Tag: square flower bucket

Determination of the nature of Al genotoxicity is currently at the initial stages of investigation

While defining Al responsive mechanisms is suggestive of the type of damage Al causes, it is crucial to define the genotoxic consequence of Al that triggers this response, whether real or perceived. Additionally, unanswered questions also persist regarding which factors participate in conjunction with ATR and ALT2 to respond to Al-dependent damage since clearly Al responsive stoppage of root growth is a multi-step process progressing through cell cycle arrest to terminal differentiation associated with endore duplication or DNA replication without cytokinesis. Therefore, not only is further identification of Al tolerance factors crucial to our understanding of Al response signaling, it is also of critical importance to determine how these factors function together to promote Aldependent cell cycle arrest causing terminal differentiation and subsequent plant growth inhibition. While the genotoxic consequences of Al in plants have yet to be elucidated, it is clear from our als3-1 suppressor mutagenesis approach that components of the DNA damage response machinery are mediating root growth inhibition in response to the likely negative impact of Al on DNA structure, integrity,flower display buckets or conformation. The identification of ATR and ALT2 as mediators of Al-dependent root growth inhibition presents new strategies and opportunities to engineer crop species capable of growing in Al toxic soils.

Based on the critical roles of ATR and ALT2 in mediating Al-dependent root growth inhibition and the current knowledge gained from the field of plant DNA damage, further studies need to be done to identify mediators and effectors within the ATR- and ALT2-mediated Al response pathway, especially those responsible for controlling cell cycle arrest, damage repair, and subsequent promotion of endocycling at the root apical meristem to stop root growth. Our understanding of the genomic consequences caused by Al is still in the beginning stages, and more work is needed. Continued testing of DNA damage response mutant responses to Al can give us the opportunity to elucidate further how genomic maintenance factors are involved in this biological problem. In addition to the value of gaining a better understanding the role of DNA damage response factors and cell cycle checkpoints in mediating Al-dependent DNA damage, Al toxicity represents a novel and biologically relevant model to study ATR dependent mechanisms in the DNA damage response in general.In previous studies, seeds of als3-1 were mutagenized with ethyl methanesulfonate and M2 seedlings were screened for roots capable of sustained growth in the presence of 0.75 mM AlCl3 in a soaked gel environment. Identified seedlings were rescued and allowed to set seeds, after which progeny were rescreened to identify bona fide als3-1 suppressors. In order to further study Al-dependent terminal differentiation of the Arabidopsis root, an als3-1 suppressor mutant was chosen from this screen that was capable of sustained root growth in comparison to als3-1 in the presence of a range of AlCl3 concentrations for further analysis. Subsequent work showed this mutant to be an allele of SUPPRESSOR OF GAMMA RESPONSE1 .

Since six mutant alleles have been previously published , this suppressor will be referred to as sog1-7.The sog1-7;als3-1 double mutant was studied further to determine if the als3- 1 suppression resulted from increased Al resistance or tolerance. Internalization of Al has been associated with deposition of the β-1,3-glucan, callose, in the plasmodesmata between cells in the root tip . Seedlings of Col-0 wild type, als3-1, and sog1-7;als3-1 were grown hydroponically for 6 days in 0 μM AlCl3 , and then exposed to either 0 or 25 μM AlCl3 . This is a concentration that causes inhibition of wild-type root growth in hydroponic growth conditions for 24 hours. After these treatments, the seedlings were stained with Aniline Blue to detect callose with the use of fluorescent microscopy. Roots of sog1- 7;als3-1 accumulated callose similarly to both Col-0 wild type and als3-1 which is consistent with plants being tolerant to internalized Al . This suggests that while callose deposition is correlated with Al toxicity and has been suggested to be integral to Al dependent stoppage of root growth, it may not primarily responsible for Al inducible growth inhibition . To determine whether sog1-7;als3-1 showed Al-responsive gene expression, it was tested whether sog1-7;als3-1 showed increases in transcripts known to be induced following Al exposure, as would be expected for enhanced Al tolerance rather than increased Al exclusion. For this experiment, seedlings of Col-0 wild type, als3-1, and sog1-7;als3-1 were grown hydroponically for 6 days, after which seedlings were exposed to 0 or 25 μM AlCl3 for 24 hours. Following this, roots were collected and total RNA was isolated for a Northern analysis with the Al-inducible probes ALS3 and ALMT1 . When grown in the presence of Al, Col-0 wild type, als3-1, and sog1-7;als3-1 all resulted in an increase in expression of both Al-responsive genes.

This further supports characterization of sog1-7 as an Al tolerant mutation, as sog1-7 suppresses the hypersensitivity of als3-1 following the internalization of Al . To quantify total Al that accumulated in the root tissue of Col-0 wild type, als3-1, and sog1-7;als3-1, dried and ashed root tissue was subjected to inductively coupled plasma-optical emission spectrometry . For this experiment, seedlings were grown hydroponically for 6 days in the absence of Al, after which roots were exposed to 0 or 50 μM AlCl3 for 24 hours. Root tips were subsequently harvested, washed with nutrient medium, dried, and then ashed in pure HNO3 in preparation for analysis. All Al-treated root samples showed significant and equivalent accumulation of Al, demonstrating that the sog1-7 mutation is not excluding Al internalization to suppress the als3-1 hypersensitive response . Considering the quantitative uptake of Al by root tissue along with callose deposition and Al-inducible gene expression, evidence supports that the sustained root growth for the sog1-7;als3-1 mutant is due to enhanced Al tolerance rather than Al exclusion from the root tip.A map-based cloning approach was used to identify the nature of the als3-1 suppressor mutation. For this, the als3-1 line carrying the suppressor mutant in the Col-0 background was crossed to an als3-1 line that had been introgressed into the La-0 background . Because of the recessive nature of the als3-1 suppressor mutation, F2 progeny from the cross were grown on gel plates soaked with 0.75 mM AlCl3 ,flower bucket and seedlings with roots that were capable of sustained growth were rescued. Following isolation of genomic DNA, PCR-based analyses were conducted and showed that the als3-1 suppressor mutation localized to the top arm of Arabidopsis chromosome 1 . Fine mapping resulted in a genetic window that allowed identification of candidate genes for sequence analysis. The als3-1 suppressor mutation was subsequently found to be in exon 4 of At1g25580, which was previously reported as the ATM-regulated transcription factor SOG1 that is responsible for initiation of endoreduplication following exposure to DNA damage agents . The als3-1 suppressor mutation represents an amino acid substitution in the predicted NAC domain of this NAM , ATAF1/ATAF2, CUC  family transcription factor . To confirm the suppression of the als3-1 phenotype is caused by a single base change in At1g25580, functional complementation was subsequently performed using a full-length genomic SOG1 construct that was previously reported . Seedlings of Col-0 wild type, als3-1, sog1-7;als3-1, and sog1-7;als3-1 carrying a wild-type genomic version of SOG1 were grown in the presence of 0.75 mM AlCl3 in a soaked gel environment. After 7 days of growth, roots were assessed for terminal differentiation. Introduction of a wild-type genomic version of SOG1 into sog1-7;als3-1 fully restored Al hypersensitivity to sog1-7;als3-1, as demonstrated by the transgenic root being terminally differentiated in a manner indistinguishable from Al-treated als3-1 . While there have been six previously published alleles of sog1, only one allele has been maintained since publication, sog1-1 .

This sog1 mutant represents a single amino acid mutation from R to G at residue 155 of SOG1. In order to determine if this allele could also suppress the als3-1 phenotype, the double mutant, sog1-1;als3-1 was generated. Subsequently, seedlings of Col-0 wild type, als3-1, sog1-1;als3-1 and sog1-7;als3-1 were grown in the presence of 0.75 mM AlCl3 in a soaked gel environment. After 7 days of growth root tips were assessed for terminal differentiation. The sog1-1 allele was capable of suppressing the extreme Al response of als3-1 in a manner indistinguishable from sog1-7, since both sog1-1;als3-1 and sog1-7;als3-1 failed to exhibit the severe root growth inhibition seen for Al-treated als3-1 . To analyze sog1-7 roots growth without the als3-1 mutation in the genetic background, sog1-7 was backcrossed to Col-0 wild type, and homozygous sog1-7 F2 progeny were identified by PCR analysis. Col-0 wild-type and sog1-7 seedlings were then grown for 7 days in the absence or presence of increasing concentrations of AlCl3 in a soaked gel environment, after which root lengths were measured. In the absence of als3-1, the sog1-7 mutant roots showed greater growth than wildtype roots in the presence of a range of normally highly inhibitory levels of AlCl3 . This indicates that SOG1 has a prominent role in actively halting root growth following Al treatment. To determine if SOG1 expression is regulated by Al, real-time PCR analysis was performed. Col-0 wild-type seedlings were grown in a hydroponic environment for 6 days and subsequently treated with 0, 25, or 100 μM AlCl3 for 24 hours. Root tissue was collected, total RNA was isolated for cDNA synthesis and RT-PCR was performed using SOG1 specific PCR oligonucleotide primers . There was no indication that SOG1 is transcriptionally induced by Al. Similarly, seedlings of sog1-7 were grown in a 0 μM AlCl3 hydroponic environment for 7 days and subsequently analyzed with real-time PCR and the sog1- 7 mutation was not found to affect transcript stability since Col-0 wild type and sog1-7 showed comparable levels of SOG1 transcript . In previous studies, loss-of-function mutations in cell cycle checkpoint factors ATR and ALT2 resulted in increased root growth in the presence of Al . This tolerance was correlated with failure to arrest cell cycle progression in conjunction with forced quiescent center differentiation. In order to determine if this is also true for roots of a sog1 loss of-function mutant, sog1-7 was crossed to either a transgenic Arabidopsis line carrying a reporter for cell cycle progression, CYCB1;1:GUS , or a reporter for QC status, QC46:GUS . Seedlings of Col-0 wild type and sog1-7 carrying the CYCB1;1:GUS reporter were grown in the absence or presence of 0.75 mM AlCl3 in a soaked gel environment for 7 days, after which they were stained for GUS activity. Col-0 wild type carrying the CYCB1;1:GUS reporter results in a substantial increase in GUS activity following exposure to Al . This is consistent with a large number of root cells being incapable of exiting the G2 phase of mitosis and incapable of proceeding into actual cell division. Unlike previous reports for the atr-4 and alt2-1 loss-of-function mutations where GUS reporter levels were eliminated , sog1-7 carrying CYCB1;1:GUS had substantially reduced levels of the CYCB1;1:GUS reporter compared with Col-0 wild type . This may indicate that the role of SOG1 in Al-dependent inhibition of cell cycle progression at the G2 phase, while likely acting in conjunction with ATR and ALT2, may also function through other factors to prevent CYCB1;1 turnover. Consistent with prior results, it was found that Al treatment results in loss of the QC as measured by QC46 dependent GUS activity that is localized to the root stem cells . For this analysis, QC46:GUS transgenic seedlings in either the Col-0 wild type or sog1-7 backgrounds were grown for 7 days in the absence or presence of 1.50 mM AlCl3 in a soaked gel environment, after which seedlings were stained to visualize the QC. Both Col-0 wild-type and sog1-7 roots had QC46:GUS accumulation in the absence of Al . Treatment with high levels of Al in Col-0 wild type resulted in the loss of the QC, but not in sog1-7 . This indicates that SOG1 plays an active role in differentiation of the QC following Al treatment and likely functions as a step in the transition to endore duplication in the root tip.In support of this model, it was found that Al treatment leads to terminal differentiation in conjunction with substantial increases in cell and nucleus size in als3-1 roots. For this analysis, Col-0 wild- type, als3-1, atr-4;als3-1, alt2-1;als3-1, and sog1-7;als3-1 plants were grown in the absence or presence of 0.75 mM AlCl3 in a soaked gel environment for 7 days, after which seedlings were fixed and stained with 4’,6-diamidino-2-phenylindole .

Our setting offers us an advantage because voters are profit-maximizing agricultural producers

As climate models become a primary tool for studying the atmospheric role of land surface processes, a question for current climate models is whether they can adequately distinguish and accurately simulate surface energy partitioning over different vegetation types. Plants contribute a large fraction of latent heat flux through evaporation of water from leaf surfaces and transpiration from deeper soil layers when stomata open during photosynthesis. Plants also affect net radiation by altering the surface albedo. A change in plant height can change the boundary layer turbulence by influencing surface roughness, and therefore the total energy exchange via latent and sensible heat fluxes [Davin and de Noblet-Ducoudre, 2010]. In most climate models, several important vegetation parameters are prescribed according to satellite observations and ground measurements. These parameters are not necessarily accurate at the site-scale due to the algorithm and validation methods used in retrieving satellite data or aggregating ground data [Yang et al., 2006]. Validation of surface fluxes over different vegetation types can help identify deficiencies in key parameters and model formulations to target for improving model performance. The aim of this work is to examine energy partitioning and surface climate simulated by a recently coupled regional climate model, WRF3-CLM3.5, for four major vegetation types across the United States, and to identify the model’s strengths and deficiencies to help prioritize model improvements. As the next-generation mesoscale numerical model,flower bucket the standard version of WRF includes relatively simple land surface schemes, which potentially constrain model applications for studying the land surface and ecosystem atmosphere feed backs.

The newly coupled model improved the surface process simulation in California [Subin et al., 2011], but has not been validated at the continental scale. We used the standard version of the Weather Research and Forecasting model version 3.0 [Skamarock et al., 2008], AmeriFlux site observations [Wofsy and Hollinger, 1998], and CERES data [Wielicki et al., 1996; Young et al., 1998] to evaluate energy flux partitioning. We analyzed the bias in surface climate variables by comparing to PRISM datasets [Di Luzio et al., 2008]. We focused on four dominant vegetation types with adequate representation in the AmeriFlux network . Both WRF and CLM have deficiencies that should be resolved in future versions to reduce the warm bias. The large warm bias in the standard version of WRF suggests there are problems in WRF. For example, the downward solar radiation bias contributes substantially to the warm bias based on a one-year sensitivity test that artificially reduced downward solar radiation by 30% . Reducing downward solar radiation is not simple because it is associated with many factors. Previous work [Markovic et al., 2008; Wild et al., 2001] suggests the overestimate of downward solar radiation at the surface could be either due to less cloud cover for cloudy days or less sky absorption of downward solar radiation for clear days. Ignoring aerosols in the model may also contribute to excess downward solar radiation [Wild, 2008]. The negative precipitation bias in the Midwest suggests that an underestimate of cloud cover may contribute to excess downward solar radiation in the Midwest. Further validation with WRF3-CLM3.5 focusing on the cloud cover and clear sky absorption are strongly encouraged but are beyond the scope of this paper. Fortunately, the newer WRF3.2 includes boundary layer physics and microphysics that could improve the overall simulation. A one-year sensitivity test using standard WRF3.2 with the MYNN boundary scheme [Nakanishi and Niino, 2009] and Thompson microphysics scheme [Thompson et al., 2008] showed a reduction in the downward solar radiation by 30 W m-2 , in T_max by 3K, and in T_min by 2K. With respect to CLM, the large warm bias in the Midwest could be due in part to 1) the missing irrigation scheme, and 2) the lower crop leaf area index used in the model.

A large area in the Midwest is covered by irrigated agriculture according to global irrigation maps [Siebert et al., 2005]. Without an irrigation scheme, WRF3-CLM3.5 may overestimate temperature by 3-5K in summer in the Midwest [Lobell et al., 2009; Sacks et al., 2009]. Considering the strong coupling between soil moisture and precipitation in the Midwest [Koster et al., 2004], low soil moisture could reduce cloud cover and enhance the downward solar radiation, further heating the land surface and contributing to a positive feedback in this region and producing a large warm bias. Also, the much lower maximum leaf area index used in the model could reduce LE and therefore increase H and near-surface temperature. The simulated seasonal variation in LAI is much lower than the direct measurements at the Bo1 site [Wilson and Meyers, 2007]. Mandatory marketing organizations have been an important agricultural policy tool in the United States for 80 years. These organizations include agricultural marketing orders, commissions, councils and check-off programs. They can serve many purposes, including supply control , setting of quality and grading standards, market or production research, limiting of unfair trade practices and generic commodity promotion. The intended purposes differ across MMOs and are outlined in each organization’s governing documents. The creation of a MMO is a political process, and considerable discretion is given to the Secretary of Agriculture in determining the value of these MMOs. In addition, many MMOs require approval through a vote of eligible producers for creation, continuation and termination. The outcome of this referendum then informs the Secretary’s decision for the future for the organization, and, in some cases, may dictate it. Producer referenda are held at regular intervals for most MMOs to ensure they are continuing to provide positive net benefits to producers. These referenda are the focus of our research. Specifically, we examine how market power among agricultural producers relates to voting power in a referendum to form, terminate or continue a MMO with a generic promotion provision. These referenda are interesting for several reasons. First, the voting rules used in determining the outcome of these referenda often depend on both the number of producers and the quantity of output they produce, suggesting that market structure matters in determining the outcome. Second, they provide an opportunity for us to study grower behavior regarding mandatory collective action organizations, which can shed light on the costs and benefits to growers of these organizations as well as on attitudes to collective action more broadly.

One of the most common types of MMOs is a marketing order. Although voting rules differ somewhat across MMOs, for the purposes of this paper, we consider voting rules for Federal marketing orders, as they are typical of the type of voting rule used by many MMOs. We model the supply side of the market for a homogeneous agricultural commodity as consisting of a single firm with a cost advantage and multiple firms with heterogeneous higher costs. This cost structure is intended to represent the supply environment in many industries,square flower bucket where there is an increasing gap between a few dominant producers and many smaller ones. We assume buyers of the commodity do not exercise market power. Finally, we focus on demand-increasing generic commodity promotion as the means by which an MMO benefits producers. Generic promotion is increasingly one of the primary roles of MMOs in the United States, in part due to the passage of the Research and Commodity Promotion Act of 1996, which created of a new category of federal check-off program with a major emphasis on generic promotion.1 We focus on a pair of voting rules commonly used together for Federal marketing orders and examine the voting power of the dominant and fringe firms. For this analysis, we consider what Felsenthal and Machover call “I-power.” This class of power measure address a voter’s influence over the decision to be made. The power measure we use is Banzhaf Power . The Banzhaf Power Index is calculated by considering all possible “winning” coalitions of voters—those coalitions that could pass a proposed action if all members of the coalition favored it, given the voting rule. A voter is “critical” if the coalition would no longer pass the proposed action if the voter left that coalition. The Banzhaf Power Index is defined as the number of times a given voter is critical out of the total number of possible vote combinations in the industry. Running simulations of these markets under various assumptions about costs and market structure and industry-calibrated market parameters, we calculate the Banzhaf Power Index value and market share of each firm. The Banzhaf Power Index assumes implicitly that voters vote for the action with a probability of 0.5. Some have challenged the usefulness of this type of measure given this naive assumption about voter behavior . However, developing a better model requires more information about voters, which can be hard to obtain. In most situations, voter preferences or correlations between preferences are difficult to measure and the factors that underly them may be challenging to identify.This voter characteristic allows us to incorporate our knowledge of theory of the firm to better predict the voter behavior given cost and market parameters.

Building on the probability theory approach to Banzhaf’s index identified by Straffin , and the behavior of profit-maximizing producers in the neoclassical theory of the firm to develop a second measure we call “Feasible” Banzhaf Power. To calculate this measure, we incorporate the information about each producer’s profit-maximizing voting choice and then assume that a producer votes in accordance with his profit-maximizing choice with a randomly drawn idiosyncratic probability. This probability represents the probability that a producer is optimizing some objective function other than profit-maximization that yields him or her to a different voting choice. For example, the producer could have the objective of minimizing government intervention, regardless of its effect on his profits. We find that market power and cost heterogeneity do indeed matter in determining the voting power of producers in MMO referenda, whether or not producer behavior is incorporated. Furthermore, incorporating information on producer behavior substantially affects our estimate of voting power. We also find that disparate preferences of firms with heterogeneous costs in situations where some producers wield market power can reduce the Feasible Banzhaf Power Index value for the low cost firm, even when the low cost firm produces a substantial share of industry output. Finally, we find that the different voting rules faced by producers in MMO referenda yield distinct differences in voting power in markets with heterogeneous producers. Our contributions to the literature are threefold. First, we contribute to both the voting power and agricultural economics literature, as to the best of our knowledge we are the first authors to examine marketing order referenda through the lens of voting power. Second, we contribute to the voting power literature by connecting the work on voting preferences and empirical voting power measures to the neoclassical theory of the firm in the form of our Feasible Banzhaf Power Index. This index is useful in that it incorporates information about behavior to provide a more realistic measure of voting power in settings with firms in the role of voter. And finally, through the analysis of voting power measures, we provide new insights about the potential challenges agricultural producers face in adapting their MMOs in a rapidly changing economic landscape. As agricultural market structures have changed over time, agricultural economists have moved away from the long-held assumption of perfect competition in some agricultural settings. Our work shows how the marriage of voting power methodology and agricultural economics can shed new light on how market power and cost heterogeneity interact with agricultural institutions in changing markets. The remainder of the paper proceeds as follows. In Section II, we give a brief history of MMOs and discuss the relevance of our work to agricultural policy. In Section III, we relate our work to the relevant literature in agricultural economics and political science. In Section IV, we present our theoretical model. In Section V, we discuss our simulations and calibration methodology. Section VI includes the presentation and discussion of our results, and Section VII concludes. MMOs were first authorized at the federal level by the Agricultural Adjustment Act of 1933 and the Agricultural Marketing Agreement Act of 1937. Initially, they were a policy response to ongoing low and volatile returns to agriculture in the 1920s and 1930s.