Farmer preferences for milpa diversity and genetically modified maize in Mexico: a latent class approach

Maize, the second most globally important staple crop after wheat, originated in Mexico, where it is typically grown as part of a set of associated crops and practices called the milpa system. This ancient mode of production is practiced today in ways that vary by cultural context and agro-environment. Milpas generate private economic value, in terms of food security, diet quality and livelihoods, for the twomillion farm households who manage them. Furthermore, milpas generate public economic value by conserving agrobiodiversity, especially that of maize landraces, which have the potential to contribute unique traits needed by plant breeders for future crop improvement. In this way, milpas contribute to global food security in maize. However, the sustainability of the milpa system has been threatened by offfarm employment opportunities, long-distance migration, the increasing commercialization and intensification of maize production. Most recently, the milpa system has been negatively impacted by the contamination of maize landraces by genetically modified (GM) maize, cultivation of which is currently prohibited in Mexico. Here, we employ a choice experiment to estimate Mexican farmers’ valuation of three components of agrobiodiversity (crop species richness, maize variety richness and maize landraces), and examine their interest in cultivating GM maize. Choice experiment data, household level social, economic and demographic data, community level economic development data, and information on milpa production characteristics, and farmers’ attitudes and perceptions with regards to GM food and crops were collected from 420 farm households across 17 communities in three states of Mexico. Using these data, we analyzed the heterogeneity of farmer preferences using a latent class model, which can be used to simultaneously identify sample segments having homogenous preferences for milpa attributes, as well as farmer characteristics affecting preferences. We further identified the characteristics of farmers who are most likely to continue growing maize landraces and managing milpa systems, as well as those least likely to accept GM maize. Specifically, we identified three distinct segments of farmers: (i) Landrace Conservationists derive the highest private economic value from continued management of landraces and the highest economic loss from the possible adoption of GM maize. These farmers are young, dislike GM foods and crops, and are mainly located at the Oaxaca site, where transgenic constructs have been found in maize landraces. (ii) Milpa Diversity Managers derive the highest economic value from managing all of the agrobiodiversity components of the milpa, and suffer fewer losses from management of GM maize. These are older farmers, who are curious and like to experiment with maize varieties. (iii) Marginalized Maize Producers derive little value from crop species and maize variety richness, receive minimal value from maize landraces, and also experience the smallest negative impact from the adoption of GM maize. These farmers are located in the most isolated communities, have the lowest level of productivity, and oversee the largest milpa areas. They are also the most tightly integrated into the maize output markets. These novel findings have implications for debates concerning the adoption of GM maize in Mexico and its associated costs and benefits, as well as for the design of targeted, cost-effective conservation programs on farms

Building the case for biofortification: measuring and maximizing impact in the HarvestPlus program

This paper describes the research and related activities that HarvestPlus undertook at each stage of the research process—discovery, proof of concept, delivery at scale—to establish and continuously strengthen the evidence base for program impact. Structured around the program’s theory of change, the evidence base includes estimates of the magnitude of potential impacts on key development outcomes as well as support for key assumptions that underlie outcomes along the impact pathway from release of biofortified varieties through adoption by farmers, consumption by consumers, and ultimately, to improved nutritional status. The HarvestPlus experience has important lessons for research for development (R4D) programs, many of which struggle to demonstrate progress towards outcomes and impacts throughout the research process.Keywords: Research for Development (R4D), Impact Assessment, Theory of Change, Micronutrient Deficiencies, Crop Varietal Improvemen

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences

Orange maize in Zambia: crop development and delivery experience

Biofortified vitamin A “orange” maize can help address the adverse health effects of vitamin A deficiency. By 2016, HarvestPlus and its partners had developed six orange maize varieties and delivery efforts have reached more than 100,000 farming households in Zambia. HarvestPlus has established the proof of concept, that vitamin A maize varieties can be developed without compromising yield levels and that these varieties can deliver sufficient quantities of vitamin A to improve nutrition. The delivery program has also shown that farmers are willing to grow orange maize varieties and consumers are willing to buy and eat orange maize products. This paper summarizes the country’s nutritional and consumer backgrounds, the crop development and release of orange maize varieties, the delivery efforts in Zambia and impact measurement. It also synthesizes lessons learned and future challenges.Keywords: Biofortification, Vitamin A Deficiency, Orange Maize, Vitamin A Maize, Zambi

Identification of optimal investments

Biofortification is regarded as a complement to supplementation, industrial fortification and dietary diversification in the fight against micronutrient deficiencies. It is important therefore to first identify areas where biofortification may have high impact and prioritize these areas for more in-depth analysis. HarvestPlus has developed the Biofortification Prioritization Index (BPI), which ranks countries globally according to their suitability for investment in biofortification interventions. HarvestPlus is also conducting ex ante micronutrient intervention portfolio analyses, designed to simulate the implementation and impact of a biofortification program in countries which have been identified as suitable candidates for investment. Micronutrient intervention portfolio studies offer the ability to distinguish production, consumption and inadequate micronutrient intake at a more disaggregated level and offer a complementary design and planning tool to simulate the implementation of biofortification and examine its potential impact and cost-effectiveness among different approaches. In addition, these studies are designed to examine multiple interventions within a country, to better understand biofortification’s role in reducing micronutrient deficiency when considered among a suite of interventions. This case study of Zambia demonstrates how these tools can be used to assess the potential impact of biofortification, quantify its cost-effectiveness and examine how it interacts with and complements other interventions. Given the long-term nature of biofortification as an intervention investment, future analyses should continue to incorporate various scenarios including continued investment in sustainable development and the effects of climate change which are likely to condition the impact of biofortification and other interventions.Keywords: Biofortification, Biofortification Priority Index (BPI), Cost-effectiveness, Household Consumption and Expenditure Surveys (HCES

Identification of N-linked glycans as specific mediators of neuronal uptake of acetylated α-Synuclein

Cell-to-cell transmission of toxic forms of α-Synuclein (αS) is thought to underlie disease progression in Parkinson disease. αS in humans is constitutively N-terminally acetylated (αS(acetyl)), although the impact of this modification is relatively unexplored. Here, we report that αSacetyl is more effective at inducing intracellular aggregation in primary neurons than unmodified αS (αS(un)). We identify complex N-linked glycans as binding partners for αS(acetyl) and demonstrate that cellular internalization of αS(acetyl) is reduced significantly upon cleavage of extracellular N-linked glycans, but not other carbohydrates. We verify binding of αS(acetyl) to N-linked glycans in vitro, using both isolated glycans and cell-derived proteoliposomes. Finally, we identify neurexin 1β, a neuronal glycoprotein, as capable of driving glycan-dependent uptake of αS(acetyl). Importantly, our results are specific to αS(acetyl) because αS(un) does not demonstrate sensitivity for N-linked glycans in any of our assays. Our study identifies extracellular N-linked glycans-and the glycoprotein neurexin 1β specifically-as key modulators of neuronal uptake of αS(acetyl), drawing attention to the potential therapeutic value of αS(acetyl)-glycan interactions

Conformational switching within dynamic oligomers underpins toxic gain-of-function by diabetes-associated amyloid

Peptide mediated gain-of-toxic function is central to pathology in Alzheimer's, Parkinson's and diabetes. In each system, self-assembly into oligomers is observed and can also result in poration of artificial membranes. Structural requirements for poration and the relationship of structure to cytotoxicity is unaddressed. Here we focus on islet amyloid polypeptide (IAPP) mediated loss-of-insulin secreting cells in patients with diabetes. Newly developed methods enable structure-function enquiry to focus on intracellular oligomers composed of hundreds of IAPP. The key insights are that porating oligomers are internally dynamic, grow in discrete steps and are not canonical amyloid. Moreover, two classes of poration occur; an IAPP-specific ligand establishes that only one is cytotoxic. Toxic rescue occurs by stabilising non-toxic poration without displacing IAPP from mitochondria. These insights illuminate cytotoxic mechanism in diabetes and also provide a generalisable approach for enquiry applicable to other partially ordered protein assemblies

Coherence lifetimes of excitations in an atomic condensate due to the thin spectrum

We study the quantum coherence properties of a finite sized atomic condensate using a toy-model and the thin spectrum model formalism. The decoherence time for a condensate in the ground state, nominally taken as a variational symmetry breaking state, is investigated for both zero and finite temperatures. We also consider the lifetimes for Bogoliubov quasi-particle excitations, and contrast them to the observability window determined by the ground state coherence time. The lifetimes are shown to exhibit a general characteristic dependence on the temperature, determined by the thin spectrum accompanying the spontaneous symmetry breaking ground state

A simple clinical scoring system to improve the sensitivity and standardization of the diagnosis of mycosis fungoides type cutaneous T-cell lymphoma: logistic regression of clinical and laboratory data

Background  The diagnosis of mycosis fungoides (MF) is notoriously difficult to establish because in the early stages, histological features may be nonspecific or merely suggestive. Objectives  To standardize the diagnosis of MF. Methods  We studied 138 patients with suspected MF referred over a 7-year period to a university department of a dermatology-based cutaneous lymphoma clinic. Six diagnostic criteria were evaluated: clinical morphology, clinical distribution, skin biopsy T-cell receptor gene rearrangement (TCR-GR), skin biopsy pan T-cell marker loss ≥ 2, skin biopsy CD4/CD8 ratio ≥ 6, and skin biopsy diffuse epidermal HLA-DR expression. These six clinical and laboratory criteria were compared by logistic regression analysis in patients with histologically diagnosed MF and those with benign disease. Results  Of the 138 patients, 74 had histology of MF, 47 of benign dermatoses and 17 were indeterminate. Close associations were found between a histological diagnosis of MF and TCR-GR (odds ratio 14·4), classical morphology (7·5), classical distribution (2·5) and diffuse epidermal HLA-DR expression (2·8). Logistic regression models were developed depending on the availability of data (either TCR-GR or HLA-DR). Probabilities for correctly diagnosing MF compared with histology as the ‘gold standard’ were derived from these logistic regression models. A scoring system assigning point values based on these probabilities was then created in order to assist the clinician in making the diagnosis. If using TCR-GR data, a positive TCR-GR = 2·5 points, the presence of classical morphology = 2·0 points, and the presence of classical distribution = 1·5 points. A total score of ≥ 3·5 points assigns a high probability (> 85%) of having MF. If using HLA-DR expression, then the presence of classical morphology = 2·5 points, a positive diffuse epidermal HLA-DR expression = 2·0 points, and the presence of classical distribution = 1·5 points. In this case, a total score of ≥ 4·0 points assigns a high probability (> 85%) of MF. Conclusions  The logistic regression models and scoring systems integrate clinical and laboratory assessments, allow rapid probability estimation, and provide a threshold for the diagnosis of MF in an objective, standardized manner.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75520/1/j.1365-2133.2003.05458.x.pd