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Harvesting the Future: Hydroponic Agriculture and Global Food Security

Although this coating may not persist on the particles in the environment, what is clear is that the effects of chronic dosing and the effects of coating are critical data gaps that should be evaluated. Also completely lacking are more environmentally realistic exposure scenarios, such as ones using natural waters and soils and also multi-species microcosm or mesocosm studies, although such studies are underway. These studies will bring the importance of environmental transformations and indirect ecological impacts into light. It is possible that community or ecosystem level impacts may be more sensitive than individual level effects. Also more chronic and food chain transfer studies should be encouraged to deal with the possible long term effects from, or accumulations of, the likely persistent nanoceria entities. The current available data do not suggest an immediate risk from acute exposures to nanoceria from use as a fuel additive or mechanical/chemical polishing or planarization. However, the data gaps we have discussed should be addressed before a comprehensive ecological risk assessment can be performed for ceria for chronic exposures or for other exposure pathways. This review lays the foundation for such assessments and clearly identifies the areas where research is most critically needed.The Bioremediation, Education, Science and Technology partnership provides a sustainable and contemporary approach to developing new bio-remedial technologies for U. S. Department of Defense priority contaminants while increasing the representation of underrepresented minorities and women in an exciting new bio-technical field. This comprehensive and innovative bio-remediation education program provides under-represented groups with a cross-disciplinary bio-remediation curriculum and financial support, coupled with relevant training experiences at advanced research laboratories and field sites. These programs are designed to provide a stream of highly trained minority and women professionals to meet national environmental needs. The BEST partnership of institutions and participants benefit from a unique central strategy— shared resources across institutional boundaries.

By integrating diffuse resources, BEST forms a specialized “learning institution without walls,” large plastic pots for plants where participants can receive advanced training at any BEST site, and where research capabilities flow freely among the participating institutions. Ongoing faculty and student exchange programs, video taped lectures, the Rotating Scholars program, and the BEST web-site ensure that all participants are empowered with opportunities to excel. The BEST partnership consists of Lawrence Berkeley National Laboratory in Berkeley, Calif., Jackson State University in Jackson, Miss., Ana G. Méndez University System in Puerto Rico, University of Texas at El Paso , University of Southern Mississippi Gulf Coast Research Lab, and University of California at Berkeley . The BEST program contract to the partnership is man-aged by LBNL for the Army Corps of Engineers, Waterways Experiment Station in Vicksburg, Miss. WES manages the contract for the Army Corps of Engineers and is the contracting entity for DoD. The partnership formed by these participating institutions leverages existing institutional resources by strengthening intramural bio-remediation education and research capabilities, and through outreach pro-grams, to disseminate training and scientific enhancement to other Historically Black Colleges and Universities and Minority Institutions . The BEST institutions are focal points for the development and dissemination of cutting-edge research and technology for the bio-remediation of nitro-aro-matic compounds, polycyclic aromatic hydrocarbons and toxic metals. The multidisciplinary BEST partnership strategy creates a flask-to-field solution that develops laboratory research into technology, and technology into field-scale environmental applications required for the cost-effective restoration of damaged environments. This year saw the addition of the University of Southern Mississippi’s Gulf Coast Research Lab and the University of Texas at El Paso as partners in the BEST program. Both institutions provide significant new personnel and training opportunities for the BEST program. The USM Gulf Coast Research Lab investigators’ focus on PAH and heavy metal phytoremediation along shorelines provides an exciting new focus with increased field opportunities for students. The UTEP investigators are focusing on exciting new metal phy-toremediation techniques using desert plants and exciting new techniques to determine risk assessment with PAHs. This year also saw the passage of the program director-ship at LBNL from Dr. Jenny Hunter-Cevera to Dr. Terry C. Hazen in October 1999. Dr. Hunter-Cevera, who has managed the BEST program at LBNL since its inception, will be sorely missed, but her new position as president of the Maryland Biotechnology Institutes may provide increased opportunities for collaboration for the entire BEST program. Dr. Hazen, who specializes in bio-remediation field applications, has demonstrated or deployed bio-remediation technologies at more than 50 sites around the United States and in Europe. He has five patents in bio-remediation technologies that are licensed by more than 40 companies in the U.S. and Europe.

During the past year, the BEST program has provided minority research training for five high school students, 74 undergraduates, 32 graduate students, three post-doctoral fellows and 10 faculty. Students and fac-ulty investigators have given 43 presentations on BEST research at scientific meetings and have published 17 scientific papers. The program produced a full color brochure and flyers in 1999 for use in recruiting more students, and also sponsored 32 lecture/seminars on bio-remediation. Fourteen videotapes of BEST seminars at LBNL/UCB were distributed to the partner institutions. The BEST program also sponsored a phytoremediation workshop for BEST investigators and students that was attended by more than 60 participants. Additional workshops are planned for the coming year. In this report, the research is organized by subject area, and two-page briefs are presented for each of 28 BEST projects. The projects presented provide a good representation of the state-of-the-science research being done with students in the BEST program – the best of BEST.Over the next 75 years, the U.S. government will undertake what has been called the largest civil works project in world history to restore the environment damaged by previous activities at federal sites, e.g., Department of Defense military bases and Department of Energy nuclear facilities. Legislative action, resulting from concern over the accumulating hazards, has mandated pollution control measures and environmental restoration of hazardous waste at all sites. Estimates of total cleanup costs range from $230 billion to more than half a trillion dollars. Given the trend of diminishing budgets throughout the federal government, future generations could inherit both an environmental and budgetary disaster. The imprecision of the cost estimates results from the lack of knowledge of how “clean” the contaminated sites will need to be. Some of the environmental damage is permanent—cleanup technologies either do not exist or are incapable of remediating the contamination. For DoD bases being closed by the Base Realignment and Closure Program, all toxic sites must be remediated before the site is returned to public use. The projected costs of site restoration using existing technologies are staggering: the estimated cleanup cost is at least $24.5 billion for the 7,313 identified U.S. sites . The pollutants at these sites include chlorinated hydrocarbons, metals, petroleum products, explosives, mixed waste and other organics. DOE also has substantial remediation costs—estimated to be from $90 billion to $200 billion . The domestic private sector presents yet another huge set of remediation problems, dwarfed only by the international problems in Eastern Europe and Russia . There is clearly a need for new cost-effective treatment technologies. Bio-remediation, the use of microor-ganisms to detoxify hazardous waste, promises to provide economical and ecologically sound clean-up strategies. An Office of Technology Assessment analysis concluded that the U.S. does not possess a sufficient pool of qualified environmental professionals, i.e.,blueberry pot the trained scientific personnel required to support this rapidly developing multi-disciplinary field. In response to these national environmental needs, the Bio-remediation Education, Science and Technology Program, funded by DoD, was established in 1996. In a few short years, BEST has pioneered a new and successful model for environmental science and education. This partnership has a highly integrated programmatic focus on the scientific and workforce needs of DoD. Since the inception of the BEST program, a significant number of major milestones and deliverables have been achieved. They are described below. The BEST program has made these dramatic accomplishments by using an approach that combines a training-education element with an integrated research project, described later in this introduction.DoD sites throughout the United States contain highly contaminated soils, groundwater and sediments. These properties pose direct and indirect exposure hazards to humans and wildlife.

Conventional remedial solutions for contaminated soils and sediments or groundwater are slow and expensive, increase inputs to hazardous waste disposal sites, and can increase human exposure to contaminants. Bio-remediation — the use of microo ganisms to destroy hazardous contaminants or to con-vert them to harmless forms — is an emerging treatment technology that can in many instances restore contaminated environments more quickly, at lower cost and at lower human risk than alternative remediation technologies. Bio-remediation can operate in either an in situ mode where contaminants are treated in place, or in an ex situ mode where contaminants are removed from a contaminated zone for treatment . In situ bio-remediation can be used when excavation is impractical — under buildings, highways, runways, etc. In situ bio-remediation can simultaneously treat soil and groundwater in one step, without the generation of hazardous waste products. In situ contaminant degradation can be achieved by either intrinsic or enhanced bio-remediation. Intrinsic bio-remediation exploits the innate capabilities of indigenous micro-bial communities to degrade pollutants. Enhanced bio-remediation seeks to accelerate in situ microbial activity by isolating and controlling the contaminated site so that the microbial environment can be purposely manipulated to correct nutritional or gas phase limitations. Ex situ treatment seeks to further control the remedial environment by placing the contaminants in an engineered treatment system. Phytore mediation, a process in which plants and asso-ciated microbial communities are used for contaminant bio-degradation or bio-immobilization, is an important and rapidly developing mode of bio-remediation. To realize the full potential benefits of plant and microbial treatment systems at DoD sites, these bio-technologies must be developed and optimized for remediation of DoD priority contaminants by an expanded pool of qualified professionals. It was in response to these DoD environmental needs that the BEST partnership of institutions was established.In order to determine whether plants can stimulate the degradation of PAHs in soil, plant species found in literature on phytoremediation of metal-contaminated sites were selected to measure the removal of PAHs in artificially contaminated soil over a period of 62 days. The plant species used for this experiment were alfalfa , barley , tall fescue and orchard grass . The PAHs were phenanthrene and anthracene, in a mixture of 600 ppm each. As shown in Figures 1 and 2, phenanthrene and anthracene were removed from the soils with plants after 62 days. More than 98% of the phenanthrene was removed during that period while the anthracene removal was found to be between 70 and 90%. The results suggest that the rate of disappearance of phenanthrene in soil was greater than anthracene under the same conditions. From the results, it is also indicated that the disappearance of PAHs in soil depends on the bio-availability of the compounds. Because phenanthrene is approximately 10 times more soluble in water than anthracene, it was expected to be more readily available to microbial degradation than anthracene. Plant-assisted degradation of PAHs is thought to be more effective on PAHs with a higher number of rings and higher molecular weights, such as benzopyrene. Anthracene removal in the soil planted with alfalfa was greater than in the soil without plants, while all the other plants have minimal to no effect on anthracene removal compared to the control soil. Phenanthrene was removed to a greater extent in the soil with alfalfa and tall fescue compared to the control without plants . However, both barley and orchard grass showed no effects of the removal of phenanthrene during that period when compared to the soil without plants. Overall, plants had minimum effect on phenanthrene degradation while anthracene degradation was more dependent on plant species. In order to determine the effect of PAH degradation by plants on bacterial numbers in soil, bacteria were counted in soil during the course of the experiment.Parathion is a widely used organophosphate insecticide which can cause adverse neurological effects if ingested or after dermal exposure. No single microor-ganism has been isolated that is capable of completely mineralizing parathion and its metabolites. Hydrolysis of parathion significantly lowers the toxicity of the parent compound, but results in the formation of a toxic intermediate, the nitroaromatic compound p-nitrophenol.

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The clearest distinction in this figure appeared to be whether the growing sites are for-profit or nonprofit

For instance, 75 percent of the articles returned in our Web of Science search were published after 2009 and 18 percent were published in 2017-18. A more recent search of these terms in April of 2018 returns 1622 records revealing a continued growth in literature on urban agriculture. Of these records, journal articles dominate . Other records include book reviews, article reviews, proceedings papers, and meeting abstracts. The main contributing journals included Land Use Policy , Landscape & Urban Planning , Agriculture & Human Values , Sustainability , and Local Environment ; however, the sources were quite diverse. Each record represents a single document and together they form the corpus used to build the reference topic model. Prior to processing, we removed any stop words, punctuation, and URLs. We performed LDA topic modelling using the MALLET program . We produced various topic models using three granularities , and used the models with the greatest log likelihood . We then examined their topic composition and removed topics dominated by non-meaning-bearing terms including time and location indicators and general publication information . These topics were identified using the alpha hyperparameter, where relatively high values indicated that the topic was common throughout the corpus and therefore not meaningful for examining differences within our sample. After these adjustments, we determined that the 25-topic model was ideal for analysis using personal expert knowledge on urban agriculture literature. The reference topic model was created in order to perform inference on content produced by urban agriculture growing sites and regional organizations in San Diego County – in other words, to interpret the content produced by the key actors identified above . We created a corpus including all textual content from the websites of agencies in our sample,plant pot with drainage with content from each of the 48 observations contained in a single document in the corpus.

Textual content included any written descriptions on the website including history, mission and vision statements, program descriptions, excluding locations, contact, and event info. For growing sites associated with larger organizations or institutions, we also collected basic descriptive content from the parent website. By applying the reference model to all the documents, each document is characterized in terms of topic composition, allowing comparisons among documents . The output of the inferencing process is a document-topic distribution matrix, from which we computed a matrix of cosine similarities among documents. In order to visualize these similarities, we used a dimensionality reduction technique known as multidimensional scaling . In the resulting output, each document is described as a 2-D point in Cartesian coordinates, where proximity relates to similarity. The resulting discursive map displayed the inferenced website corpus, with each point representing a single growing site or organization. The location of each point relates to its particular topic composition. The distance between points is indicative of their discursive similarity – the closer two points are in the discursive map, the more similar their topic composition; the farther apart, the more dissimilar. We investigated this map, but also created a series of variations, altering the symbology of the discursive map to reflect particular features of the sites. This allowed us to examine the connections between characteristics like growing methods and topic composition. We were also interested in discovering clusters among the data points, and so we utilized k-means clustering to identify meaningful groups in our data . K-means is a heuristic algorithm that attempts to partition aninput dataset into k groups, allowing researchers to explore clusters within a dataset. Our data seemed to occupy primarily three quadrants in the discursive map, and so we chose to identify three classes. This algorithm was run for 1,000 iterations and the results with the lowest sum of squared errors – a metric that explains the difference between each observation and its corresponding k-means centroid – were chosen as representative. This analysis complemented our visual analysis of symbology patterns. The growing methods symbology illustrating the practices used by growing sites revealed a distinct, but blurry pattern between motivation and practice.

When analyzing the map using this symbology, a general pattern emerged in which technologically-advanced sites tended to group in the top-left quadrant of the map with two outliers: Go Green Agriculture and Archi’s Acres. The absence of innovation in these outliers’ top-three loadings suggested that other topics precede technology in how these growing sites describe themselves despite their use of advanced technologies. Generally, soil-based sites occupied the right side of the discursive map; however, soil-based farms such as Suzie’s Farm, Good Taste Farm, and Point Loma Farms were grouped in with the soilless sites. Growing site and organization descriptions of their processes did drive their location on the discursive map. For instance, the soilless sites often described the inventive and underrepresented practices they use to grow produce in the urban environment. However, the content did not end there. Other topics like social movements, climate change, and food access were also present among these sites. We saw a similar trend with sites using a community gardening model. When we explored the entire topic loadings of growing sites and organizations, ignoring practice-based topics like innovation and community gardening topics, we saw that the clusters have far more similarities than differences. Interestingly, these soilless sites are typically affiliated with businesses as opposed to nonprofits which dominate the right side of the map, where most soil-based sites are located . Indeed, we expected that business and nonprofit website content would vary and these results provide evidence to that effect. San Diego Food System Alliance, the leading regional nonprofit organization, is located in the center of the map. This location is not surprising in the context of neoliberal governance in which cities and regional organizations are more focused on building consensus and supporting apolitical agendas, rather than taking on political causes .The affiliation symbology illustrating the relationship between institutional affiliation and content was less coherent than the other symbologies displayed in previous figures, but still offered important insights. Growing sites were affiliated with a variety of institutions including schools, churches, organizations hosting training and educational programs, and for-profit businesses.

Education sites were located throughout the map suggesting that training and skill-building are not major dividing factors in discourse. In other words, many different types of organizations claim to focus on education. However, church, community, and school gardens tended to concentrate in the top-right section of the map, which is typically associated with soil-based community gardens. However, it cannot be assumed that the for-profit sites lack social mission. For example, Archi’s Acres, a for-profit hydroponic farm in Escondido, includes a social enterprise function focusing on training veterans in hydroponic farming. Sundial Farms, a veteran- and immigrant-owned, hydroponic farm in the Innovation cluster, is a direct result of this program. This social function features prominently in its website content: “At Archi’s, we believe a key aspect of successful business is how it meets its responsibility to the community in which it operates and the customers which make up its marketplace. We do this by integrating into our business model an opportunity to support others including our military service members and veterans.” This broader social mission may explain its topic loadings and the absence of innovation as a primary topic. The overall uniqueness of this growing site may explain its peripheral location in the discursive map. Solutions Farms, an aquaponic operation associated with Solutions for Change,growing blueberries in pots was the only nonprofit located in the for-profit dominated section of the map. The organization aims to alleviate family homelessness in the county through skill development, including training in aquaponic farming. However, innovation is the primary topic in their content, influencing their location among other sites whose discourse is focused on innovation.Multivariate clustering was performed on the discursive map to identify clusters in the sites and group them accordingly. Figure 8 contains the k-means results including three classes . Transitional sites were identified by creating a 4-class result . The topic compositions of sites in each cluster were examined and the clusters were given descriptive names reflecting their dominant topics : Innovation, Community, and Access. The transitional sites – those that broke off into their own group in the 4-class result – were signified using an overlaid line pattern. These sites were close to or straddled the center axes of the map.The Innovation cluster was distinct from the other clusters. The predominant topic amongst this group was innovation, which includes words and phrases like rooftop farming, zero-acreage farming, soilless, aquaponics, buildings, hydroponic, vertical, greenhouses, indoor, and technology as well as production, yield, growth, and quality. Unsurprisingly, all of the technologically-advanced sites resided in this cluster with the exception of Valley View Farms, which experiments with hydroponics, but focuses primarily on animal farming. Among the topic loadings in this group were community gardening, food access, social movements, climate change, water management, food production, and food security. This cluster also consisted primarily of for-profit growing sites with the exception of Roger’s Community Garden located on the University of California, San Diego campus. An interesting outlier is Go Green Agriculture, a hydroponic farm, which is located on the border of the Community cluster. This location is likely driven by its top topics, which include community gardening, location, and climate change, which are well-represented in both the Innovation and Community cluster. The Community cluster emphasized connections with local residents, primarily promoting home and community gardening – community gardening was the most prevalent topic in this cluster.

Although, this cluster overlaped considerably with the Access cluster, there was a clear emphasis on environmental topics including ecosystem conservation, water management, location, water contamination, innovation, and climate change. The social movement topic was also prevalent throughout this cluster with many of its sites expressing a dedication to alternative forms of organization. It is also worth noting that the socio-economic characteristics of the two neighborhoods are also quite different. Southeastern San Diego, specifically zip-code 92102 where Mt. Hope Community Garden is located, is a primarily Hispanic community, followed by White , African American , and Asian . The median income is at $42,464 with only 24 percent of the population exceeding $75,000 annually . The sites and organizations in this cluster also placed considerably less emphasis on environmental topics in favor of more social topics including public health, food production, and urban greening. Still, topics like ecology and climate change were present suggesting that environmental and social concerns were not mutually exclusive. The sites in the Access cluster were also predominantly affiliated with educational and training programs. Two particularly interesting examples are UrbanLife Farms and Second Chance Youth Garden. Both growing sites are wings of social justice organizations that offer job training and skills development for youth living in City Heights and Southeastern San Diego – communities that have seen considerable disinvestment and suffer from high unemployment . Other growing sites like Rolling Hills Grammar School and Literacy Garden and Olivewood Gardens and Learning Center also focus on youth programming. Not all the growing sites in this cluster work with youth. New Roots Farm concentrates on providing resettled refugees with land for farming, small-business training, and nutrition education to help them adjust to a new life away from their home country. This mission guided its topic loading of food security, social movements, and food access. The five urban agriculture supporting organizations we surveyed spanned the Community and Access clusters. Slow Food San Diego, Slow Food Urban San Diego, San Diego Roots Sustainable Food Project , and San Diego Community Garden Network are located in the Community cluster. San Diego Food System Alliance was located at the border between the Community and Access clusters suggesting that food access was a more prominent topic for the organization. Further, its central position illustrated the consensus focus of the organization, which caters to a diverse group of actors including politicians, businesses, and nonprofit organizations. Overall, the placement of the organizations made sense as they are nonprofit facilitators for other sites aimed at broader social goals like increasing food access and building community.

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Diflubenzuron is an insect growth regulator and is not listed in the draft regulations

As an example, Ogunjemiyo et al studied a more simplified crop setting, consisting of a single, highly evapotranspiring crop in an area with simplified meteorological conditions . Similar uniformity occurs throughout much of the Midwest, where mono-cultures of corn and soybean would permit the study of water vapor patterns while reducing the impact of variation in crop type. The Central Valley, with its large variety of crops and management practices, resulting in non-uniform distributions of aerodynamic roughness, ET rates, and landscape structures throughout the scene, was perhaps not the ideal location to test this approach. Unfortunately, the type of data we used, including AVIRIS– derived water vapor, and LST from MASTER, is not widely available outside of data sets acquired for the HyspIRI-Airborne Campaign. We would suggest a targeted campaign, acquiring combined AVIRIS-MASTER for agricultural studies, over more simplified and better instrumented sites would be of great benefit. Beyond advancing our ability to capture patterns of field-level ET with water vapor imagery, this imagery may prove valuable for regional analyses of water transport. There are many challenges associated with linking water vapor to crops at the field-level as outlined above, but the idea behind this work will likely hold at a smaller scale. Lo and Famiglietti found that in the Western United States the irrigation from California has been shown to increase the summer stream flow of the Colorado River by 30 percent. Water vapor imagery, if acquired more consistently and over larger areas, offers an additional tool that could be used to capture finer scale water vapor transport, to complement models and coarser scale observations from sensors such as MODIS. These large movements of water vapor have implications for climate change and land use, and call upon the need to increase monitoring of water vapor patterns in areas with large irrigation inputs. Therefore, 10 liter pot a study that examines the ability of water vapor imagery to assist in regional water transport assessments could be of high value.

CDPR’s draft use regulations, designed to address pesticide runoff and drift, could have a potentially significant economic impact on California agriculture, as well as to the supporting industries and communities, due in part to the large number of active ingredients listed in the draft regulations. Assessing the potential effects of the regulations is complicated by a number of factors. First, pest management programs for many crops, such as alfalfa, walnuts, strawberries, lettuce, rice and several others, include at least one of the CDPR’s targeted 68 active ingredients and efficacious alternatives are not always available. Often, the most common alternatives to an individual active ingredient are also subject to the draft regulations. Second, mandated buffer zones that define the minimum distance that must be left between a sprayed area and a “sensitive aquatic site,” as a function of the application method, are an important component of the regulations. Third, the amount of field acreage affected by buffers depends on the distribution of crop acreage relative to the location of a sensitive aquatic site. Fourth, the draft regulations propose to use the definition of sensitive aquatic site as “any irrigation or drainage ditch, canal, or other body of water in which the presence of pesticides could cause adverse impacts on human health or aquatic organisms.” This article focuses on the potential economic impacts of the draft regulations for rice production in Colusa and Butte counties due to the listing of two selected active ingredients. It is drawn from a larger report that considers the economic effects of the draft regulations for 20 county-crop pairs. The analyses are performed at the county level because the distribution of crop acreage relative to the location of sensitive aquatic sites is an important determinant of potential economic impacts.According to the National Agricultural Statistics Service , California’s rice crop is the second largest in the United States, accounting for 22% of the value of national rice production. Rice is the tenth most valuable crop grown in California, contributing 2.8% to the total value of production in 2009. In 2009 there were 563,974 acres of rice in California.

The statewide average yield was 4.38 tons per acre, production totalled 2,472,614 tons, and the price of rice was $390 per ton with a total farm gate value of $963,526,000. The top rice-producing counties in California by value are Colusa, Sutter, Butte, Glenn, and Yuba, according to county agricultural commissioners’ data reported by NASS. Rice is the most valuable crop in both Colusa and Butte counties. In 2009 rice accounted for 40.7% and 33.9% of total crop value in Colusa and Butte counties, respectively. Colusa was the top rice-producing county in the state, accounting for 25% of the value of all California rice. In 2009 Colusa County farmers grew 152,400 acres of rice, which yielded an average of 4.5 tons per acre, and produced a total of 685,800 tons of rice; the price was $355 per ton, for a total value of production of $243,459,000. In 2009 Butte County farmers grew a total of 103,416 acres of rice, which yielded an average of 4.7 tons per acre and produced a total of 486,055 tons of rice; the price was $379 per ton, for total value of production of $103,265,000. Together, Butte and Colusa counties accounted for 44% of California rice production in 2009.According to data from Demars and Zhang , a draft report under preparation for CDFA, there was a total of 250,800 acres of rice in Butte and Colusa counties in 2009, divided among 4,947 different fields. For that report they used Geographic Information System technology to combine U.S. Geological Survey National Hydrography Dataset and California Department of Water Resources land-use layer data into a common projected coordinate system. These were then run through a custom script that reported the amount and percent of crop land bordering sensitive aquatic sites. Affected Acreage Demars and Zhang concluded that while the actual acreage that would be in 25-ft. buffers was a small share of total acreage , the number of fields affected was a large share of the total number of fields . Thus, the increased management costs due to the buffers could be substantial. Under a 150-ft. buffer, both the acreage in buffers and the number of fields affected were substantial shares of the total: 19% and 96.5%, respectively. We used Demars and Zhang’s findings, along with base yield information from county agricultural commissioners’ reports, cost information from UC Cooperative Extension cost studies, and estimates of yield reduction from the scientific literature to estimate the changes in gross and net revenues for the two counties in response to the regulations.

The most important active ingredients for rice production that would be prohibited for use in buffers under the draft regulations are propanil , which is used as a cleanup herbicide for weed control, and lambda-cyhalothrin , a pyrethroid insecticide which is used to control rice water weevil. Weeds are the most important pest in rice, reducing yields by 17% in the United States as a whole compared with 8% and 7% losses yield losses due to insects and diseases, respectively. Thus,drainage gutter weed control through a combination of water management, herbicide application, and other methods is crucial for sustaining the productivity of U.S. rice-cropping systems. Propanil is the most widely used herbicide in rice. It is a relatively inexpensive material, to which water grass weeds in rice have not yet developed resistance, unlike other available herbicides, including thiobencarb, cyhalofopbutyl, and bensulfuron-methyl. Thus, growers are able to use it as a cleanup herbicide post-planting, following the application of one or more other active ingredients. Most propanil in Butte and Colusa counties is ground-applied, so there is relatively little scope for growers to reduce the impact of the draft regulations by changing from aerial to ground applications. Because of widespread herbicide resistance among common weed species in rice fields, it is difficult to identify post-planting alternatives to propanil as part of an effective weed management program. There are a few cultural alternatives, including increasing the depth of water in order to “drown” weeds, severely drying the field to desiccate sedges, or using flooding to germinate weeds early and then kill them preplant with a broad-spectrum herbicide such as glyphosate. However, none of these methods are a perfect substitute for propanil. Each compromises the efficiency of the production system and may result in considerable yield loss. In order to compute the effects of the draft regulations on total and net revenues, we specify that propanil is used as a cleanup spray, except in the 25-ft. buffer where no cleanup application is made, and that only half of total field acreage requires a cleanup spray. Based on the scientific literature, we assume that rice yields decline by 40% in the untreated buffer. The per-acre cost of treatment declines by 100% in the buffer because no cleanup spray is applied. Also, the uncontrolled weeds in the non-treated buffer zones will produce large quantities of seeds, thereby fortifying the weed seed bank and ultimately increasing weed populations over time. The rice water weevil is one of the most economically damaging invertebrate pests in California rice. Root pruning by larvae reduces growth, tillering, and yield of affected plants. Buffer zone requirements are particularly problematic for rice water weevil management due to its life cycle and distribution in rice fields. This insect overwinters in grassy areas around rice fields; these areas are usually associated with sensitive aquatic sites such as sloughs and ditch banks. In early spring the rice water weevil moves to flooded rice fields but does not tend to establish very far into the fields. A 25-ft. buffer would encompass most of the area where damage from rice water weevil would be expected to occur. Lamda-cyhalothrin is the major insecticide currently used to control rice water weevil. In 2009 all applications of lambda-cyhalothrin in Butte and Colusa counties were made by air, according to CDPR Pesticide Use Reporting data. This is driven by the timing of post planting applications; rice fields are treated with lambda-cyhalothrin when the rice plants have one to three leaves.

At this stage of development, water movement and soil disturbance caused by the equipment used for ground applications can uproot rice plants, reducing stands. Thus, the timing of the application must be changed in order to change the application method and avoid the 150-ft. buffer requirement. Lamda-cyhalothrin applications made after the three-leaf stage of rice are not effective against the rice water weevil. Recent scientific research findings indicate that pre-flood applications of lambda-cyhalothrin can be effective, although this approach has not been adopted widely by growers.The UC Integrated Pest Management Guidelines for rice water weevil list two alternative chemical controls to lambda-cyhalothrin: -cypermethrin and diflubenzuron . -cypermethrin is a pyrethroid that is also listed in the draft regulations. Hence, it would not be a viable alternative to replace lambda-cyhalothrin if the draft regulations were implemented.However, diflubenzuron is also not available as an alternative buffer treatment because of label restrictions that require a 25-ft. vegetative buffer between ground application areas and bodies of water. Given these limitations, growers concerned with rice water weevils would likely use a preventive, pre-flood ground application of lambda-cyhalothrin if the draft regulations were implemented. In order to evaluate the economic effects of the draft regulations on rice water weevil management costs and associated rice revenues, we compare the current post-flood aerial application method to pre-flood ground application to eligible acreage under the draft regulations. Rice water weevils tend to be economic pests near field edges, and growers do not usually treat entire fields. We proxy this management pattern by assuming that the land within 100 feet of the edge of a field represents, roughly, the land that is treated currently. Under the draft regulations, acreage within 25 feet of a sensitive aquatic site cannot be treated with a ground application. We assume that acreage within this buffer is left untreated, and that lambda-cyhalothrin is groundapplied on the remaining eligible acreage within 100 feet of the field edge. Based on the scientific literature, we assume that the acreage treated with a pre-flood ground application sustains a 15% yield loss and the untreated acreage sustains a 23% yield loss.

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This interpretation correlates well with the position of three TGAT core motifs

Transcription factor binding sites were identified by consulting multiple online prediction tools which quickly found over two hundred predicted cis-motifs, many of which had low probability scores. The odds of identifying functional cis-motifs were increased in a few select cases by adding 5bp sequences on either side of the core motif, based on previously identified target sites for WUS , ARF1, and ARR1. The enlarged biding sites were then mapped to the CLV3 genomic sequence, tolerating up to 2 mis-matches in the flanking regions. In order to account for the presence of transcription factors whose cis-motifs are not currently known, MEME analysis were employed to identify motifs shared between genes that are co-expressed with CLV3. Overall, 231 potential cis-motifs and transcription factor binding sites were identified. Most were randomly distributed over the entire CLV3 genomic sequence, but irregular clusters could be recognized near the coding region. The largest cluster occurred in the upstream 500bp of the 5’ promoter, while up to three smaller clusters occurred in the 3’ enhancer region . The list of potential factors was then filtered to include those found inside the previously identified CLV3 regulatory regions, which left just 157 predictions . Many of the remaining predictions were found to have overlapping sequences, though it is unclear how well this might predict their actual function in-vivo. One notable example of this phenomenon is a predicted MYB-like binding site located at -155bp, which was predicted by four different databases. In other cases, two structurally different transcription factors were predicted to have overlapping cis-motifs, such as the bZIP/homeodomain pair Opaque-2/ALFIN-1 in the 3’ enhancer region. Interestingly,large plastic pots for plants the data also revealed four partial miR414 targets, three of which overlapped with the DNA/Mariner family transposable element At2gTE50670 in the 3’ enhancer , and the fourth occurred in the 3rd exon.

In an alternative approach to identify unknown cis-motifs, phylogenetic footprinting was used to compare CLV3 orthologous sequences from different species. In this method, functional regulatory structures can be identified by their conservation over evolutionary time, which often requires little more than performing a sequence alignment. The method is also quite robust, as previous studies found that the identified footprints matched 80 and 85% of known transcription factor binding sites. To begin this analysis, three CLV3 orthologs were identified by their syntenic relationships within the Brassicaceae using the tools in the Brassica Genome.org database. Their cDNA sequences were aligned with 27 CLE family paralogs identified in A. thaliana in order to identify features that were unique to CLV3 orthologs, before expanding the search to additional species. This analysis revealed three potentially unique traits that might be used to distinguish orthologs from the multitudes of closely related CLE genes. These included three consecutive histidines at the C terminal end of the CLE motif, a C-terminal oligo extension, and a 3-exon gene structure, all of which had been previously identified in the CLV3 sub-group. Additional orthologs were then identified using tBlastn searches against the AtCLV3 protein, for which nine species which met the criteria described above: Brachypodium distachyon, Oryza sativa, Ricinus communis, Glycine max, A. thaliana, Arabidopsis lyrata and Brassica rapa, Capsella grandiflora, and Camelina sativa. No AtCLV3 orthologs were identified in the gymnosperms, basal angiosperms, or the Asteriids using these search parameters. The Euphorbiaceae and Fabaceae each contributed one species in the closely related Eurosiids I, while the monocots are represented by two species in the Poaceae. As a result, this sampling is heavily biased towards the Brassicaceae family , which provide more than half of the total number of species. In order to footprint the promoter regions, initial sequence alignments were performed using 8kb genomic fragments, containing up to 5kb of upstream and downstream sequences on either side of the coding region. However, little or no homology was found when all nine orthologs were aligned simultaneously. This was not improved by removing monocot clade, as the two grass orthologs failed to align with each other.

Repeating this pattern, both R. communis and G. max also failed to alignment with each other, or with any of the remaining orthologs. In contrast, conserved regions became clearly visible when the five Brassicaceae species were aligned separately . This result appears to reflect the optimum degree of sequence divergence for this gene, as previous studies have found that orthologs outside of the Brassicaceae were less informative due excessive divergence, whereas sequences obtained entirely within the Brassicaceae have been found to have too little divergence . Three of the remaining species had complete genomic sequences, while the other two consisted of two contigs separated by a gap of unknown size. In the B. rapa ortholog, the gap was located in the 3’ region, and was flanked by 256 and 452 base pair sequences that did not align with any of the other Brasssicaceae orthologs, despite strong sequence conservation in the surrounding regions. This indicates the recent insertion of a large DNA fragment, potentially >700bp in size. Attempts to locate the source of the two end-fragment sequences in the B. rapa genome with BLAST searches, unexpectedly found that each was present in multiple copies, and were distributed across several different chromosomes. No evidence of transposable element sequences were found, so the flanking regions were here interpreted to be contaminating scaffold sequences from the original genome assembly. A similar gap of unknown size occurred in C. grandiflora, where one contig aligned with the CDS and 3’ UTR, while the entire 5’ upstream contig failed to align with any other ortholog. In both cases, the non-aligning sequences were removed from the analysis, providing a final alignment consisting of four orthologs in the 5’ promoter region, and five orthologs spanning the CDS and 3’ UTR. Overall, the five orthologs shared between 27% and 65% sequence similarity, and grouped into two closely related pairs. One pair contained C. grandiflora and C. sativa, and the other contained A. thaliana and A. lyrata. In contrast, B. rapa was found to be distinct from all other Brassicaceae orthologs, which accurately recapitulates its predicted evolutionary relationship with the rest of the family. Upon closer inspection, the coding regions were found to be 79-93% similar, which dropped to just 14-34% in regions with no significant alignments. The initial alignment was considerably fragmented, with many insertions, deletions, and isolated nucleotides. In many cases, the position of these features varied with the settings in the alignment software, and were here interpreted to be artifacts of the alignment procedure.

To correct such artifacts, isolated nucleotides were manually adjusted left or right to maximize local sequence alignments within ±5bp. Where variation in the length of tandem repeats was apparent, gaps were introduced into one or more ortholog sequences to accommodate the largest number of repeats present. Conserved regions were then identified by using a 5bp sliding window to identify regions with more than 60% identity. This window is unusually small compared to previous studies that have used 15-50bp sliding windows, but was chosen here to more accurately reflect the minimum size of known transcription factor binding sites. Where large contiguous conserved regions were found, the presence of small 1-3bp indels within their sequences were used to break them into smaller fragments, as disruption of these sites indicates that they do not contain functional cis-motifs. scattered in the 3’ UTR. Several predicted transcription factor sites were found within the coding regions, but these were interpreted to be non-functional, as previous GUS-reporter systems did not reveal any significant regulatory elements within this region. Among other notable features was a predicted signal peptide in the first exon, identified with signal P 4.0,blueberry pot which was almost entirely conserved and is consistent with the secretion of the mature CLV3 oligopeptide. In addition, the second exon was found to be completely conserved with no In all, 42 conserved regions were identified, ranging in size from 5 to over 111bp long. Fourteen footprints were found in the coding sequence, of which nine of were clustered around the three exons. Only one footprint was found entirely within in the 5’ UTR, and the remaining four were intervening gaps. The second exon also completely overlapped with several predicted transcription factors, including HOX2a, aswell as cytokinin and gibberellic acid responsive motifs. This suggests as-yet unrecognized functional role for the second exon, which might explain why it has been retained in a family that consists largely of single exon genes. The 3rd exon was also highly conserved, although curiously the most conserved region only partially overlapped with the CLE motif and instead included part of the C-terminal extension. In the 3’ UTR, the footprints were found to overlap with potential zinc-finger and MYB binding sites, as well as a cytokinin responsive ARR10 site. In the upstream regulatory region, the 5’ promoter contained ten conserved footprints, eight of which formed a large and nearly contiguous block near the TSS. The two isolated footprints were located at -204bp and -167bp upstream, corresponding to the palindromic Motif#2 and the redundantly predicted MYB binding site, respectively. In the remaining footprints, additional predictions were found for an overlapping AGL15/CBF site, an auxin response element, overlapping GT1 and AGAMOUS sites, and one prediction for a TATA-less promoter. The latter may be related to the position of the only recognizable TATA box-like sequence, which at – 68bp upstream, which is more than double the usual 25-35bp described for other TATA-based promoters. In contrast, the 3’ enhancer region contained seventeen footprints arranged in roughly three clusters, spanning a region nearly 600 bp long. Two of these clusters closely corresponded with the previously noted clusters of predicted transcription factor sites, while the third was distinctly isolated and had no predicted transcription factors. Together, the footprints contained one of the three known WUS binding sites , two predicted AtHB1 binding sites, a cytokinin responsive element , several bZIP motifs, a KNOX-like site, and a predicted cis-motif forNPR1. Strikingly, the majority of the footprints also overlapped with a DNA transposable element in A. thaliana, At2TE50665 . It has previously been implied that WUS controls CLV3 expression in a concentration dependent manner, which is consistent with the close proximity of two demonstrated WUS binding sites .

The region around these two sites also contains several other TAAT cores within a single stretch about 100bp long, much of which is represented by four conserved footprints, which together might form a WUS binding site cluster. However, only the +970 WUS binding site was found to be perfectly conserved, while the other TAAT cores displayed mutations or were interrupted by indel sequences in one or more orthologs. Instead, when the region around the known WUS binding sites was examined in more detail with a 5bp sliding window, a strikingly periodic pattern was observed, where four different conserved motifs were found to be regularly spaced about 15 bp apart. In order from 5’-3’, these motifs were identified as CCGTTGGG, AGTAC, TTGTCAA, and TAATTAATGG , the latter two of which correspond to a predicted W-box motif, and the +970 WUS binding site. In addition, a perfectly conserved sequence was found just 25-36 bp downstream in all orthologs, which consisted almost entirely of tandem repeats containing ATG. The ATG repeats also overlapped with a predicted ALFIN-1 homeodomain/Opaque-2 binding site, suggesting that this sequence may actually represent a modified bZIP motif, or perhaps an atypical homeodomain binding site containing a TGAT core motif. It is not clear how many potential binding sites are present in these ATG repeats, but in consideration of the size of the conserved region, it seems likely that they could accommodate up to three transcription factor proteins simultaneously.The potential functional role of the TGAT motifs is further supported by the observation that they are 4x over-represented in the surrounding 124 bp conserved region, while the TAAT cores actually are 5x under-represented. In addition, pair-wise distance measurements between the two cores revealed a skewed distribution, where few sites were found closer together than the median value of 5bp. When several median-length pairs were aligned, this corresponded to the 13bp motif TAATnnWnnTGAT. When this motif was subjected to Patmatch searches of the A. thaliana genome, it was found to be 26x over represented among the genes directly targeted by WUS. Multiple copies of the 13bp motif were also found in several target genes, including two in the 3’ enhancer of AtCLV3.