells (pbNK). This resulted in a very different KIR repertoire for dNK capable of binding C1 or C2 epitopes compared with pbNK. We also show that, although maternal KIR2DL1 binding to C2 epitope educates dNK cells to acquire functional competence, the effects of other iNKR on dNK responsiveness are quite different from those in pbNK. This provides a basis for understanding how dNK responses to allogeneic trophoblast affect the outcome of pregnancy. Our findings suggest that the mechanisms that determine the repertoire of iNKR and the effect of self-MHC on NK education may differ in tissue NK cells compared with pbNK.This work was supported by Wellcome Trust Grants 090108/Z/09/Z and 085992/Z/08/Z, as well as by British Heart Foundation Grant PG/09/077/27964. P.R.K. was the recipient of a Wellcome Trust Ph.D. studentship.This is the final version of the article. It first appeared from the American Association of Immunologists via http://dx.doi.org/10.4049/​jimmunol.150122

A KIR B centromeric region present in Africans but not Europeans protects pregnant women from pre-eclampsia.

In sub-Saharan Africans, maternal mortality is unacceptably high, with >400 deaths per 100,000 births compared with <10 deaths per 100,000 births in Europeans. One-third of the deaths are caused by pre-eclampsia, a syndrome arising from defective placentation. Controlling placentation are maternal natural killer (NK) cells that use killer-cell immunoglobulin-like receptor (KIR) to recognize the fetal HLA-C molecules on invading trophoblast. We analyzed genetic polymorphisms of maternal KIR and fetal HLA-C in 484 normal and 254 pre-eclamptic pregnancies at Mulago Hospital, Kampala, Uganda. The combination of maternal KIR AA genotypes and fetal HLA-C alleles encoding the C2 epitope associates with pre-eclampsia [P = 0.0318, odds ratio (OR) = 1.49]. The KIR genes associated with protection are located in centromeric KIR B regions that are unique to sub-Saharan African populations and contain the KIR2DS5 and KIR2DL1 genes (P = 0.0095, OR = 0.59). By contrast, telomeric KIR B genes protect Europeans against pre-eclampsia. Thus, different KIR B regions protect sub-Saharan Africans and Europeans from pre-eclampsia, whereas in both populations, the KIR AA genotype is a risk factor for the syndrome. These results emphasize the importance of undertaking genetic studies of pregnancy disorders in African populations with the potential to provide biological insights not available from studies restricted to European populations.This work was supported by the Wellcome Trust (090108/Z/09/Z, 085992/Z/08/Z, 089821/Z/09/Z), the British Heart Foundation (PG/ 09/077/27964), the Centre for Trophoblast Research at the University of Cambridge, a Wellcome Trust Uganda PhD Fellowship in Infection and Immunity held by Annettee Nakimuli, funded by a Wellcome Trust Strategic Award (084344), the US National Institutes of Health (AI017892), and the UK Medical Research Council (G0901682).This is the accepted manuscript of a paper published in PNAS (A Nakimuli, O Chazara, SE Hiby, L Farrell, S Tukwasibwe, J Jayaraman, JA Traherne, J Trowsdale, F Colucci, Emma Lougee, RW Vaughan, AM Elliott, J Byamugishaa, P Kaleebu, F Mirembe, N Nemat-Gorgani, P Parham, PJ Norman, A Moffett, PNAS 2015, 112, 845-850

Structural studies of integral membrane GPCR accessory proteins

GPCR accessory proteins regulate the strength, efficiency and specificity of signal transfer upon receptor activation. Due to the inherent difficulties of studying membrane proteins in vitro and in vivo, little is known about the structure and topology of these small accessory proteins. Two examples of GPCR accessory proteins are the Melanocortin-2 receptor accessory protein (MRAP) and the Receptor-activity-modifying protein (RAMP) family. MRAP and RAMP1 are the main focus of this thesis in which they are thoroughly characterised by solution-state NMR and further biophysical techniques.The single-pass transmembrane domain protein MRAP regulates the class A GPCR melanocortin receptors. It is specifically required for trafficking the melanocortin-2-receptor from the endoplasmic reticulum to the cell surface and subsequent receptor activation. A remarkable characteristic of MRAP is its proposed native dual-topology, which leads to an antiparallel homodimeric conformation. Investigation of the biochemical and biophysical properties of MRAP revealed an α-helical transmembrane domain, and an α-helical N-terminal LD(Y/I)L-motif. Further efforts concentrated on establishing the homodimeric conformation of MRAP in vitro. RAMP1 facilitates receptor trafficking and alters the ligand specificity of the GPCR Class B receptors calcitonin receptors and calcitonin receptor-like receptors. Moreover, RAMP1 is required to act as a Calcitonin-gene-related peptide (CGRP) receptor (RAMP1). RAMP1 has been shown to form stable parallel homodimers in the absence of its cognate receptor. Its dimerisation and the possible dimerisation motif PxxxxP-motif were studied extensively.With the goal of understanding the mechanism of dimerisation and the role of GPCR accessory proteins I have used solution-state NMR in detergent micelles as my main technique. NMR provides unique possibilities for understanding the structure and dynamics of such small membrane proteins

Enhanced bacterial cancer therapy delivering therapeutic RNA interference of c-Myc

BackgroundBacterial cancer therapy was first trialled in patients at the end of the nineteenth century. More recently, tumour-targeting bacteria have been harnessed to deliver plasmid-expressed therapeutic interfering RNA to a range of solid tumours. A major limitation to clinical translation of this is the short-term nature of RNA interference in vivo due to plasmid instability. To overcome this, we sought to develop tumour-targeting attenuated bacteria that stably express shRNA by virtue of integration of an expression cassette within the bacterial chromosome and demonstrate therapeutic efficacy in vitro and in vivo.ResultsThe attenuated tumour targeting Salmonella typhimurium SL7207 strain was modified to carry chromosomally integrated shRNA expression cassettes at the xylA locus. The colorectal cancer cell lines SW480, HCT116 and breast cancer cell line MCF7 were used to demonstrate the ability of these modified strains to perform intracellular infection and deliver effective RNA and protein knockdown of the target gene c-Myc. In vivo therapeutic efficacy was demonstrated using the Lgr5creERT2Apcflx/flx and BlgCreBrca2flx/flp53flx/flx orthotopic immunocompetent mouse models of colorectal and breast cancer, respectively. In vitro co-cultures of breast and colorectal cancer cell lines with modified SL7207 demonstrated a significant 50–95% (P < 0.01) reduction in RNA and protein expression with SL7207/c-Myc targeted strains. In vivo, following establishment of tumour tissue, a single intra-peritoneal administration of 1 × 106 CFU of SL7207/c-Myc was sufficient to permit tumour colonisation and significantly extend survival with no overt toxicity in control animals.ConclusionsIn summary we have demonstrated that tumour tropic bacteria can be modified to safely deliver therapeutic levels of gene knockdown. This technology has the potential to specifically target primary and secondary solid tumours with personalised therapeutic payloads, providing new multi-cancer detection and treatment options with minimal off-target effects. Further understanding of the tropism mechanisms and impact on host immunity and microbiome is required to progress to clinical translation

Evaluation of post-stocking survival and movement of hatchery-reared juvenile bloater (Coregonus hoyi) stocked across bathymetric depths in Lake Ontario

Bloater (Coregonus hoyi), extirpated from Lake Ontario in the 1980s, have been stocked annually since 2012 with limited success in re-establishing a self-sustaining population. In this study, hatchery-raised juvenile bloater were tagged with acoustic telemetry high-resolution predation tags and stocked over three depths in Lake Ontario (5, 50, and 100m) in 2022 and 2023 to quantify survival, causes of mortality, and movement. Time-to-event modelling generated a three-week survival estimate of 38% (31-46%; 95% Confidence Interval) across both years, with lower survival in year 1 (12%; 12-38%) than year 2 (44%; 33-59%). The deepest depth (100m) yielded the highest survival, with mortality due to predation more common at shallower depths, while non-predation mortality, potentially from compression barotrauma, was more prevalent in deeper water. Rapid dispersion following release was observed in both years, with greater distances travelled in 2023. This study revealed low initial survival for stocked bloater that varied between years and stocking depth and highlighted different potential sources of mortality associated with depth, while providing new information for consideration of stocking techniques in large lakes.The presentation of the authors' names and (or) special characters in the title of the pdf file of the accepted manuscript may differ slightly from what is displayed on the item page. The information in the pdf file of the accepted manuscript reflects the original submission by the author

Determining the Impact of Hogget Breeding Performance on Profitability under a Fixed Feed Supply Scenario in New Zealand

peer-reviewedHoggets (ewe lambs aged 4 to 16 months) can be bred from approximately 8 months of age for potentially increased flock production and profit, however most New Zealand hoggets are not presented for breeding and their reproductive success is highly variable. Bio-economic modelling was used to analyse flock productivity and profit in four sets of scenarios for ewe flocks with varying mature ewe (FWR) and hogget (HWR) weaning rate combinations. Firstly, hogget breeding was identified to become profitable when break-even HWRs of 26% and 28% were achieved for flocks with FWRs of 135% and 150%, respectively. Secondly, relatively smaller improvements in FWR were identified to increase profit to the same level as larger improvements in HWR. Thirdly, a high performing flock with FWR and HWR both ≥ the 90th percentile currently achieved commercially, was the most profitable flock modelled. Fourthly, a FWR was identified with which a farmer not wishing to breed hoggets could have the same profit as a farmer with a flock achieving current industry average FWR and HWR. Overall, the relative profit levels achieved by the modelled flocks suggest that more farmers should consider breeding their hoggets, though improvements in FWRs should be prioritised

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing

Organoids with a type 1 collagen scaffold to model bacterial cancer therapy

Bacterial cancer therapy (BCT) is emerging as an important option for the treatment of solid tumours, with promising outcomes in preclinical trials. Further progress is hampered by an incomplete understanding of how oncotropic bacteria, such as attenuated strains of Salmonella enterica serovar Typhimurium, colonise tumours and the responses of both the bacteria and tumour cells to this colonisation. To model this, we developed organoids that are permissive for bacterial colonisation, replacing the conventional commercially available extracellular matrix (e.g., Matrigel) with a type I collagen matrix scaffold. A comparison of the two extracellular matrices indicated that type 1 collagen permitted an initial infection efficiency more than 5-times greater than with Matrigel. In addition, subsequent growth within type 1 collagen expanded bacterial cell numbers by over 10-fold within 4 days of infection. These organoids allow for the visualisation of bacterial chemoattraction, cell invasion and subsequent population of the interior lumen, and will permit the future optimisation of BCT. In addition, by establishing patient-derived organoids, we demonstrate a platform for developing future personalised treatments exploiting BCT