Irrigated Crop-Share Leasing Arrangements in Kansas

Farm Management,

Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata

BACKGROUND: There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution. RESULTS: We generated a set of 66 intergenic sequences in Arabidopsis lyrata, a close relative of Arabidopsis thaliana. The intergenic regions included transposable element (TE) remnants and regions flanking the TEs. We verified orthology of these amplified regions both by comparison of existing A. lyrata – A. thaliana genetic maps and by using molecular features. We compared substitution rates among the 66 intergenic loci, which exhibit ~5-fold rate variation, and compared intergenic rates to a set of 64 orthologous coding sequences. Our chief observations were that the average rate of nucleotide substitution is slower in intergenic regions than in synonymous sites, that rate variation in both intergenic and coding regions correlate with GC content, that GC content alone is not sufficient to explain differences in rates between intergenic and coding regions, and that rates of evolution in intergenic regions correlate negatively with gene density. CONCLUSION: Our observations indicated that mutation rates vary among genomics regions as a function of base composition, suggesting that previous observations of "selective constraint" on non-coding regions could more accurately be attributed to a GC effect instead of selection. The negative correlation between nucleotide substitution rate and gene density provides a potential neutral explanation for a previously documented correlation between gene density and polymorphism levels within A. thaliana. Finally, we discuss potential forces that could contribute to rapid synonymous rates, and provide evidence to suggest that transcription-related mutation contributes to rate differences between intergenic and synonymous sites

Bibliography of socio-economic studies : fisheries of the northeast U.S.

This bibliography of social and economic studies of the fisheries of the Northeast United States (Maine to North Carolina) includes annotated listings for each entry and an index of key words for cross-referencing. We have attempted to include all studies published since 1970, and a selected group of particularly significant studies done earlier. The major focus has been on commercial fisheries, but recreational fishing studies have also been included when possible. In addition to studies of the Northeast United States fisheries, studies of Canadian fishing subsidies, European and other markets, have been included because of their relevance to the regional industry. All stages of the fishing industry's operation - harvesting, processing, distribution, marketing - are included, along with management and policy oriented material.Prepared for the National Marine Fisheries Service Contract NA-81-FA-C-00018 and for The Pew Memorial Trust, also for the Department of Commerce, NOAA Office of Sea Grant under NA-80AA-D-0077 (E/L-1) and the Institution's Marine Policy and Ocean Management Program

Plant cysteine oxidase oxygen-sensing function is conserved in early land plants and algae

All aerobic organisms require O2 for survival. When their O2 is limited (hypoxia), a response is required to reduce demand and/or improve supply. A hypoxic response mechanism has been identified in flowering plants: stability of proteins with N-terminal cysteine residues is regulated in an O2-dependent manner by the Cys/Arg branch of the N-degron pathway. Oxidation of these cysteine residues is catalysed by plant cysteine oxidases (PCOs) which destabilises proteins in normoxia; PCO inactivity in hypoxia results in protein stabilisation. Biochemically, the PCOs are sensitive to O2 availability and can therefore act as plant O2 sensors and regulation of the stability of proteins such as Group VII ethylene response factors (ERF-VIIs) can initiate adaptive responses to hypoxia. It is not known whether oxygen-sensing mechanisms exist in other phyla from the plant kingdom. Known PCO targets are only conserved in flowering plants, however PCO-like sequences are conserved in all planta. We sought to determine whether PCO-like enzymes from the liverwort, Marchantia polymorpha (MpPCO) and the freshwater algae, Klebsormidium nitens (KnPCO) have a similar function to PCO enzymes from Arabidopsis thaliana . We report that MpPCO and KnPCO show O2-sensitive N-terminal cysteine dioxygenase activity towards known AtPCO ERF-VII substrates as well as a putative endogenous substrate, MpERF-like, which was identified by homology to the Arabidopsis ERF-VIIs transcription factors. This work confirms functional and O2-dependent PCOs from Bryophyta and Charophyta, indicating the potential for PCO-mediated O2-sensing pathways in these organisms and suggesting PCO O2-sensing function could be important throughout the plant kingdom

A comparative state-level analysis of carbon capture and storage (CCS) discourse among U.S. energy stakeholders and the public

AbstractPerceptions of the potential of emerging technologies like carbon capture and storage (CCS) are constructed not just through technical and economic processes but also through discourse, i.e. through compelling narratives about what a technology is, what a technology might become and why it is needed and preferable to competing technologies. The influence of discourse is particularly important in the innovation phases prior to commercialization when innovation activities are focused on research, development and demonstration, and when feasibility and costs of alternatives systems cannot yet be tested by market dynamics. This paper provides a state-level comparative analysis of CCS discourse in the U.S. to provide insights about the socio-political context in which CCS technology is advancing and being considered in four different states: Massachusetts, Minnesota, Montana, and Texas. This research combines analysis of interviews of state-level energy stakeholders and media analysis of state-level newspapers. In semi-structured interviews, state-level energy policy stakeholders were asked to explain their perceptions of the potential opportunities and risks of CCS technology within their unique state context. Interview texts were coded to assess the frequency and extent of various different frames of CCS opportunities and risks including technical, political, economic, environmental, aesthetic, and health/safety. A similar coding scheme was applied to analysis of state-level newspaper coverage of CCS technology. Here, the frequency of these different framings of CCS opportunities and risks in state-level print media was assessed. This analysis demonstrates wide variation in state-level CCS discourse and perceptions of the potential opportunities and risks associated with CCS technology. This mixed-methods approach to characterizing the socio-political context for CCS advancement in these four states contributes to improved understanding of state-level variation in energy technology innovation, provides valuable information about energy technology development in these specific states, and also offers insight into the very different sub-national discourses associated with emerging low-carbon energy technologies in the U.S

Dynamic regulation of AtDAO1 and GH3 modulates auxin homeostasis

The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by AtDAO1/2 and conjugation by GH3s. Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product oxIAA, an increase in the conjugated forms IAA-Asp and IAA-Glu of 438-fold and 240-fold respectively, while auxin remains close to wild type. By fitting parameter values to a mathematical model of these metabolic pathways we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1. We then quantified gene expression in plantae, and found that transcripts of AtDAO1 and GH3 genes are increased in response to auxin, over different time scales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, while auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues, in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development

Lessons Learned from the First 10 Years of the Oaks and Prairies Joint Venture’s Grassland Restoration Incentive Program (GRIP)

The Oaks and Prairies Joint Venture (OPJV) was formed in 2008 as a public-private partnership of agencies and organizations working across jurisdictional boundaries in portions of Texas and Oklahoma, USA. The OPJV’s major focus is reversing declines of bird populations by supporting strategic habitat conservation (biological planning, conservation design, conservation delivery, mission-based monitoring, and assumption-driven research) for northern bobwhite (Colinus virginianus), grasslandobligate species, and their respective habitats. Our objective for this paper is to document and share a decade of lessons learned in developing a partnership-based native grassland conservation program to meet grassland bird conservation targets. We share lessons learned about how to manage partnership-based, large-scale habitat incentive programs to better target project locations and habitat practice types. To establish initial shared purpose, OPJV partners drew from population and habitat objectives in various state, national, and international bird conservation plans, stepped down to ecoregion levels, to establish the OPJV Grassland Bird Conservation Business Plan. The plan has 4 strategies directly contributing to the achievement of OPJV grassland bird biological objectives that are directly supported by OPJV staff or resources (or both). The overall objective for 2015–2025 was 619,978 ha (1,532,000 acres) improved within 40 focal counties, representing 1/3 of all counties in the OPJV. Our main strategy was to provide financial incentives through the OPJV Grassland Restoration Incentive Program (GRIP) to private landowners for conducting beneficial grassland bird habitat management practices. Since inception in 2013, GRIP has treated over 44,515 ha (110,000 acres) on private lands in Texas and Oklahoma, with the goal of maintaining highquality grassland bird habitat on treated hectares for ≥5 years. In 2017, OPJV partners working with USDA Natural Resources Conservation Service, began a 5-year, $6.1 million partnership to provide additional technical and financial assistance to private landowners interested in grassland conservation through the Regional Conservation Partnership Program (RCPP). A project scoring system was designed to strategically encourage individual projects to include prescribed fire—one of the lowest cost practices per hectare—as a recurring practice to maintain program-achieved grassland improvements. Post-inception of the RCPP, the area treated with prescribed fire increased from approximately 809 ha (2,000 acres)/year to 3,237 ha (8,000 acres)/ year, while maintaining average annual hectares of all other beneficial practices. Beginning in 2013, bird point count surveys were conducted annually to monitor northern bobwhite and grassland bird populations, including a subset of points under the National Bobwhite Conservation Initiative (NBCI) Coordinated Implementation Plan. To date, nearly 25,000 individual point counts have been performed in Texas (n = 20,111) and Oklahoma (n = 4,558). Working together, OPJV partners have made significant progress toward meeting grassland bird habitat and population objectives, while tracking progress and improving methods. However, there is still considerable work ahead

Hsp90 governs dispersion and drug resistance of fungal biofilms

Fungal biofilms are a major cause of human mortality and are recalcitrant to most treatments due to intrinsic drug resistance. These complex communities of multiple cell types form on indwelling medical devices and their eradication often requires surgical removal of infected devices. Here we implicate the molecular chaperone Hsp90 as a key regulator of biofilm dispersion and drug resistance. We previously established that in the leading human fungal pathogen, Candida albicans, Hsp90 enables the emergence and maintenance of drug resistance in planktonic conditions by stabilizing the protein phosphatase calcineurin and MAPK Mkc1. Hsp90 also regulates temperature-dependent C. albicans morphogenesis through repression of cAMP-PKA signalling. Here we demonstrate that genetic depletion of Hsp90 reduced C. albicans biofilm growth and maturation in vitro and impaired dispersal of biofilm cells. Further, compromising Hsp90 function in vitro abrogated resistance of C. albicans biofilms to the most widely deployed class of antifungal drugs, the azoles. Depletion of Hsp90 led to reduction of calcineurin and Mkc1 in planktonic but not biofilm conditions, suggesting that Hsp90 regulates drug resistance through different mechanisms in these distinct cellular states. Reduction of Hsp90 levels led to a marked decrease in matrix glucan levels, providing a compelling mechanism through which Hsp90 might regulate biofilm azole resistance. Impairment of Hsp90 function genetically or pharmacologically transformed fluconazole from ineffectual to highly effective in eradicating biofilms in a rat venous catheter infection model. Finally, inhibition of Hsp90 reduced resistance of biofilms of the most lethal mould, Aspergillus fumigatus, to the newest class of antifungals to reach the clinic, the echinocandins. Thus, we establish a novel mechanism regulating biofilm drug resistance and dispersion and that targeting Hsp90 provides a much-needed strategy for improving clinical outcome in the treatment of biofilm infections

Systems analysis of auxin transport in the Arabidopsis root apex

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin’s shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues