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Creators/Authors contains: "McNamara, John"

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  1. Abstract The US agriculture and food systems research and education system remains the envy of the world, and the US Department of Agriculture and the Land-Grant University system lead the public and private partnerships that have improved agricultural productivity and human health phenomenally for over 160 years. The continuation of these improvements relies on equitable access to trustworthy data—particularly in genetics and phenomics—and the ability to leverage such data to address future scientific challenges. In this article, we discuss the growing need in agriculture for phenomic databases that follow findable, accessible, interoperable, and reproducible data (FAIR) guidelines, as well as the need for public policy supporting a sustainable funding model for these databases. 
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    Free, publicly-accessible full text available August 25, 2026
  2. Abstract Advances in agricultural genetic, genomic, and breeding (GGB) technologies generate increasingly large and complex datasets that need to be adequately managed and shared. While several agricultural biological databases maintain and curate GGB data, not all scientists are aware of them and how they can be used to access and share data. In addition, there is the need to increase scientists’ awareness that appropriate data archiving and curation increases data longevity and value and bolsters scientific discoveries’ reproducibility and transparency. The AgBioData Education working group aims to address these unmet needs and developed a modular curriculum for educators teaching the basics of biological databases and the findable, accessible, interoperable, and reusable (FAIR) principles to undergraduate and graduate students (https://www.agbiodata.org/). The present paper provides an overview of the topics covered within the curriculum, called ‘AgBioData Curriculum for Ag FAIR Data,’ its audience and modalities, and how it will positively impact all the different stakeholders of the agricultural database ecosystem. We hope the modular curriculum presented here can help scientists and students understand and support database use in all aspects of improving our global food system. Database URL: https://zenodo.org/records/14278084 
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  3. Synopsis Early marine invertebrates like the Branchiopoda began their sojourn into dilute media some 500 million years ago in the Middle Cambrian. Others like the Mollusca, Annelida, and many crustacean taxa have followed, accompanying major marine transgressions and regressions, shifting landmasses, orogenies, and glaciations. In adapting to these events and new habitats, such invertebrates acquired novel physiological abilities that attenuate the ion loss and water gain that constitute severe challenges to life in dilute media. Among these taxon-specific adaptations, selected from the subcellular to organismal levels of organization, and constituting a feasible evolutionary blueprint for invading freshwater, are reduced body permeability and surface (S) to volume (V) ratios, lowered osmotic concentrations, increased osmotic gradients, increased surface areas of interface epithelia, relocation of membrane proteins in ion-transporting cells, and augmented transport enzyme abundance, activity, and affinity. We examine these adaptations in taxa that have penetrated into freshwater, revealing diversified modifications, a consequence of distinct body plans, morpho-physiological resources, and occupation routes. Contingent on life history and reproductive strategy, numerous patterns of osmotic regulation have emerged, including intracellular isosmotic regulation in weak hyper-regulators and well-developed anisosmotic extracellular regulation in strong hyper-regulators, likely reflecting inertial adaptations to early life in an estuarine environment. In this review, we address osmoregulation in those freshwater invertebrate lineages that have successfully invaded this biotope. Our analyses show that across 66 freshwater invertebrate species from six phyla/classes that have transmuted into freshwater from the sea, hemolymph osmolalities decrease logarithmically with increasing S:V ratios. The arthropods have the highest osmolalities, from 300 to 650 mOsmoles/kg H2O in the Decapoda with 220–320 mOsmoles/kg H2O in the Insecta; osmolalities in the Annelida range from 150 to 200 mOsmoles/kg H2O, and the Mollusca showing the lowest osmolalities at 40–120 mOsmoles/kg H2O. Overall, osmolalities reach a cut-off at ∼200 mOsmoles/kg H2O, independently of increasing S:V ratio. The ability of species with small S:V ratios to maintain large osmotic gradients is mirrored in their putatively higher Na+/K+-ATPase activities that drive ion uptake processes. Selection pressures on these morpho-physiological characteristics have led to differential osmoregulatory abilities, rendering possible the conquest of freshwater while retaining some tolerance of the ancestral medium. 
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