858 results for Journal article, Lincoln University Research Archive

  • Integrated analysis of gene network in childhood leukemia from microarray and pathway databases

    Chaiboonchoe, Amphun; Samarasinghe, Sandhya; Kulasiri, D.; Salehi-Ashtiani, K.

    Journal article
    Lincoln University

    Glucocorticoids (GCs) have been used as therapeutic agents for children with acute lymphoblastic leukaemia (ALL) for over 50 years. However, much remains to be understood about the molecular mechanism of GCs actions in ALL subtypes. In this study, we delineate differential responses of ALL subtypes, B- and T-ALL, to GCs treatment at systems level by identifying the differences among biological processes, molecular pathways, and interaction networks that emerge from the action of GCs through the use of a selected number of available bioinformatics methods and tools. We provide biological insight into GC-regulated genes, their related functions, and their networks specific to the ALL subtypes. We show that differentially expressed GC-regulated genes participate in distinct underlying biological processes affected by GCs in B-ALL and T-ALL with little to no overlap. These findings provide the opportunity towards identifying new therapeutic targets. © 2014 Amphun Chaiboonchoe et al.

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  • Evaluation of parameter uncertainties in nonlinear regression using Microsoft Excel Spreadsheet

    Hu, W.; Xie, J.; Chau, Henry; Si, B. C.

    Journal article
    Lincoln University

    Background Nonlinear relationships are common in the environmental discipline. Spreadsheet packages such as Microsoft Excel come with an add-on for nonlinear regression, but parameter uncertainty estimates are not yet available. The purpose of this paper is to use Monte Carlo and bootstrap methods to estimate nonlinear parameter uncertainties with a Microsoft Excel spreadsheet. As an example, uncertainties of two parameters (α and n) for a soil water retention curve are estimated. Results The fitted parameters generally do not follow a normal distribution. Except for the upper limit of α using the bootstrap method, the lower and upper limits of α and n obtained by these two methods are slightly greater than those obtained using the SigmaPlot software which linearlizes the nonlinear model. Conclusions Since the linearization method is based on the assumption of normal distribution of parameter values, the Monte Carlo and bootstrap methods may be preferred to the linearization method.

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  • Variation in the Yak calpastatin gene (CAST)

    Yang, G.; Zhou, Huitong; Hu, J.; Luo, Y.; Hickford, Jonathan G. H.

    Journal article
    Lincoln University

    Calpastatin (CAST) is a specific inhibitor of calpain (calcium-dependent cysteine protease). This study investigated the potential for variation in yak (Bos grennies) CAST. PCR-SSCP analysis of exon 6 of yak CAST revealed three unique patterns (named A-C). Sequencing of the amplicons revealed two nucleotide substitutions. One substitution (c.398G/C) would nominally change the amino acid sequence (p.S133T) of yak calpastatin. The variant sequence A which carried c.398C was the most common in the yaks tested (95.1%). This is the first report that found yak CAST is variable, and as in pigs, sheep and cattle, this variation may affect animal production traits.

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  • An association between lifespan and variation in IGF1R in sheep.

    Byun, Seung O.; Forrest, R. H.; Frampton, C. M.; Zhou, Huitong; Hickford, Jonathan G. H.

    Journal article
    Lincoln University

    Longevity in livestock is a valuable trait. When productive animals live longer fewer replacement animals need to be raised. However, selection for longevity is not commonly the focus of breeding programs as direct selection for long-lived breeding stock is virtually impossible until late in the animal's reproductive life. Additionally the underlying genetic factors or genes associated with longevity are either not known, or not well understood. In humans, there is evidence that insulin-like growth factor 1 receptor (IGF1R) is involved in longevity. Polymorphism in the IGF1R gene (IGF1R) has been associated with longevity in a number of species. Recently, 3 alleles of ovine IGF1R were identified, but no analysis of the effect of IGF1R variation on sheep longevity has been reported. In this study, associations between ovine IGF1R variation, longevity and fertility were investigated. PCR-single strand conformational polymorphism (PCR-SSCP) was used to type IGF1R variation in 1716 New Zealand sheep belonging to 6 breeds and 36 flocks. Ovine IGF1R C was associated with age when adjusting for flock (present 5.5 ± 0.2 yr, absent 5.0 ± 0.1 yr, P = 0.02). A general linear mixed effects model suggested an association (P = 0.06) between age and genotype, when correcting for flock. Pairwise comparison (least significant difference) of specific genotypes revealed the difference to be between AA (5.0 ± 0.1 yr) and AC (5.6 ± 0.2 yr, P = 0.02). A weak negative Pearson correlation between fertility and longevity traits was observed (r = -0.25, P < 0.01). The finding of an association between variation in IGF1R and lifespan in sheep may be useful in prolonging the lifespan of sheep.

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  • Nitrous oxide fluxes, soil oxygen, and denitrification potential of urine- and non-urine-treated soil under different irrigation frequencies

    Owens, J.; Clough, Timothy J.; Laubach, J.; Hunt, J. E.; Venterea, R. T.; Phillips, R. L.

    Journal article
    Lincoln University

    © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. 5585 Guilford Rd., Madison, WI 53711 USA. All rights reserved. Despite increased use of irrigation to improve forage quality and quantity for grazing cattle (Bos taurus, Linnaeus), there is a lack of data that assess how irrigation practices influence nitrous oxide (N2O) emissions from urine-affected soils. Irrigation effects on soil oxygen (O2) availability, a primary controller of N2O fluxes, is poorly understood. It was hypothesized that increased irrigation frequency would result in lower N2O emissions by increasing soil moisture and decreasing soil O2 concentrations. This would favor more N2O reduction to dinitrogen (N2). We examined effects of high (3-d) versus low (6-d) irrigation frequency with and without bovine urine addition to pasture. Nitrous oxide fluxes were measured daily for 35 d. Soil O2, temperature, and water content were continuously measured at multiple depths. Inorganic nitrogen, organic carbon, and soil pH were measured at 6-d intervals. Measurements of denitrification enzyme activity with and without acetylene inhibition were used to infer the N2O/(N2O + N2) ratio. The N2O/(N2O + N2) ratio was lower under high- compared with low-frequency irrigation, suggesting greater potential for N2O reduction to N2 with more frequent irrigation. Although N2O fluxes were increased by urine addition, they were not affected by irrigation frequency. Soil O2 decreased temporarily after urine deposition, but O2 dynamics did not explain N2O dynamics. Relative soil gas diffusivity (DP/DO) was a better predictor of N2O fluxes than O2 concentration. On a freedraining soil, increasing irrigation frequency while providing the same total water volume did not enhance N2O emissions under ruminant urine patches in a grazed pasture.

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  • Optimizing land use for the delivery of catchment ecosystem services

    Doody, D.; Withers, P. J. A.; Dils, R. M.; McDowell, Richard; Smith, V.; McElarney, Y. R.; Dunbar, M.; Daly, D.

    Journal article
    Lincoln University

    © The Ecological Society of America. Despite widespread implementation of best management practices, sustainable farming is neither practical nor possible in certain locations, where protecting water quality and promoting agricultural production are likely to be incompatible. Some strategic prioritization of land-use options and acceptance of continually degraded waterbodies may be required to ensure optimization of multiple ecosystem services in catchments (also known as watersheds or drainage basins). We examine approaches to prioritization and propose catchment buffering capacity as a concept to manage the pressure–impact relationship between land use and aquatic ecosystems. Catchment buffering capacity can be considered as a continuum of biogeochemical, hydrological, and ecological catchment properties that define this relationship. Here, we outline a conceptual framework to assist prioritization: (1) establish a water-quality target, (2) quantify the gap in compliance to achieve the desired target, (3) assess catchment sensitivity to change, and (4) determine the adaptive capacity of catchment communities to reach the target.

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  • Happiness, welfare and ethics: dissonant consequences and conflicting values

    Clydesdale, G.

    Journal article
    Lincoln University

    This paper draws attention to an uncomfortable ethical issue with regard to happiness and welfare. The introduction of Western healthcare to Africa has resulted in significant population growth, with implications for human and animal welfare. However, the issue of population control or withdrawing health aid raises serious ethical concerns. This paper introduces the ethical problem and the factors giving rise to it. It then provides an exploratory analysis of the various ethical positions from which this problem can be viewed, with an eye to maximising human and animal welfare. Recent psychological work on welfare is considered when discussing the different ethical approaches. The discussion highlights the fact that conflicts in values can occur, and ways of resolving these are discussed.

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  • Plant mutualisms with rhizosphere microbiota in introduced versus native ranges

    Shelby, N.; Duncan, Richard P.; van der Putten, W. H.; McGinn, K. J.; Weser, Carolin; Hulme, Philip E.

    Journal article
    Lincoln University

    © 2016 The Authors. Journal of Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society. The performance of introduced plants can be limited by the availability of soil mutualists outside their native range, but how interactions with mutualists differ between ranges is largely unknown. If mutualists are absent, incompatible or parasitic, plants may compensate by investing more in root biomass, adapting to be more selective or by maximizing the benefits associated with the mutualists available. We tested these hypotheses using seven non-agricultural species of Trifolium naturalized in New Zealand (NZ). We grew seeds from two native (Spain, UK) and one introduced (NZ) provenance of each species in glasshouse pots inoculated with rhizosphere microbiota collected from conspecifics in each region. We compared how plant biomass, degree of colonization by rhizobia and arbuscular mycorrhizal fungi (AMF), and the growth benefit associated with each mutualist differed between provenances (native and introduced populations) when grown with soil microbiota from each region. We also tested whether the growth benefit of colonization by mutualists was correlated with the extent to which alien plants were distributed in the introduced range. Rhizobia colonization was generally lower among introduced relative to native provenances. In NZ soils, 9% of all plants lacked rhizobia and 16% hosted parasitic nodules, whereas in native-range soils, there was no evidence of parasitism and all but one plant hosted rhizobia. Growth rates as a factor of rhizobia colonization were always highest when plants were grown in soil from their home range. Colonization by AMF was similar for all provenances in all soils but for four out of seven species grown in NZ soils, the level of AMF colonization was negatively correlated with growth rate. In general, introduced provenances did not compensate for lower growth rates or lower mutualist associations by decreasing shoot–root ratios. Synthesis. Despite differences between introduced and native provenances in their associations with soil mutualists and substantial evidence of parasitism in the introduced range, neither level of colonization by mutualists nor the growth benefit associated with colonization was correlated with the extent of species’ distributions in the introduced range, suggesting mutualist associations are not predictive of invasion success for these species.

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  • Quantification and comparison of shelterbelt carbon stocks within and between an organic mixed-cropping farm and a conventional dairy farm

    Welsch, Johannes; Hale, Roderick J.; Buckley, Hannah L.; Case, Bradley S.

    Journal article
    Lincoln University

    Although woody ecosystems provide a key carbon sink to compensate for current and future greenhouse gas emissions, the potential utility of such sinks within agroecosystems has not yet been fully investigated. We quantified shelterbelt carbon variability, within above- and below-ground pools, for two contrasting farms: a conventional dairy farm and an organic mixed-cropping farm. Shelterbelts comprised deciduous, evergreen and mixed-native species occurring on silt loams, as well as adjacent paddock soils for comparison. Considering all above- and below-ground components, woody shelterbelts contained up to fifteen times more carbon (>600 t C ha-1) than sampled paddock soils (c. 45 t C ha-1). Carbon quantities within organic farm shelterbelt soils were 2.5 times higher than dairy farm soils, suggesting a potential land use effect. Soil carbon comprised about 10 % of total ecosystem carbon within shelterbelts. This study indicates that farm shelterbelts can serve a role as relevant carbon sinks within New Zealand agroecosystems.

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  • Use of social media in the Australian and New Zealand wine industries

    Forbes, S. L.; Goodman, S.; Dolan, R.

    Journal article
    Lincoln University

    Wineries are keen to adopt social media, but they struggle to identify the return on investment and there appears to be a distinct level of strategy regarding adoption. Sharon L Forbes, from the Faculty of Agribusiness and Markets at Lincoln University, New Zealand; together with Steve Goodman and Rebecca Dolan, from the Marketing & Management department of The University of Adelaide's Business School, have surveyed wineries about social media use and the perceived benefits.

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  • Translocations of North Island kokako, 1981-2011

    Innes, J.; Molles, Laura; Speed, H.

    Journal article
    Lincoln University

    The North Island kokako (Callaeas wilsoni) is a threatened endemic passerine whose distribution has declined greatly on the New Zealand mainland due primarily to predation by ship rats (Rattus rattus) and brushtail possums (Trichosurus vulpecula). It persists in 21 populations, of which 10 (48%) have been established by translocation, and 1 has been supplemented by translocation. Of the 11 populations subject to translocation, 4 are on islands and the remainder are on the mainland; 7 translocations have resulted in successful new or supplemented populations and another 4 translocations are in progress. Translocations to another 5 sites did not establish breeding populations for various reasons. In total, there were 94 translocations of 286 kokako to the 16 sites, and the number released at a site averaged 18 (range 3-33) birds. Kokako were released at a site over an average period of 49 months (range 1-159 months) with a mean of 3 birds (maximum 10) released per day. The small numbers of kokako released and the long time required to complete a translocation were due to the difficulty and high expense of catching kokako. Translocations will continue to be important for the conservation of this species, to establish further new populations and to limit inbreeding depression and allele loss in existing populations.

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  • Sexually dimorphic vocalisations of the great spotted kiwi (Apteryx haastii)

    Dent, J. M.; Molles, Laura

    Journal article
    Lincoln University

    © The Ornithological Society of New Zealand Inc. Kiwi (Apteryx spp.) are the most vocal of the ratites. Of the 5 Apteryx species only 2 have previously been subject to detailed vocal analysis: the North Island brown kiwi (A. mantelli) and the little spotted kiwi (A. owenii). This paper describes the vocalisations of the great spotted kiwi (A. haastii), the largest of the Apteryx species. Acoustic recorders were installed near the breeding den sites of 7 great spotted kiwi pairs residing in Hawdon Valley, Canterbury between November 2012 and March 2013. A total of 133 whistle vocalisations from 10 individuals were subject to detailed temporal and spectral analysis. Male and female syllables were found to be sexually dimorphic; syllables in male calls tended to be longer and more highly pitched than their female counterparts. Despite this dimorphism, patterns of intra-call variation were consistent between the sexes. It appears that intra-call variation is a trait which varies markedly within the Apteryx genus.

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  • "Acoustic anchoring" and the successful translocation of North Island kokako (Callaeas cinerea wilsoni) to a New Zealand mainland management site within continuous forest

    Molles, Laura; Calcott, A.; Peters, D.; Delamare, G.; Hudson, J. D.; Innes, J.; Flux, I.; Waas, J. R.

    Journal article
    Lincoln University

    In Jul and Aug 2005, 18 North Is kokako (Callaeas cinerea wilsoni) were released into a 450-ha area of New Zealand native forest subject to intensive control of introduced mammalian predators. The area, Ngapukeriki (near Omaio, Bay of Plenty, New Zealand), lies within a 13,000-ha matrix of native and exotic forest subject to lower and variable degrees of predator control. In contrast to most previous kokako translocations, this project employed 3 tactics to maximise the likelihood that kokako would remain in the target area: 1) many birds were released in a short period; 2) playback of kokako song was broadcast in the release area (potentially creating an “acoustic anchor”); and 3) a kokako pair was held at the release site in an aviary. Most birds approached to within 20 m of playback speakers, some approaching repeatedly. Several interactions between released birds were observed, including vocal interactions and instances of birds associating with one another temporarily. Visits to the aviary pair were rare. On 13 Apr 2006, all 8 trackable birds and 4 birds whose transmitters had failed remained in the core management area; locations of remaining birds (with lost or non-functional transmitters) were unknown. At least 5 territorial pairs had formed, and 1 chick was known to have fledged. To our knowledge, this was the 1st time song playback had been used as an attractant in a terrestrial bird reintroduction.

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  • Regulation of UV-induced flavonoid production in Marchantia polymorpha: a role in the evolution of plants for land colonisation?

    Jordan, B.; Albert, N.; Clayton, W.; Deroles, S.; Schwinn, K.; Davies, K.

    Journal article
    Lincoln University

    Plants are thought to have colonized the land around 500 million years ago. One of the major challenges the first pioneers faced was protection against UV radiation. UV has severe detrimental effects on plant cells and was at particularly high levels during the period of land colonisation because the ozone layer was not fully developed. Seed plants use a mix of secondary metabolites as UV ‘sunscreens’, and of these the flavonoid group of phenylpropanoids is of particular importance.

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  • Dry matter yield and radiation use efficiency of four autumn sown top flowering annual clover

    Nori, H.; Moot, D. J.; Black, A. D.

    Journal article
    Lincoln University

    Monocultures of arrowleaf (Trifolium vesiculosum), balansa (T. michelianum), gland (T. glanduliferum) and Persian (T. resupinatum) clovers were sown on four dates in autumn and winter 2010. Dry matter (DM) accumulation was dependent on the duration of crop growth which was influenced by the time of sowing. Autumn sown crops which flowered latest had a longer duration of vegetative growth and consequently produced the highest dry matter yields. In the establishment year, autumn sown crops produced up to 17.5 t DM/ha for balansa, 12.5 t DM/ha for Persian, 11.0 t DM/ha for gland and 9.4 t DM/ha for arrowleaf at physiological maturity (P<0.05). Thus, over the two years ‘Bolta’ balansa and ‘Mihi’ Persian clovers were the highest yielding and easiest to regenerate from seed in monocultures. ‘Cefalu’ arrowleaf failed to regenerate in the second year due to low population of seedling emergence. ‘Prima’ gland clover was low yielding because it flowered and matured without fully utilising the growing season.

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  • Dry matter and sheep production of four dryland tall fescue-clover pastures 4-6 years after establishment

    Black, A. D.; Moir, J. L.

    Journal article
    Lincoln University

    Effects of tall fescue cultivar (‘Advance’ and ‘Flecha’) and clover species (white and subterranean (sub) clovers) combinations on pasture dry matter (DM) and sheep production were assessed in years four (2011/12), five (2012/13) and six (2013/14) after establishment in dryland, Canterbury. ‘Advance’ pastures yielded less total herbage than ‘Flecha’ pastures (13.9 cf. 16.5 t DM/ha) but more fescue (8.6 cf. 5.9 t DM/ha) and 2.1 t DM/ha clover in year four, 13.5 t DM/ha total herbage with more fescue (8.0 cf. 4.1 t DM/ha) and 1.9 t DM/ha clover in year five, and 11.7 t DM/ha total herbage, 5.4 t DM/ha fescue and 0.8 t DM/ha clover in year six. Sub clover pastures yielded more total, fescue and clover herbage (16.9, 8.8 and 3.2 t DM/ha) than white clover pastures (13.5, 5.7 and 1.0 t DM/ha) in year four, more fescue in year five (7.2 cf. 4.9 t DM/ha), and more clover in year six (1.2 cf. 0.3 t DM/ha). Sheep liveweight gain was greater for sub than white clover pastures in year four (939 cf. 431 kg/ha) and five (697 cf. 481 kg/ha) and 689 kg/ha in year six. Therefore, sub clover and ‘Advance’ were generally more productive than white clover and ‘Flecha’, but both fescues showed similar persistence after 6 years.

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  • Role of needle surface waxes in dynamic exchange of mono- and sesquiterpenes

    Joensuu, J.; Altimir, N.; Hakola, H.; Rostas, Michael; Raivonen, M.; Vestenius, M.; Aaltonen, H.; Riederer, M.; Bäck, J.

    Journal article
    Lincoln University

    Biogenic volatile organic compounds (BVOCs) produced by plants have a major role in atmospheric chemistry. The different physicochemical properties of BVOCs affect their transport within and out of the plant as well as their reactions along the way. Some of these compounds may accumulate in or on the waxy surface layer of conifer needles and participate in chemical reactions on or near the foliage surface. The aim of this work was to determine whether terpenes, a key category of BVOCs produced by trees, can be found on the epicuticles of Scots pine (Pinus sylvestris L.) and, if so, how they compare with the terpenes found in shoot emissions of the same tree. We measured shoot-level emissions of pine seedlings at a remote outdoor location in central Finland and subsequently analysed the needle surface waxes for the same compounds. Both emissions and wax extracts were clearly dominated by monoterpenes, but the proportion of sesquiterpenes was higher in the wax extracts. There were also differences in the terpene spectra of the emissions and the wax extracts. The results, therefore, support the existence of BVOC associated to the epicuticular waxes. We briefly discuss the different pathways for terpenes to reach the needle surfaces and the implications for air chemistry.

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  • Is kanuka and manuka establishment in grassland constrained by mycorrhizal abundance?

    Davis, M.; Dickie, I. A.; Paul, T.; Carswell, F.

    Journal article
    Lincoln University

    Two indigenous small tree and shrub species, kanuka (Kunzea ericoides) and manuka (Leptospermum scoparium), have potential as reforestation species in New Zealand as they are forest pioneer species that can invade grassland naturally from present seed sources. The aim of this study was to determine if establishment of kanuka and manuka from seed in grassland distant from stands of these species might be constrained by lack of appropriate mycorrhizal fungi. Both species were grown in an unsterilised grassland soil from a low productivity montane site assumed to be devoid of appropriate mycorrhizal fungi and inoculated with sterilised or unsterilised O-horizon or mineral soil from beneath three kanuka and three manuka communities expected to contain such fungi. Inoculation with unsterilised O-horizon soil improved kanuka biomass by 36-92%, depending on the source of the inoculant. Inoculation did not improve manuka biomass. No ectomycorrhizal infection was observed on either kanuka or manuka in samples examined under binocular microscope. The biomass response by kanuka to inoculation may be due to introduction of more effective arbuscular mycorrhizal fungi from kanuka communities or possibly to the introduction of soil microorganisms. Testing of inoculation under field conditions will be essential to determine whether establishment of either species in grassland soil by seeding is seriously constrained by lack of appropriate mycorrhizal fungi or soil microorganisms.

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  • Modeling dynamic processes in smallholder dairy value chains in Nicaragua: a system dynamics approach

    Lie, H.; Rich, Karl

    Journal article
    Lincoln University

    In Nicaragua, the production of dairy and beef is the most important source of household income for many smallholder producers. However, erratic volumes and quality of milk limit the participation of small- and medium-scale cattle farmers into higher-value dairy value chains. This research uses a system dynamics (SD) approach to analyze the Matiguás dairy value chain in Nicaragua. The paper presents the conceptual framework of the model and highlights the dynamic processes in the value chain, with a focus on improving feeding systems to achieve higher milk productivity and increased income for producers. The model was developed using a participatory group model building (GMB) technique to jointly conceptualize and validate the model with stakeholders.

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  • Phosphorus fertilization by active dust deposition in a super-humid, temperate environment – Soil phosphorus fractionation and accession processes

    Eger, A.; Almond, Peter C.; Condron, Leo M.

    Journal article
    Lincoln University

    The inventory of soil phosphorus (P) is subject to significant changes over time. The main primary form, bedrock-derived apatite P, becomes progressively lost through leaching, or transformed into more immobile and less plant-accessible, secondary organic and mineral forms. Here we studied the rejuvenating effect of dust deposition on soil P along an active dust flux gradient downwind of a braided river. Along the gradient, we measured soil P fractions to 50 cm depth of six Spodosols and one Inceptisol, supplemented by tree foliage P concentrations. While an increasing dust flux correlates with a twofold increase of foliar P and soil organic P along the gradient, apatite P declines from ~50 to 3 g m⁻² and total P shows no response. Compared to dust-unaffected Spodosols, depth distribution of total P becomes increasingly uniform and organic P propagates deeper into the soil under dust flux. Further, the effect of topsoil P eluviation attenuates due to higher organic P content and the zone of high apatite P concentrations associated with un-weathered subsoil becomes progressively removed from the upper 50 cm. We interpret these patterns as being consistent with upbuilding pedogenesi and conclude that dust-derived mineral P is assimilated in the organic surface horizon and does not reach the mineral soil. Dust-derived mineral P is temporarily stored in the living biomass and returns to the soil with plant and microbial detritus as organic P, which is subsequently buried by further dust increments. We further conclude that (1) the efficiency of P fertilization of the ecosystem by dust accession is higher than through P advection in dust-unaffected Spodosols and (2) organic P may serve as an important source of labile P in a high-leaching environment. ©2013. American Geophysical Union. All Rights Reserved.

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