Complexity of animal breeding choice making.

The last decades of developments in animal breeding, genetics, genomics and data recording technologies have allowed the evaluation of larger numbers of animal and animal traits than ever before. This should help make animal breeding choices more informed, but it also makes them far more complex. This complexity may be overwhelming farmers, thus compromising realization of potential genetic gain in livestock industries. However, the effect of complexity of animal breeding choices on farmers' selection of animals has received very little theoretical consideration to date. This paper reviews the theoretical principles of complex decisions, contextualizes the findings to the field of animal breeding, and analyses how farmers and the animal breeding industry are currently dealing with complexity. According to the findings of the analyses of complex decisions in other fields, the complexity of animal breeding choices is likely to lead to farmers using conscious or unconscious simplifying strategies (heuristics) to handle such complexity. When these heuristics are ineffective, poor selection decisions and a potential loss of genetic progress can be expected. Further, studies using survey experiments to understand farmer behaviour and selection preferences may be compromised by the complexity of the survey´s choice tasks. Thus, while many animal breeding industries recognize the complexity of animal breeding choices for farmers and attempts are made to assist farmers in their choice making, the effectiveness of these attempts is not well quantified and understood. We discuss three areas of research that could be key to disentangling how, and by how much, animal breeding choice complexity affects farmers' decisions.

Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes.

BACKGROUND: Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. METHODS: The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection. A deterministic simulation model was used to predict selection differentials and the flow of genetic superiority through the different tiers. Cumulative discounted economic benefits were calculated based on trait gains achieved in each of the tiers and considering the extra revenue and associated costs of applying recording, genotyping and selection practices in the multiplier tier of the breeding scheme. RESULTS: Performance recording combined with genomic or parentage information in the multiplier tier reduced the genetic lag between the nucleus and commercial flock by 2 to 3 years. The overall economic benefits of improved performance in the commercial tier offset the costs of recording the multiplier. However, it took more than 18 years before the cumulative net present value of benefits offset the costs at current test prices. Strategies in which recorded multiplier ewes were selected as replacements for the nucleus flock did modestly increase profitability when compared to a closed nucleus structure. Applying genomic selection is the most beneficial strategy if testing costs can be reduced or by genotyping only a proportion of the selection candidates. When the cost of genotyping was reduced, scenarios that combine performance recording with genomic selection were more profitable and reached breakeven point about 10 years earlier. CONCLUSIONS: Economic benefits can be generated in multiplier flocks by implementing performance recording in conjunction with either DNA pedigree recording or genomic technology. These recording practices reduce the long genetic lag between the nucleus and commercial flocks in multi-tiered breeding programs. Under current genotyping costs, the time to breakeven was found to be generally very long, although this varied between strategies. Strategies using either genomic selection or DNA pedigree verification were found to be economically viable provided the price paid for the tests is lower than current prices, in the long-term.

Expression of P. falciparum var genes involves exchange of the histone variant H2A.Z at the promoter.

Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes.

Simulating the Commercial Implementation of Gene-Editing for Influenza A Virus Resistance in Pigs: An Economic and Genetic Analysis.

The development of swine Influenza A Virus resistance along with genetic technologies could complement current control measures to help to improve animal welfare standards and the economic efficiency of pig production. We have created a simulation model to assess the genetic and economic implications of various gene-editing methods that could be implemented in a commercial, multi-tiered swine breeding system. Our results demonstrate the length of the gene-editing program was negatively associated with genetic progress in commercial pigs and that the time required to reach fixation of resistance alleles was reduced if the efficiency of gene-editing is greater. The simulations included the resistance conferred in a digenic model, the inclusion of genetic mosaicism in progeny, and the effects of selection accuracy. In all scenarios, the level of mosaicism had a greater effect on the time required to reach resistance allele fixation and the genetic progress of the herd than gene-editing efficiency and zygote survival. The economic analysis highlights that selection accuracy will not affect the duration of gene-editing and the investment required compared to the effects of gene-editing-associated mosaicism and the swine Influenza A Virus control strategy on farms. These modelling results provide novel insights into the economic and genetic implications of targeting two genes in a commercial pig gene-editing program and the effects of selection accuracy and mosaicism.

Market Intelligence and Incentive-Based Trait Ranking for Plant Breeding: A Sweetpotato Pilot in Uganda.

Crop breeding programs must accelerate crop improvement, spur widespread adoption of new varieties and increase variety turnover they are to meet the diverse needs of their clients. More comprehensive quantitative approaches are needed to better inform breeding programs about the preferred traits among farmers and other actors. However, the ability of current breeding programs to meet the demands of their clients is limited by the lack of insights about value chain actor preference for individual or packages of traits. Ranking traits based on monetary incentives, rather than subjective values, represents a more comprehensive, consistent, and quantitative approach to inform breeding programs. We conducted a large pilot in Uganda to assess the implementation of a novel approach to trait ranking, using a uniquely large sample of diverse sweetpotato value chain actors. We found meaningful differences in trait ranking and heterogeneity among different actors using this approach. We also show our approach's effectiveness at uncovering unmet demand for root quality traits and at characterizing the substantial trait demand heterogeneity among value chain players. Implementing this approach more broadly for sweetpotato and other crops would increase the effectiveness of breeding programs to improve food security in developing countries.

Antibody recognition of heterologous variant surface antigens after a single Plasmodium falciparum infection in previously naive adults.

Antibodies to variant surface antigens (VSA) including Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) have been associated with protective antimalarial immunity that appears to be variant-specific. This study of adult returned travelers with a single acute P. falciparum infection investigated whether a primary antibody response includes IgG specific for heterologous VSA. We found that 11 of 14 patients had IgG reactive with up to six P. falciparum lines expressing different heterologous PfEMP1 variants, measured by flow cytometry (reactivity greater than two times the mean of the negative control sera was defined as "positive"), with high reactivity (greater than four times the mean of the negative controls) detected in three patients. The dominant variant(s) recognized differed between seropositive individuals. Despite previous evidence that antibody responses to heterologous VSA are short-lived, seven patients had detectable IgG at > 20 weeks post-infection. Together these data suggest that a single P. falciparum infection can be sufficient to induce antibodies reactive with several PfEMP1 variants, although the repertoire of target epitopes they recognize may still be restricted.

VAR2CSA is the principal ligand for chondroitin sulfate A in two allogeneic isolates of Plasmodium falciparum.

Malaria during pregnancy causes serious disease that is associated with sequestration in the placenta of Plasmodium falciparum infected erythrocytes that adhere to several host receptors, including chondroitin sulfate A (CSA). The principal CSA binding ligand associated with placental sequestration is the P. falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the var2csa gene. We disrupted the var2csa gene in two allogeneic parasites and ablated CSA binding. However, in one parasite line we were able to re-select for adhesion to bovine trachea CSA associated with transcription of two var genes, var-CS2 and varP. Parasites transcribing parts of var-CS2 and varP were present in the placentae of some infected women but the mutant parasites that transcribed var-CS2 and varP were recognized by sera from men and pregnant women independent of parity. This work raises the possibility that the PfEMP1 molecules encoded by var-CS2 and varP may be minor contributors to placental malaria but also confirms the importance of the immunodominant, conserved var2csa PfEMP1s in pregnancy associated malaria and strengthens the case for var2csa as a pregnancy-specific malaria vaccine.

Early safety and efficacy of percutaneous left atrial appendage suture ligation: results from the U.S. transcatheter LAA ligation consortium.

BACKGROUND: Transcatheter left atrial appendage (LAA) ligation may represent an alternative to oral anticoagulation for stroke prevention in atrial fibrillation. OBJECTIVES: This study sought to assess the early safety and efficacy of transcatheter ligation of the LAA for stroke prevention in atrial fibrillation. METHODS: This was a retrospective, multicenter study of consecutive patients undergoing LAA ligation with the Lariat device at 8 U.S. sites. The primary endpoint was procedural success, defined as device success (suture deployment and <5 mm leak by post-procedure transesophageal echocardiography), and no major complication at discharge (death, myocardial infarction, stroke, Bleeding Academic Research Consortium bleeding type 3 or greater, or cardiac surgery). Post-discharge management was per operator discretion. RESULTS: A total of 154 patients were enrolled. Median CHADS2 score (congestive heart failure, hypertension, age ≥ 75 years, diabetes mellitus, prior stroke, transient ischemic attack, or thromboembolism [doubled]) was 3 (interquartile range: 2 to 4). Device success was 94%, and procedural success was 86%. A major complication occurred in 15 patients (9.7%). There were 14 major bleeds (9.1%), driven by the need for transfusion (4.5%). Significant pericardial effusion occurred in 16 patients (10.4%). Follow-up was available in 134 patients at a median of 112 days (interquartile range: 50 to 270 days): Death, myocardial infarction, or stroke occurred in 4 patients (2.9%). Among 63 patients with acute closure and transesophageal echocardiography follow-up, there were 3 thrombi (4.8%) and 13 (20%) with residual leak. CONCLUSIONS: In this initial multicenter experience of LAA ligation with the Lariat device, the rate of acute closure was high, but procedural success was limited by bleeding. A prospective randomized trial is required to adequately define clinical efficacy, optimal post-procedure medical therapy, and the effect of operator experience on procedural safety.

Ectopic recombination of a malaria var gene during mitosis associated with an altered var switch rate.

The Plasmodium falciparum var multigene family encodes P. falciparum erythrocyte membrane protein 1, which is responsible for the pathogenic traits of antigenic variation and adhesion of infected erythrocytes to host receptors during malaria infection. Clonal antigenic variation of P. falciparum erythrocyte membrane protein 1 is controlled by the switching between exclusively transcribed var genes. The tremendous diversity of the var gene repertoire both within and between parasite strains is critical for the parasite's strategy of immune evasion. We show that ectopic recombination between var genes occurs during mitosis, providing P. falciparum with opportunities to diversify its var repertoire, even during the course of a single infection. We show that the regulation of the recombined var gene has been disrupted, resulting in its persistent activation although the regulation of most other var genes is unaffected. The var promoter and intron of the recombined var gene are not responsible for its atypically persistent activity, and we conclude that altered subtelomeric cis sequence is the most likely cause of the persistent activity of the recombined var gene.

Antigenic differences and conservation among placental Plasmodium falciparum-infected erythrocytes and acquisition of variant-specific and cross-reactive antibodies.

Background. Pregnant women are infected by Plasmodium falciparum with novel antigenic phenotypes that adhere to chondroitin sulfate A (CSA) and other receptors in the placenta. The diverse and variant parasite protein P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is encoded by var genes, is a ligand for CSA and a major target of antibodies associated with protective immunity.Methods. Serum samples from pregnant women exposed to malaria were tested for immunoglobulin G, adhesion-inhibitory antibodies, and agglutinating antibodies to different CSA-binding isolates expressing conserved var2csa-type genes and to parasite isolates from infected placentas. Parasite isolates also were examined to assess PfEMP1 expression, the effect of trypsin treatment of infected erythrocytes on parasite adhesion and cleavage of PfEMP1, and inhibition of adhesion by rabbit antiserum raised against a CSA-binding isolate.Results. Findings demonstrated that (1) there are significant antigenic differences between CSA-binding isolates that correspond with polymorphisms in var2csa; (2) there are differences in the properties of PfEMP1 and antibody reactivity between CSA-binding and placental isolates, which express multiple PfEMP1 forms; (3) acquired antibodies target diverse and cross-reactive epitopes expressed by CSA-binding infected erythrocytes, and cross-reactive antibodies are not necessarily cross-inhibitory; and (4) the breadth of antibody reactivity is greater among multigravidae than among primigravidae.Conclusions. Immunity may be mediated by a repertoire of antibodies to diverse and common epitopes. Strategies based on vaccination with a single domain or isolate might be hindered by antigenic diversity.

Broad analysis reveals a consistent pattern of var gene transcription in Plasmodium falciparum repeatedly selected for a defined adhesion phenotype.

Transcription of the majority of the members of the Plasmodium falciparum var multigene family were analysed in two isolates by a quantitative approach. Both of these isolates had been repeatedly selected for adhesion to chondroitin sulphate A (CSA) and one had also been selected for adhesion to hyaluronic acid (HA). These adhesion phenotypes are expressed by many parasites isolated from placentae and are associated with malaria disease in pregnancy. Increased transcription of the var gene var2csa, or its homologue IT4 var4, was associated with the CSA and HA adhesion phenotypes in all parasites suggesting that it was the dominant, if not the only, var gene that encoded adhesion to CSA in these allogeneic isolates. Some var genes were consistently transcribed at higher levels than others regardless of expressed adhesion phenotypes suggesting a transcriptional hierarchy. Unspliced or partial transcripts were detected for most var genes tested. These atypical var gene transcripts may have implications for the regulation of var gene transcription.

Cross-reactive surface epitopes on chondroitin sulfate A-adherent Plasmodium falciparum-infected erythrocytes are associated with transcription of var2csa.

Malaria in pregnancy is associated with placental accumulation of Plasmodium falciparum-infected erythrocytes (IE) that adhere to chondroitin sulfate A (CSA). Adhesion is mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1), a variant parasite protein expressed on the surface of IE and encoded by var genes. Rabbit antiserum was generated against the CSA-adherent P. falciparum line CS2, in which the dominant var transcribed is var2csa, a relatively conserved var gene that has been associated with CSA adhesion. Anti-CS2 recognized genetically distinct CSA-adherent P. falciparum lines but not CD36-adherent parent lines. Reactivity with anti-CS2 correlated with the level of adhesion to CSA. Fluorescence-activated cell sorting according to binding of anti-CS2 showed reactivity was associated with CSA adhesion and transcription of var2csa. These data are consistent with the hypothesis that var2csa encodes a PfEMP1 expressed on the surface of IE, which mediates adhesion to CSA and is relatively conserved between genetically distinct strains of P. falciparum.