Economics of managing acid soils in dryland mixed cropping systems: comparing gross margins with whole-farm analysis derived using a business process model

A 12-year experiment designed to show the benefits of applying lime to acid soils when growing annual pasture, perennial pasture, and annual crops in rotations with annual or perennial pastures, provides the context for comparing methods of economic analysis. In this study enterprise gross margins are compared with whole-farm cumulative monthly cash flows derived using a business process model. The current study gave gross margins comparable with those of a recently published study based on the first 12 years of the same field experiment at Book Book near Wagga Wagga in southern NSW (Li et al., 2010). Both gross margin analyses indicated positive results for all treatments. However, because key fixed and capital cost items were not taken into account in the gross margin analysis the financial benefits of the treatments were overstated. In the whole-farm analysis, a full set of accounts (including fixed and capital costs) was developed for the experimental combinations of prime lamb and dryland cropping enterprises and used to generate a monthly cash flow sequence for each treatment over the 12-year term of the experiment. This full financial analysis, where all costs are included, showed all mixed treatments (cropping and grazing) accumulated unsustainable losses over the period of the trial. The grazing-only treatments generated positive cash lows over the 12 year period, but 2 accumulated high levels of debt in the initial years. None of these outcomes were predicted by gross margins, which were consistently positive for all treatments. This paper concludes that the analysis of trial results benefits from interpretation in the context of whole-farm analysis, verified by district experience. Relying on gross margin analysis alone would have supported loss-making outcomes in this trial. This conclusion has important ramifications for analysis of all systems trials.Agribusiness,

Subsoil Acidity Determines Survival of Lucerne on a Highly Acidic Soil

Lucerne (Medicago sativa) is one of most productive perennial species in southern Australia. However, productivity is severely restricted under acid soils (Irwin et al. 2001). Fenton et al. (1996) reported that lucerne performs poorly if soil pH was below 5 and exchangeable aluminium was over 5%. It is estimated that there are 24 m ha of acidic subsoil in southern Australia (Dolling et al. 2001). A long-term liming experiment, 1992 to 2010, aimed to ameliorate subsoil acidity via a vigorous liming program (Li et al. 2001). This paper reports survival of lucerne during the 3rd cycle of the experiment from 2004 to 2009

Lucerne for Acid Soils: A Field Evaluation of Early Generation Aluminium Tolerant Genotypes

The development of lucerne germplasm tolerant of acidic soil conditions has long been a research objective of international significance. Many initiatives have previously failed to produce genotypes with adequate improvement in tolerance to be deemed economically viable and as a consequence, still no cultivar of lucerne exists that has improved adaptation to acidic soils. An Australian research program spanning the previous decade sought to redress this issue by developing lucerne genotypes with significantly enhanced tolerance to aluminium (Al) toxicity. Using recurrent selection in hydroponic solution culture, populations selected comprised individuals which displayed enhanced seedling root growth following a pulse of Al toxic solution (Scott et al. 2008). A subsequent pot experiment showed that these populations exhibited up to 40% increase in seedling root length when grown in an acidic soil with high Al concentration, though there was a differential response observed between the elite populations (Hayes et al. 2011). The current study tested the hypothesis that lucerne establishment in the field would be higher in populations selected in high Al solution culture when grown in an acidic soil environment

Simulating collective behavior in the movement of immigrants by using a spatial prisoner’s dilemma with move option

The movement of immigrants is simulated by using a spatial Prisoner’s Dilemma (PD) with move option. We explore the effect of collective behavior in an evolutionary migrating dynamics. Simulation results show that immigrants adopting collective strategy perform better and thus gain higher survival rate than those not. This research suggests that the clustering of immigrants promotes cooperation

Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, \u3cem\u3eFrankliniella occidentalis\u3c/em\u3e

Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually

Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, \u3cem\u3eFrankliniella occidentalis\u3c/em\u3e

Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually

A new ensemble coevolution system for detecting HIV-1 protein coevolution

Background: A key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect position-specific coevolution within and between different proteins. However, an ensemble coevolution system that integrates different methods to improve the detection of HIV-1 protein coevolution has not been developed. Results: We integrated 27 sequence-based prediction methods published between 2004 and 2013 into an ensemble coevolution system. This system allowed combinations of different sequence-based methods for coevolution predictions. Using HIV-1 protein structures and experimental data, we evaluated the performance of individual and combined sequence-based methods in the prediction of HIV-1 intra- and inter-protein coevolution. We showed that sequence-based methods clustered according to their methodology, and a combination of four methods outperformed any of the 27 individual methods. This four-method combination estimated that HIV-1 intra-protein coevolving positions were mainly located in functional domains and physically contacted with each other in the protein tertiary structures. In the analysis of HIV-1 inter-protein coevolving positions between Gag and protease, protease drug resistance positions near the active site mostly coevolved with Gag cleavage positions (V128, S373-T375, A431, F448-P453) and Gag C-terminal positions (S489-Q500) under selective pressure of protease inhibitors. Conclusions: This study presents a new ensemble coevolution system which detects position-specific coevolution using combinations of 27 different sequence-based methods. Our findings highlight key coevolving residues within HIV-1 structural proteins and between Gag and protease, shedding light on HIV-1 intra- and inter-protein coevolution. Reviewers: This article was reviewed by Dr. Zoltán Gáspári. © Li et al

An integrated map of HIV genome-wide variation from a population perspective

Background: The HIV pandemic is characterized by extensive genetic variability, which has challenged the development of HIV drugs and vaccines. Although HIV genomes have been classified into different types, groups, subtypes and recombinants, a comprehensive study that maps HIV genome-wide diversity at the population level is still lacking to date. This study aims to characterize HIV genomic diversity in large-scale sequence populations, and to identify driving factors that shape HIV genome diversity. Results: A total of 2996 full-length genomic sequences from 1705 patients infected with 16 major HIV groups, subtypes and circulating recombinant forms (CRFs) were analyzed along with structural, immunological and peptide inhibitor information. Average nucleotide diversity of HIV genomes was almost 50% between HIV-1 and HIV-2 types, 37.5% between HIV-1 groups, 14.7% between HIV-1 subtypes, 8.2% within individual HIV-1 subtypes and less than 1% within single patients. Along the HIV genome, diversity patterns and compositions of nucleotides and amino acids were highly similar across different groups, subtypes and CRFs. Current HIV-derived peptide inhibitors were predominantly derived from conserved, solvent accessible and intrinsically ordered structures in the HIV-1 subtype B genome. We identified these conserved regions in Capsid, Nucleocapsid, Protease, Integrase, Reverse transcriptase, Vpr and the GP41 N terminus as potential drug targets. In the analysis of factors that impact HIV-1 genomic diversity, we focused on protein multimerization, immunological constraints and HIV-human protein interactions. We found that amino acid diversity in monomeric proteins was higher than in multimeric proteins, and diversified positions were preferably located within human CD4 T cell and antibody epitopes. Moreover, intrinsic disorder regions in HIV-1 proteins coincided with high levels of amino acid diversity, facilitating a large number of interactions between HIV-1 and human proteins. Conclusions: This first large-scale analysis provided a detailed mapping of HIV genomic diversity and highlighted drug-target regions conserved across different groups, subtypes and CRFs. Our findings suggest that, in addition to the impact of protein multimerization and immune selective pressure on HIV-1 diversity, HIV-human protein interactions are facilitated by high variability within intrinsically disordered structures. © 2015 Li et al.; licensee BioMed Central