PRODUCTION AGRICULTURE AS A KNOWLEDGE CREATING SYSTEM

Production Economics,

The Role and Responsibility of the Public

It\u27s the title of the conference—the court of public opinion—and the topic of this panel. Professor Christopher Schroeder of Duke Law School is joined by media and public policy professor Kim Gross, senior attorney for the Institute for Justice Scott Bullock, and litigation director of the ACLU Steve Shapiro to contemplate both the influence of the media on public opinion and ways to use the media as an advocacy tool. Gross discusses her research into the influence of media coverage on the public, followed by Bullock and Shapiro who explain the ways in which public interest law may choose to incorporate a media strategy into a larger legal battle. Questions/themes/discussion topics Media framing How media coverage can influence public opinion Factors that influence the media\u27s power How the Duke lacrosse case differs from typical crime coverage Legal strategies of public interest organizations Winning in the court of law, but losing in the court of public opinion Losing in the court of law, but winning in the court of public opinio

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad

Western Gull Foraging Behavior as an Ecosystem State Indicator in Coastal California

With accelerating climate variability and change, novel approaches are needed to warn managers of changing ecosystem state and to identify appropriate management actions. One strategy is using indicator species—like seabirds as ecosystem sentinels—to monitor changes in marine environments. Here, we explore the utility of western gulls (Larus occidentalis) breeding on Southeast Farallon Island as a proxy of ecosystem state in coastal California by investigating the interannual variability in gull foraging behavior from 2013 to 2019 in relation to upwelling conditions, prey abundances, and overlap with humpback whales (Megaptera novaeangliae) as gulls frequently feed in association with whales. Western gulls have a flexible diet and forage on land and at-sea. We combined gull GPS tracking data during the incubation phase, ecosystem survey data on multiple predator and prey species, and derived oceanographic upwelling products. When foraging at sea, gulls overlapped with cool upwelled waters. During 2015–2017, 25% more gull foraging trips visited land than in other years, where land trips were on average ∼8 h longer and 40% further than sea trips, which coincided with high compression of coastally upwelled waters (habitat compression) in 2015–2016. Gull foraging behavior was related to local prey abundances, where more foraging occurred near shore or on land when prey abundances were low. However, visual surveys indicated that ∼70% of humpback whale observations co-occurred with gulls, and the year with the most foraging on land (2017) corresponded to regionally low relative whale abundances, suggesting gull movement patterns could be an indicator of whale presence. Further, both whales and gulls forage near-shore under high upwelling habitat compression and low krill abundance. Hence, the deployment of year-round tags on gulls with the capability of near real-time data accessibility could provide important fine-scale metrics for conservation and management of the threatened yet recovering eastern Pacific humpback whale population between infrequent and coarse surveys. Entanglement in fishing gear and ship strikes are major inhibitors to whale recovery and have increased concomitantly with human use of ocean resources. Moreover, as climate variability and change increase, novel indicators should be explored and implemented to inform marine spatial planning and protect species across multiple scales from new risks

Impact of a Tropical Cyclone on Terrestrial Inputs and Bio-Optical Properties in Princess Charlotte Bay (Great Barrier Reef Lagoon)

In January 2013, tropical cyclone Oswald caused widespread flooding in the North-East coast of Australia, and large and highly episodic inputs into Princess Charlotte Bay (PCB, northern Great Barrier Reef). Freshwater outflows from the Normanby and Kennedy rivers, the two main rivers draining the adjacent catchments, resulted in drastic changes in physical, biogeochemical and optical properties within PCB. On 31 January, 2 days after the peak riverine discharge from the Normanby river, nutrients and dissolved organic matter contents peaked under the influence of large outflows from the Kennedy river into the western section of the bay (5.8 μM for dissolved inorganic nitrogen, 6.9 g m−3 for dissolved organic carbon and 6.1 m−1 for the colored dissolved organic matter absorption coefficient at 412 nm). In the eastern section of the bay, the situation appeared more ‘mixed’, with a suspended solids concentration reaching 23.1 g m−3 close to the Normanby river mouth. The main phytoplankton bloom occurred in the transition zone between the Kennedy and Normanby flood plumes, and was dominated by diatoms with a chlorophyll a concentration reaching 14.6 mg m−3. This study highlights the need to better describe the critical spatial and temporal scales of variability of key biogeochemical and optical properties after a major flood event. The data collected is key to improve the accuracy of ocean color remote sensing algorithms and regional biogeochemical budgets following highly episodic inputs

A phase 2a randomized clinical trial of intravenous vedolizumab for the treatment of steroid-refractory intestinal acute graft-versus-host disease

Steroid-refractory (SR) acute graft-versus-host disease (aGvHD) remains a significant complication after allogeneic hematopoietic cell transplantation. Systemic corticosteroids are first-line therapy for aGvHD, but apart from ruxolitinib, there are no approved treatments for SR aGvHD. Vedolizumab is approved for treatment of ulcerative colitis and Crohn\u27s disease, and may be effective for treatment of SR intestinal aGvHD. We conducted a phase 2a trial (NCT02993783) to evaluate the clinical efficacy, tolerability, and safety of vedolizumab 300 and 600 mg for SR intestinal aGvHD. This study was terminated before full enrollment was completed because early results failed to demonstrate positive proof-of-concept in efficacy. Before termination, 17 participants had enrolled and an early response in intestinal aGvHD was observed in 11 and eight participants at days 15 and 28, respectively. All adverse events observed were consistent with those expected in a population with SR intestinal aGvHD. Overall, vedolizumab did not meet the primary efficacy endpoint (overall response at day 28), likely owing to premature study drug discontinuation, lack of efficacy, and the competing risks inherent with a population with advanced SR intestinal aGvHD. Nevertheless, this study provides valuable insights into the considerations needed when conducting studies in patients with SR intestinal aGvHD

Comparison of Machine Learning Algorithms for Predictive Modeling of Beef Attributes Using Rapid Evaporative Ionization Mass Spectrometry (REIMS) Data

Ambient mass spectrometry is an analytical approach that enables ionization of molecules under open-air conditions with no sample preparation and very fast sampling times. Rapid evaporative ionization mass spectrometry (REIMS) is a relatively new type of ambient mass spectrometry that has demonstrated applications in both human health and food science. Here, we present an evaluation of REIMS as a tool to generate molecular scale information as an objective measure for the assessment of beef quality attributes. Eight different machine learning algorithms were compared to generate predictive models using REIMS data to classify beef quality attributes based on the United States Department of Agriculture (USDA) quality grade, production background, breed type and muscle tenderness. The results revealed that the optimal machine learning algorithm, as assessed by predictive accuracy, was different depending on the classification problem, suggesting that a “one size fits all” approach to developing predictive models from REIMS data is not appropriate. The highest performing models for each classification achieved prediction accuracies between 81.5–99%, indicating the potential of the approach to complement current methods for classifying quality attributes in beef

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species