A Preliminary Analysis of the Benefits of Introducing Apomixis into Rice

The objective of this research is to undertake an ex ante economic analysis of basic scientific research that aims to identify the gene(s) that control apomictic reproduction, with the ultimate aim of transferring the characteristic into commercially important crops. This paper reports very preliminary results, using the introduction of apomixis into rice as a case study. Apomixis is a natural, asexual method of plant reproduction resulting in offspring that are genetically identical to the mother plant. Apomixis promises to revolutionize plant breeding by providing a system for crop improvement that allows any desired variety, including hybrids, to breed true. This ability will make both breeding and seed production more efficient. It offers the opportunity for plant breeders to more readily develop varieties that are specifically adapted to local conditions, using, and thus conserving, greater genetic diversity. Apomixis will also allow resource-poor farmers to replant the seed they produce from locally bred varieties year after year, a strategy not possible with today's commercial hybrid varieties. Global changes in aggregate welfare, resource allocation, production and price levels are calculated using the global economy-wide computable general equilibrium model known as GTAP. Preliminary modeling results suggest that the overall welfare gains associated apomictic rice could be substantial.Agribusiness, Agricultural and Food Policy, Crop Production/Industries, Environmental Economics and Policy, Farm Management, Institutional and Behavioral Economics, Land Economics/Use, Production Economics, Research Methods/ Statistical Methods,

Nonmarket valuation of water quality: Addressing spatially heterogeneous preferences using GIS and a random parameter logit model

The spatial distribution of agri-environmental policy benefits has important implications for the efficient allocation of management effort. The practical convenience of relying on sample mean values of individual benefits for aggregation can come at the cost of biased aggregate estimates. The main objective of this paper is to test spatial hypotheses regarding respondents' local water quality and quantity, and their willingness-to-pay for improvements in water quality attributes. This paper combines choice experiment and spatially related water quality data via a Geographical Information System (GIS) to develop a method that evaluates the influence of respondents' local water quality on willingness-to-pay for river and stream conservation programmes in Canterbury, New Zealand. Results showed that those respondents who live in the vicinity of low quality waterways are willing to pay more for improvements relative to those who live near to high quality waterways. The study also found that disregarding the influence of respondents' local water quality data has a significant impact on the magnitude of welfare estimates and causes substantial underestimation of aggregated benefits

How important is reputation for New Zealand wine makers?

The wine industry in New Zealand has been maturing over the past few decades, with consumers becoming more sophisticated and wineries responding by increasing their production of premium varieties. In addition, there have been several legal changes and subsequent changes to the distribution and marketing of wine in New Zealand that have made wine more widely available. It is therefore an interesting and dynamic time to gain a more comprehensive understanding of the relative effects of regional reputation and producer-specific quality on the willingness to pay for domestically produced premium table wine in New Zealand. Previous empirical work suggests that New Zealand consumers rely on both expert opinion and regional reputation when determining their willingness to pay for wine produced domestically. The current paper extends this work by considering the development of a winery‟s reputation in more detail. Hedonic price analysis is used to determine the price premia associated with a range of indicators of both individual and collective reputation. Preliminary statistical results are presented and interpreted within the context of a growing body of international literature on wine economics

Dairy industry scenarios: Informing dairy farm systems for the future

The purpose of the Dairy Farm Systems for the Future project is to explore how best to identify and design farming systems best suited to the changing environment and farmer circumstances. The first step in the project was to describe that changing business environment to develop a better understanding by farmers, industry and researchers of possible, plausible future scenarios for dairying in New Zealand. These scenarios are now providing reliable and comprehensive information, a context, for the design and rigorous evaluation of a range of farming systems best suited to each possible, plausible future. The scenarios were developed through a series of workshops and research phases throughout 2014/15. The process involved 68 industry stakeholders (25 organisations plus farmers/farm consultants) and resulted in the development of four scenarios. The scenario development process, outlined in this report, looked beyond the current views (the base scenario) to come up with three very different futures that the dairy industry could be facing in 10 years' time. The futures reflect the interpretation of 16 specific local and global uncertainties/risks. In-depth research into the level of variation in, and the implications of, each uncertainty informed the scenario building process.DairyNZ, Ministry for Primary Industrie

Genome-wide meta-analysis of muscle weakness identifies 15 susceptibility loci in older men and women

© 2021, The Author(s). Low muscle strength is an important heritable indicator of poor health linked to morbidity and mortality in older people. In a genome-wide association study meta-analysis of 256, 523 Europeans aged 60 years and over from 22 cohorts we identify 15 loci associated with muscle weakness (European Working Group on Sarcopenia in Older People definition: n = 48,596 cases, 18.9% of total), including 12 loci not implicated in previous analyses of continuous measures of grip strength. Loci include genes reportedly involved in autoimmune disease (HLA-DQA1p = 4 × 10−17), arthritis (GDF5p = 4 × 10−13), cell cycle control and cancer protection, regulation of transcription, and others involved in the development and maintenance of the musculoskeletal system. Using Mendelian randomization we report possible overlapping causal pathways, including diabetes susceptibility, haematological parameters, and the immune system. We conclude that muscle weakness in older adults has distinct mechanisms from continuous strength, including several pathways considered to be hallmarks of ageing

Genome-wide meta-analysis of muscle weakness identifies 15 susceptibility loci in older men and women.

Low muscle strength is an important heritable indicator of poor health linked to morbidity and mortality in older people. In a genome-wide association study meta-analysis of 256,523 Europeans aged 60 years and over from 22 cohorts we identify 15 loci associated with muscle weakness (European Working Group on Sarcopenia in Older People definition: n = 48,596 cases, 18.9% of total), including 12 loci not implicated in previous analyses of continuous measures of grip strength. Loci include genes reportedly involved in autoimmune disease (HLA-DQA1 p = 4 × 10-17), arthritis (GDF5 p = 4 × 10-13), cell cycle control and cancer protection, regulation of transcription, and others involved in the development and maintenance of the musculoskeletal system. Using Mendelian randomization we report possible overlapping causal pathways, including diabetes susceptibility, haematological parameters, and the immune system. We conclude that muscle weakness in older adults has distinct mechanisms from continuous strength, including several pathways considered to be hallmarks of ageing

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p