Tag: horticulture

In 1977 the Boston Urban Gardens was formed through a coalition of black community organizers, white activists, and other Boston residents to better coordinate gardening efforts in the city . In Oakland, the Black Panther Party grew gardens for subsistence on open spaces and on the properties of facilities used for BPP activities . Nationally, community garden received significant support and became increasingly institutionalized by the end of the 1970s. Between 1976 and 1993 the USDA ran an Urban Agriculture Program in 26 cities providing technical and financial support to gardeners. In 1982, $17 million worth of food was produced by community gardeners supported by the Urban Agriculture Program . In 1979 the American Community Gardening Association was formed at a conference of community gardeners from across the nation. Their early mission included publicizing the work of gardens, providing mechanisms for information exchange and establishing deeper relationships between gardening groups . In the 1980s the ACGA was deeply concerned with land tenure, a sentiment we will see reflected in the San Francisco League of Urban Gardeners as well. The May 1982 and fall 1987 issues of the Journal of Community Gardening, the ACGA’s national publication, were devoted to the topics of site permanence, advocacy to change the place of gardening in city master plans and housing developments, and opinions on gardeners organizing to secure sites through ownership, land trusts, and long-term leases . In 1982, Diane Gonsalves argued community gardens should not be made portable stating, “the displacement of gardens undermines the commitment of the gardeners,plant pot with drainage depriving neighborhoods of an important stabilizing factor, in much the same way that housing displacement does” .

Gonsalves laments that gardens “remain invisible to planners. Architects, politicians, and policy makers” and “are treated like carpets that can be rolled up and moved elsewhere atwill” . In spring 1983, the ACGA published an infographic on tips for saving a garden entitled “Stop the Bulldozers!” . On the other hand, in the 1987 ACGA publication on land tenure, Gerson was advocating for gardeners to accept that gardeners will sometimes lose sites: “When it comes time to leave, you do so. Regrettably. But you don’t cry, whine, or fuss, nor do you encourage your gardeners to do so” ). Gerson argued that ‘creating a fuss’ damages the reputation of community gardening at large, and in an environment where “developers will win 98% of the time” gardeners need to know gardens are not forever. During this period from the late 1960s to the 1970s, collective urban gardening experienced a revival across the country. But by the mid-1980s community gardening was in decline. Shifts in federal and state funding left many gardening programs without the funds to support their staff or work. Yet, the commitments and sometimes projects of this era have survived to the present. During the community gardening period, San Francisco Bay Area urban agriculture communities started to develop as a vanguard leading many conceptual and political efforts to support gardening and urban improvement through agriculture. Home gardening was embraced as a key piece of sustainability of the rapidly growing communal living movement in the Bay Area. By 1971 there were more than 300 communes in the region connected by the weekly newsletter Kaliflower in which articles described home gardening techniques among other things . Kaliflower authors drew inspiration from the Diggers, a spin off from the San Francisco Mime Troupe who advocated for community self-sufficiency and practices such as dumpster diving, labeled “garbage yoga”, and theater aimed to “politicize a new way of living in the city” .

Urban communes became the launching ground for a network of Food Conspiracies, collectives who pooled food stamps, bought bulk food and shared other food resources, and later the San Francisco People’s Food System . In Berkeley, community activist Helga Olkowski and doctoral student William Olkowski, Helga’s husband, created many opportunities for Bay Area residents to learn about sustainable living. Together they developed classes at UC Berkeley on food growing, promoted the use integrated pest management across the Bay Area, started the first recycling center in the US, and help start Antioch College West, an alternative college in San Francisco with a focus on ecology. For six years, William Olkowski conducted research and education on the UCB Gill Tract Farm in Albany, now the site of an urban garden and land battle . The Olkowskis are potentially best known for the publication of two books on urban food production: The City People’s Book of Raising Food and Integral Urban House: Self-reliant Living in the City. The latter was one of the first books on “urban homesteading Lower down on the peninsula, John Jeavons and his colleagues at Ecology Action in Palo Alto started an urban farm in 1971 to conduct research on intensive food production methods. Ecology Action grew food and taught ecological agricultural practices on this farm until their lease ran out in 1980. Jeavons, a former student of UCSC’s Orin Martin, lamented, “like so much other agricultural land in the United States, our lovingly tended beds succumbed to the press of urbanization” . While their farm was initially imagined as a piece of the urban Bay region, the difficulty of maintaining land access pushed Ecology Action to find a permanent site in Northern California. Their bio-intensive method of food production requires long-term soil building, ideally over a 50-year period, and other practices that were not viable in land markets dominated by short-term leases and the loss of land to development.

However, by the 1980s, another force in bio-intensive and sustainable local agriculture was growing as a commercial venture in both rural and urban California. In 1982 the renowned Berkeley restaurant, Chez Panisse started growing and buying local produce . By 1986, Chez Panisse and fourteen other high-end restaurants were buying from a small urban farm, Kona Kai Farms Market Garden, in an industrial neighborhood in Berkeley . Sustainable gardening and local food sources for commercial purposes were deeply connected to the Bay Area environmental movements of the sixties, seventies, and eighties. In addition to experiments in home agriculture as connected to sustainable and often communal living, the Bay Area was enlivened with other acts to reimagine urban relationships to land, food, and people. In 1969 in Berkeley, People’s Park became a national example of a continued community occupation of land leading to the creation of community gardens, open space, and much more . In a decades-long, often violent struggle, student activists, environmentalists and social justice advocates occupied UC Berkeley land in what was considered a revolutionary act to create space for humans and nature in resistance to development. In San Francisco, artists from the San Francisco Mime Troupe, inspired by the diggers, started an urban farm as a piece of “life theater.” Here art, agriculture, and community gathering were combined to radically rethink human-nature relations . Another urban farm, the Farm, was created when project leaders, Sherk and Wickert, leased 1.5 acres of land by the side of the freeway. Community activists worked with the Trust for Public Land and the city eventually agreed to buy 5.5 acres and develop it into a park. Between 1974 and 1987 “The Farm” or Crossroads Community included artists, poets, punks, vegetables, livestock,pots with drainage holes and many others in an experiment in non-hierarchical radical ecology. At the same time, the lot next to The Farm became a key gathering space for low rider cars and Chicano cultural activists. People’s Park was an inspiration to Low Riders looking to carve out a space of their own in the mission district . After 1980, diminishing funds for community arts projects and shifting use of the space led to the decline of The Farm as it had been. The City was not accepting of the radical vision of the space and began development of a more traditional urban park, which still exists today as Portrero Del Sol Park and adjacent community gardens. During the 1970’s, Community garden programs housed under municipal departments began popping up across the country. Over forty percent of contemporary community gardening programs began in 1975 . Many of California’s contemporary community gardening programs were initiated in this period. In 1977 the California Council on Community Gardening stated “Community gardening improves the quality of life for all people by beautifying neighborhoods; stimulating social interaction; producing nutritious food; encouraging self-reliance, conserving resources; and creating opportunities for recreation and education” . San Jose’s first community garden was started in 1976 by a coalition of residents from senior associations, the Food Bank, San Jose State University students in environmental studies, UC Cooperative Extension, and San Jose Parks and Recreation. The 5-acre garden, located on land previously used for a City nursery, was named Mi Tierra and was led and tended by mainly Mexican-American residents . A year later the City started its official community gardening program. In 1993 Mi Tierra was evicted when the San Jose Ice Center was built on the land, and Mi Tierra became Nuestra Tierra community garden on another site. The garden was moved again in 2000 when the land was scheduled to be made into a golf course . This has been a common story for San Jose gardens; all of the community gardens started in the seventies have been moved from their initial sites when the City or other landholder developed the land.

In 1999 when the 25-year-old West Side Garden was evicted in order to build a library, Lilyann W. Brannon with the help of other gardeners fought the prospect of loosing more garden land. Lilyann W. Brannon, a prominent environmental activist and leader of the United New Conservationists, an environmental group started in the seventies at San Jose State University, objected to the City’s position that a community garden is an interim use until development takes place. She advocated that the City zone sites for permanent community gardens, stating: “I would like to see some dignity given to the urban agriculture” . John Dotter, San Jose community garden program director for many years, noted that community gardens and cultural gardens have been an essential space in San Jose for many groups of immigrants to continue the expression of agricultural and community identities . In a valley with rich history of farming in Japanese, Mexican, and other ethnic communities, gardens bridge rural and urban immigrant communities.In addition to San Jose, both Oakland and San Francisco initiated community garden programs in the seventies. In 1973, the San Francisco Board of Supervisors created a community gardening program under the Department of Public Works Street Tree Program and hired a coordinator to run the gardens . The greenhouse at the Laguna Honda Hospital, the site of the former victory garden, was put to use growing plants for distribution to community gardens. At the same time the coordinator assisted residents in finding sites for gardens and in obtaining insurance. When the Comprehensive Employment Training Act began providing federal funding for positions for urban improvement, San Francisco hired CETA workers to run community garden and art projects. By 1975 fourteen full-time workers were employed . Using CETA funding, Contra Costa County hired seven staff members to develop a gardening program inspired by San Francisco’s program . The state of California hired a community gardening coordinator to be housed under the Office of Appropriate Technology and published a 1977 report on the state of community gardens . The significant energy across the state was funneled into the creation of the California Council for Community Gardening , a precursor to the American Community Gardening Association . The Council organized statewide conferences, a communication network, and information sharing forums. By 1979 there were 75 community gardens managed by the San Francisco Department of Public Works. However due to the passage of Proposition 13 and the end of CETA funding, the community gardens program had already begun its decline. By 1980 the community garden program was no longer functioning . The Contra Costa program lost all but one staff member. The California Council for Community Gardening began its decline and folded in 1985. Organizer Mark West wind concluded the project ultimately did not continue because “each of us was too dedicated to our primary focus – our own projects in our own communities” . In San Francisco, Pam Pierce, Steve Michaels, and other gardeners continued the work of helping to support gardens under the name of the Urban Agriculture Coalition .

In July 2006 in South Central Los Angeles, over 300 gardeners were evicted after public land became private through backroom deals. This eviction became perhaps the most publicized and scandalous urban farming land dispossession in U.S. history. Three years later in Albany, CA in the face of UC Berkeley’s plans to develop their last plot of urban agricultural land, a coalition of over thirty groups began a fifteen-year process resulting in an urban garden and community-university partnership. Today activists struggle to maintain access to the land for the future. Both of these cases, despite being gardens on public land engaging hundreds of community members, demonstrate the insecure access to land gardeners struggle with across cities in the US. Their stories are telling. The Los Angeles South Central Farm garden site, which was over ten acres, was obtained by the City of LA in the mid-1980s through eminent domain for the purpose of creating a trash incinerator facility . Local citizens successfully opposed the building of the incinerator, and in response to the 1992 social uprising spurred by the Rodney King beating and long term effects racism and poverty in south central LA, the site was purposed as a community garden. The local food bank saw the garden as a means to address a lack of food retailers and social marginalization of residents. Garden construction began in 1994. Gardeners, mainly recent Mexican and Central American immigrants and Latinos, farmed 350 plots, producing rich agroecological environments with fruit trees, dense plantings of vegetables and flowers,growing strawberries vertical system and difficult to find herbs and culinary ingredients.

Gardeners came to the farm to grow food for their families, practice or learn agricultural traditions from those still practicing their knowledges, feel more at home and socialize, and support family businesses . In a study of the farm’s biodiversity, Peña estimated there were 100-150 plant varieties, many varieties of which were difficult to find in the US outside of huertos familiares in Latino communities. In 1995, the development company that had lost the property to eminent domain in the 80s made its first attempt to buy back the property, but the City Council did not approve the deal . The developer sued arguing that he was denied his right to buy back the land that was taken with the purpose to build a trash incinerator. In 2004 the gardeners were given their eviction notices after the city as a result of an out-of-court settlement sold the property back to the developer for $5.05 million . In response to the eviction notices, the gardeners organized to form the South Central Farmers Feeding Families. The gardeners and their allies went through a roller coaster journey of successes then eventual failure in the courts. Local residents, internationally known actors, and city politicians supported the effort to keep the gardeners on the land. In April 2006, the Trust for Public Land and LA Mayor Villaraigosa’s office negotiated an option to buy the land, but the developer was now seeking $16.3 million for the property . When the coalition raised the funds to meet the asking price, the developer rejected the offer and, starting in June, barred gardeners from the land and demolition begun . Mares and Peña argue that the struggle over South Central Farm represented a turning point for the environmental justice movement. Latino immigrants had reproduced village-based forms of community self-organization, integrated agricultural traditions into a new place, and challenged undemocratic urban planning and policy. Many city officials had expressed support for the South Central Farmers, a group of Latino residents, including many undocumented immigrants. Still, in the end the city sided with an interpretation of the case as a simple matter of a developer’s right to his property .

The incident demonstrated that many local government officials who claimed to support the work of gardeners would only go so far in standing up to business interests, despite arguments that the sale of the city land was illegal . Gardeners who assumed city land would be secure from development saw the land sold out from under them. Despite the eventual development of the land, the gardeners’ resistance to claims by the developer galvanized a community and demonstrated their political power .In Berkeley, urban agriculture advocates struggled for fifteen years to gain a tenyear agreement for a garden on public land. In 1997 after learning of UC’s plans to develop a large tract of agricultural research land for commercial purposes, a coalition of over 30 groups began resisting the development and proposed instead an urban agriculture research and education center. For over seven decades the farm was used by the Division of Biological Control for research on integrated pest management, but in 1998 a research agreement was made between the UC Department of Plant and Molecular Biology and Novartis, a biotechnology corporation, which granted Novartis the right to license discoveries in exchange for a $25 million donation to the department . As a result, by 2001 the DBC was no longer allowed to use the land and was defunded by the university. Students, faculty and others organized against this “biotech buyout”, leading to the infamous tenure battle of Ignacio Chapela.1 At the same time students, faculty, and community partners were organizing to try to gain a better foothold for sustainable agriculture research at the University. Starting in the mid-1990s, the University of California Berkeley decided to sell the development rights to the unused south side of Gill Tract that was adjacent to UC Berkeley family student housing. UC students, neighbors, and urban garden advocates led by Peter Rosset and others at Food First organized to resist the development and advocated for the creation of a sustainable urban agriculture training center 1997.

The UC moved ahead with planning the development at the same time it was seeing unprecedented tuition hikes, increased recruitment of out-of-state students, and increased investment in real estate and development on UC campuses . In 2004 the UC Regent’s released a Master Plan for Developing the University Village with details of Capital Projects Division’s plans to develop the entire tract with a shopping center, senior center complex, and recreation and open spaces . The Associated Students of the University of California and the Student Organic Garden Association at UC Berkeley released statements opposing the development of the land and supporting the creation of a garden/farm . Between 2004 and the early 2010s, the UC sought the necessary zoning changes and approvals from the city of Albany as well as solicited interested developers, including Whole Foods and Sprouts grocery stores.The occupation initially lasted three weeks during April 2012, until UC police stepped in to end the occupation. The land was reoccupied in May, 2013, when protesters again cleared grasses, tilled, and planted. This occupation was broken up by UC police, re-established, and then raided again. At the same time students and garden advocates were working with faculty, such as Miguel Altieri, and the College of Natural Resources,growing vegetables in vertical pvc pipe to develop a community-university partnership for use of the land. Today that partnership project manages a collectively run garden called the Gill Tract Community Farm located on part of the northern portion of the land. In addition, UC faculty continue to conduct agricultural experiments on the north side, while the south side is still slated for development. Occupy the Farm persists as a movement and many of the original occupiers now garden as a part of the partnership. OTF activists have also developed a connection with the MST 2 , organizing events that connect food and land sovereignty work in the global south to the struggle for the Gill Tract Farm. Occupy the Farm works to highlight the UC’s shift towards increasing privatization while little support is given to projects that support local agriculture, food security, or otherwise serve the local ecological and human communities. For example, OTF activists protested the December 2013 hiring of Robert Lalanne as the first ever ‘vice chancellor for real estate’ for UC Berkeley. On October 1, 2014, members of OTF and the Cal Progressive Coalition occupied the office of Capital Projects holding a sit-in until Chancellor Dirks met with the occupiers and provided several important documents about the Gill Tract development, which activists had been promised in May . This action was conducted as a part of a call for National Days of Action for Land and Food Sovereignty put forth by the US Food Sovereignty Alliance. The idea for these days of action came out of meetings at the second US Food Sovereignty Alliance Annual Assembly in 2013. The first was held in Oakland in 2011.

Organizing around land and food in the US context arose as an important theme for Alliance members, as well as for researchers. Food First initiated the Land & Sovereignty in the Americas’ Collective, which in October 2014 released its first informational brief on land and resources grabs in the US . OTF and others engaged in these actions have sought to bring land politics to the forefront of the struggles for sustainable agriculture and food sovereignty. These two urban agriculture projects aimed to enact better food systems, both as a part of contemporary food movements and as a part of the local struggles of their immediate geographic communities. The South Central Farm arose in the mid-1990s in Los Angeles in the same time and place as the community food security movement, as a solution to the hunger and lack of healthy food options in a majority African American, Latino, and Mexico and Central American immigrant community. Organizing for use of the Gill Tract Farm began in 1997 and for nearly two decades has focused on the need for public educational resources to be allocated towards sustainable agriculture. Advocates have stressed the environmental significance of preserving one of the last pieces of farmland in the East Bay. In 2010 the advocacy received a new boost of energy when Occupy the Farm activists identified the farm as important to the broader community project of reclaiming commons. Due to the intensity of their struggle, both of these stories gained positions of prominence in contemporary food movements. These examples demonstrate the fact that gardeners are most frequently not the owners or decision makers of land use choices for the parcels of land that they farm. This disconnect of land ownership and use has led to a significant problem for contemporary urban agriculture: tenure insecurity even on public land. But the stories go beyond highlighting struggles for tenure strictly for gardening. Both stories incite both outrage and debate in gardening communities on the topics of how urban space can and should be used in recreating food systems. Urban agriculturalists construct and define urban utopian projects that intend to reconfigure the city in more ideal forms. Ultimately, each project made food activists distinguish their positions on the appropriate uses, governance, and ownership of urban land in situations where gardeners are not immediately empowered to make land use decisions. Gardens are part of  socio-ecological processes that create urban space, and gardeners are a part of the urban movements that struggle for ideal landscapes. Drawing on Lefebvre, urban political ecology understands space as socially produced through a history of practices, representations, and experiences . Gardeners change the production of urban spaces through actions like advocating for use of public lands, changing investors’ decisions on buying particular parcels, or passing legislation to increase access to space for gardens. Adopted as a strategy for change in various movements, community gardens in urban settings can have multiple and contrasting meanings of community and garden . Gardeners debate the questions: What kind of city do we want to live in? How do we want to eat and work, interact with nature, and engage with our neighbors and governmental agencies within that city? Can gardens help us transform cities today or prefigure new cities of our futures? Can we change the economic, political, social, ecological landscapes of cities through garden projects? These questions are central to the project of urban political ecology, which serves as a guiding framework for this dissertation. Urban political ecology brings together theories of production, space, justice and agency to understand socioecological landscapes .

The first uses a lagged dependent variable approach and the second employs a difference-in-difference framework. Both approaches yield similar estimates, indicating that during the period under examination the subsidy increased support for the incumbent party by 6.2% to 7.5%. While this increase might seem relatively modest, we emphasize that this result is the estimated effect of receiving the subsidy in a single year of a multi-year program and that the individual effects of the subsidy are likely to be attenuated because non-recipients may have also benefitted indirectly, for example through reduced food prices. The main contribution of this paper is to add to the growing empirical literature on the political benefits of poverty-reduction programs . We draw from the new wave of agricultural subsidy programs in Africa to demonstrate that such programs can alter political preferences even in settings like Malawi, where entrenched ethno-regional partisan ties might be expected to limit the political effects of government sponsored programs. In doing so, the paper also contributes to the literature specifically related to the political economy of agricultural subsidies . The findings have important implications for the larger literature on distributive politics and on our understanding of voter behavior in Africa. The conventional wisdom in scholarship on patronage and clientelism, particularly in Africa, is that ruling parties build and maintain support by channeling material favors to core supporters . One of the key debates in the empirical literature on voter behavior in Africa’s emerging democracies is whether government performance affects voters’ political preferences in contexts where social identities, particularly ethnicity, are salient. The analysis presented here shows that distributive programs need not be targeted to core supporters to be politically beneficial to incumbents,greenhouse benches suggesting that leaders in Africa’s emerging democracies may be able to enhance their support by implementing anti-poverty programs that do not discriminate against non-partisans or out groups at the local level.

Should incumbent leaders expect to reap political rewards from implementing targeted antipoverty programs? On the one hand, the answer may seem obvious. The theoretical literature on retrospective voting suggests that voters reward parties that implement desired policies . To the extent that distributive programs lead to real improvements in welfare, voters may well compensate the incumbent at the ballot box. Studies from emerging democracies in the developing world find evidence of such a link. De la O shows that in Mexico a large-scale anti-poverty cash transfer program that provided benefits to lowincome families increased voter turnout and support for the incumbent party. In Brazil, Zucco reports similar effects when examining a cash transfer program aimed at low income families with children. Manacorda et. al show that a short-term poverty relief program in Uruguay had similar effects, increasing support for the incumbent party that launched the program. Pop-Eleches and Pop-Eleches examine a program that distributed coupons to poor families for the purchase of reduced-priced computers and found that beneficiaries were significantly more likely to support parties of the governing coalition. Finally, Harding and Harding and Stasavage present evidence from Ghana and Kenya that voters reward incumbents for improving roads and expanding access to primary education. There are at least two channels through which targeted subsidy programs like the agricultural subsidy we examine in this paper might affect voter preferences. First, retrospective theories of economic voting suggest that when such programs have a positive effect on individual economic welfare, voters will reward the party responsible for implementing the program. Agricultural programs are generally highly visible initiatives that have a direct effect on material well-being for large numbers of citizens. In Malawi, for example, studies have shown a strong positive relationship between expanded fertilizer use resulting from the subsidy program and crop yields . Others have linked the subsidy to dramatic increases in maize output that reduced food insecurity and brought down the price of maize in local markets .

Existing studies suggest that subsidy programs have contributed to improved evaluations of incumbent job performance in Malawi and elsewhere . This is important, because, as Harding and Stasavage argue, voters are more likely to reward incumbent leaders for programs that can be directly attributed to those political actors. The clientelism literature suggests an alternative mechanism through which subsidy programs might affect voter behavior. In contexts where the distribution of valued benefits is controlled by party agents, citizens may trade their vote for material transfers . By this logic, the receipt of subsidy coupons might be expected to strengthen patron-client bonds, solidifying support for the party that controls access to state largess. However, for reasons described below, we expect the clientelist mechanism to be less relevant in the Malawian context that we study because of weak local-level party infrastructure. At the same time, there is reason to be skeptical about anti-poverty programs’ power to influence political preferences, particularly in African contexts where voter preferences are often driven by ethnic and regional identities. Longstanding approaches to political behavior in Africa suggest that voters hold strong preferences for candidates and parties associated with their own ethnic communities and only trust co-ethnics to deliver benefits to their group . Where ethnicity underlies political preferences, voters may be unresponsive to material transfers and may be hesitant to give incumbents credit for distributive programs, even when such programs do not discriminate by ethnicity or partisanship.Moreover, the clientelism literature suggests an additional reason why voters may be unmoved by anti-poverty programs: where local monitoring systems are weak, voters may simply accept government favors but continue to vote according to pre-existing preferences . The existing empirical literature from African cases has so far offered mixed findings on the connection between government performance and voter preferences. Several recent studies provide evidence in favor of retrospective voting theories . Other studies, however, suggest that in some cases ethnicity can trump performance . With the exception of Harding and Harding and Stasavage , these works tend to focus on broad performance measures, rather than specific antipoverty programs. As such, we still know relatively little about the potential effect of particular policy initiatives. There is good reason to be skeptical about the political effects of anti-poverty programs in the Malawian context in particular. In four of five elections after the return to competitive politics in 1994, electoral results exhibited a clear ethno-regional character, with voters in the North, Center, and South lining up en masse behind the party associated with their regions and the ethnic communities in each area . Likewise, the incumbent party at the time of our study – the DPP – was particularly weak. The incumbent president, Mutharika, came to power in the 2004 election as the hand-picked successor of the retiring president, Bakili Muluzi. Mutharika was elected as the head of the United Democratic Front party, over which Muluzi continued to preside after the 2004 election. Subsequent power struggles led Mutharika to abandon the UDF and launch the DPP in 2005. As a new party, the DPP lacked even minimal infrastructure and was poorly suited to monitor clientelist exchanges at the local level. The principal contribution of this article is to show that anti-poverty programs,plant benches particularly in the form of a targeted agricultural subsidy, can affect political preferences even when ethno-regional identities are politically salient and parties lack the ability to monitor distributive exchanges.Intervening in agricultural markets has long been a central political strategy used by African leaders to build and maintain support. In the period following independence African leaders implemented a variety of agricultural policies – tariffs, price controls, subsidies, credit schemes, and so forth – to reward favored constituencies . These interventions favored urban residents and rural notables, not ordinary farmers who posed little threat to incumbent leaders. By the 1990s, governments across the continent had removed or scaled back these programs in response to fiscal constraints and donor pressure to reduce the role of the state in the economy.

In recent years, however, large-scale subsidy programs have reemerged in several countries as initiatives to combat stagnant agricultural productivity and chronic food insecurity . One estimate suggests that seven leading African countries presently spend over US$ 2 billion per year on subsidy programs . Malawi’s Agricultural Input Subsidy Programme was launched in response to a sharp decline in rainfall in the 2004/05 growing season3 that that left an estimated 4.9 million Malawians vulnerable to hunger and food insecurity . The AISP targeted poor subsistence farmers starting with the 2005/06 season. The program represented a massive expansion of efforts to alleviate food insecurity that had been initiated earlier in the decade . The program is often heralded as a success: one report, for example, credits the AISP with taking Malawi from having a 43% food deficit in 2005 to achieving a 53% food surplus in 2007—becoming a net food exporter in just two years . These claims, however, have been challenged by those questioning the validity of such statistics and by those who have studied household-level data to measure the program’s enduring effects and its ability to reduce food insecurity and poverty . The AISP’s core objective was to increase resource-poor smallholder farmers’ access to improved agricultural inputs to achieve food self-sufficiency and to increase smallholder farmers’ incomes through increased food and cash crop production . Beneficiaries received coupons to be redeemed at government-designated retailers for either seed or subsidized fertilizer. The AISP distributed three types of coupons: a fertilizer coupon, a seed coupon, and what was referred to as a flexible coupon, which could be exchanged for a variety of seed options. The program grew in subsequent years, reaching an estimated 65% of farm households at its peak in 2008/09 at a cost of approximately USD $285 million in that year, equivalent to 16% of the government’s annual budget or about $22 per citizen in a country were GDP per capita is less than $300 . Allocation decisions4 are made at the national level by officials from the Ministry of Agriculture. District allocations are based on the amount of land under cultivation and the number of farm families per district, information that is provided by village-level officials and cross-checked by agricultural extension agents. At the village level, allocation was jointly determined by the Ministry of Agriculture, District Development Committees, Area Development Committees, and Traditional Authorities. Individual beneficiaries were supposed to be identified through use of the farm household register and open meetings held by Ministry of Agriculture staff. These committees submitted to Ministry of Agriculture staff a list of names of those in need, from which the Ministry of Agriculture selected beneficiaries. District officials then transferred coupons to representatives of village committees , and these committees distributed coupons to beneficiaries. Given the multiple actors involved in the identification of recipients and the delivery of coupons, there were a number of opportunities for the government to engage in targeting.The literature on distributive politics offers contrasting views on whether incumbents should be expected to target rewards to core supporters , swing voters or some mix of the two. Empirical studies from other contexts find evidence consistent with both models . With specific regard to targeting in agricultural input subsidy programs in African countries, relevant studies found evidence of political targeting toward opposition strongholds in Ghana , core support areas in Zambia , and an absence of targeting with respect to patterns of prior electoral support in Malawi .6 More work is needed to identify the conditions under which leaders adopt alternative allocation strategies. Regardless of whether the Malawian government may have sought to reward core supporters or to court potential swing voters through the allocation of subsidy coupons across districts, we expect that the ability to target individuals at the local level was constrained in Malawi by the relatively high degree of ethnic homogeneity at the village level.The prerequisite for individual targeting is that party agents must be able to identify core supporters, opposition supporters, and possible swing voters. In most election years, ethnicity serves as a useful predictor of electoral preferences , making it possible to identify core and swing districts based on ethnic demography. However, because rural villages have little ethnic diversity, ethnicity is much less useful for identifying core and swing individuals within villages.Two additional features of the Malawian context limit the potential for village-level targeting. First, during the period under study partisan orientations were abnormally fluid, making ethnicity even less useful as a marker of party allegiances.

These groups bring together their expertise, tools, and infrastructure in a research program supported by the NSF to create and translate to practice precision agriculture technologies and systems. The Center activities are positioned to deliver outputs in agricultural-specific IoT sensor, robotics, energy, communication, and data science technologies and their integrated systems, that are responsive to the scale, environment, and socioeconomics of farming. The research program outcomes are structured to build needed fundamental knowledge, technologies, and systems with increasing complexity and scale over time and to establish trusted relationships between researchers and stakeholders to realize precision agriculture systems that contribute to a food, energy, and water secure future. The impacts of market liberalization on welfare in rural areas of less developed countries have received increasing attention from both researchers and policy makers as relatively poor countries become integrated into world markets and trade pacts. Overwhelmingly, the view of researchers and policy makers alike has been that, in less developed countries , urban residents win but rural populations lose from the elimination of own-import tariffs on agricultural commodities. The urban gain results from lower consumption costs, while the rural loss is the consequence of increased competition with imported agricultural and livestock goods, depressing both profits and wages in a sector in which LDCs presumably have a comparative advantage. This raises serious welfare concerns, because many of the world’s poor live in rural areas. An interesting corollary to this argument is that agricultural support policies in developed countries adversely affect welfare in rural LDC households by depressing world prices for farm goods . In this paper we use a disaggregated rural economy-wide modeling approach to explore the rural welfare impacts of own-country agricultural tariff reforms called for in the Central American Free Trade Agreement in four Central American countries: El Salvador, Guatemala, Honduras, and Nicaragua .

Our rural economy-wide model for each country consists of a series of interacting micro agricultural household models. Inasmuch as an agricultural household model can be viewed as a computable general equilibrium model for an individual rural household group , the disaggregated rural economy-wide model is really a nested CGEM. To facilitate comparison,dutch buckets for sale we model the same rural household groups in each of the four countries . We use the nested rural CGEMs to simulate the impacts of country-specific agricultural provisions in CAFTA on the income of each rural household group. We also perform a welfare analysis in which the economy-wide model is used to estimate the transfers that would be required to maintain all rural household groups at their pre-CAFTA welfare levels. This transfer differs from a conventional compensating variation by taking into account rural economy-wide impacts of the trade policy shock on household resource allocations, rural wages and subsistence production.Two considerations have tended to reinforce the view that agricultural trade reforms negatively affect rural welfare in LDCs. First, many rural households produce grain, for which high-income countries have a comparative advantage in production. Removing protection on grain imports thus leaves the rural economy vulnerable to competition from foreign grain producers. The combination of generous support programs for grain farmers in high-income countries with LDC tariff reform, from this perspective, inflicts damage on the LDC rural economy. Second, the effects of agricultural reforms in high-income countries are likely to be muted because in many cases LDCs already have preferential access to developed country markets for their agricultural exports. LDCs are net exporters of tropical products, for which competition with developed countries generally is not an issue. Preferential treatment covers a large share of developing country exports to the European Union and the United States, reaching over 90% of all agricultural exports to these regions for some LDCs .

The most notable preferential agreements include those between the E.U. and its members’ former colonies in Africa, the Caribbean and the Pacific, and the Everything but Arms agreement; and between the United States and Africa and Latin America via the Africa Growth and Opportunity Act and the Caribbean Basin Initiative. Because of this, the argument goes, LDCs stand to gain less than they lose from the liberalization of agricultural trade. In fact, some LDCs may lose from trade liberalization as a result of preference erosion . These considerations have been salient in the contentious debates over agricultural policy that characterized the Uruguay Round in the late 1980s and 1990s and currently plague multilateral trade negotiations under the Doha Development Agenda . Some evidence from aggregate economy-wide models suggests that the impact of agricultural trade reforms in LDCs would be positive; however, the reasons lie mostly in the effects that such reforms would have on the non-agricultural sector. Tangermann reports the finding from a GTAP model that full agricultural liberalization by high-income countries would enhance the non-agricultural terms of trade for developing countries, thus leading to income gains. However, Anderson and Valenzuela , using a GTAP model, find negative effects of own-country agricultural trade reforms on agricultural value-added in all the developing countries they considered. The implication of these findings would seem to be that the more narrowly one focuses on the LDC rural economy and on own-country tariff reforms, the greater the likelihood of finding negative welfare impacts of agricultural trade liberalization. Micro agricultural household theory suggests that the impacts of agricultural market liberalization on LDC rural welfare are not clear cut, even if LDC producers do not acquire greater access to high-income markets for their agricultural output. As producers or suppliers of factors to farms, rural household lose when the price of goods they produce decreases. However, rural households also are consumers, and it is not uncommon to find that most producers of protected goods in LDCs are not net sellers of these goods prior to reforms. Like urban households, they stand to benefit as consumers. Whether the negative production or positive consumption effect dominates is an empirical question, and the answer is likely to be different for different rural household groups. Even on the production side, a decrease in price may benefit households that are engaged in other crop activities if factor prices decrease. Even the impacts of agricultural trade reforms on factor prices are ambiguous; they depend on the relative factor intensities of the directly and indirectly affected activities.

Understanding the impacts of agricultural trade reforms on LDC rural economies thus requires an economy-wide modeling approach that embeds within it a micro-economic focus capturing both the heterogeneity of rural households and the diversity of activities in which these households participate. GTAP and other economy-wide models are useful to explore aggregate impacts of trade policy reforms; however, their high level of aggregation precludes a rural micro focus.CAFTA represents an ideal case for studying the potential impacts of agricultural trade reforms on rural welfare. In EGHN,hydroponic net pots the majority of farm households cultivate food grains. All benefit from preferential access to U.S. markets for their agricultural exports, and all are net importers of grain. Prevailing tariffs on grain imports range from 15% to 40% in El Salvador, from 20% to 35% in Guatemala, from 15% to 45% in Honduras, and from 10% to as high as 62% in Nicaragua. Tariffs on livestock products in the four countries range from 15% to 164% . With the exception of white corn, all of these tariffs would be phased out, either immediately or gradually, under CAFTA. 1 The stakes are high from a rural welfare point of view. Rural poverty ranges from 62% of all rural residents in El Salvador to 86% in Honduras. CAFTA would be implemented in a context of generally deteriorating agricultural trade balances. Between 1990 and 2003, both Guatemala and Honduras experienced a decrease in their positive agricultural trade balances while in El Salvador a surplus gave way to a steep deficit . Only in Nicaragua did a positive surplus increase, due primarily to increases in bean and meat exports. In all four countries, maize and rice imports and fruit and vegetable exports increased sharply. Sugar exports increased, but in two out of the four countries , traditional agricultural exports as a whole contracted.Maize production decreased in Guatemala and Honduras, increased slightly in El Salvador, and rose sharply in Nicaragua. Rice production contracted in El Salvador, Guatemala and Honduras while rising in Nicaragua. Beef output stagnated in El Salvador and Guatemala, fell in Honduras, and rose in Nicaragua; beef imports increased as did imports of poultry . Milk production rose in all four countries, and except in Nicaragua, milk imports increased, as well. Changes in land use mirror these trends . Between 1978 and 2001, the land area cultivated in basic grains decreased in Honduras, did not change significantly in El Salvador and Guatemala, and increased in Nicaragua. In contrast, land in other crops, including non-traditional fruits and vegetables, increased in all four countries. Only in Nicaragua did the number of cattle increase. CAFTA would be implemented in a context of demographic transformation, as migration shifts rural population internally, to cities, and internationally, mostly to the United States. Nevertheless, rural population shares remain high by international standards. In 2003, the rural share of the economically active population was 56% in Guatemala, 46% in Honduras, 42% in Nicaragua and 38% in El Salvador.

The shares of population living in rural areas ranged from 43% in El Salvador to 60% in Guatemala. According to the U.S. Census of Population, the number of EGHN-born persons living in the United States nearly doubled from 1990 to 2000, from 771,600 to 1,342,000. The rural migration response potentially has an important influence on how agricultural trade policy reforms affect rural poverty. Two other considerations are critical when modeling rural welfare effects of trade policy shocks: the heterogeneity of rural households and the diversification of these households’ activities and income sources.Tables 3a-3d present the classification of rural household groups that we use to capture the heterogeneity of the rural population in each Central American country, the criteria used to create the household categories, and the number of households in each country and in the data bases used to estimate the models. Landless households represent the largest number of rural households in all but Guatemala, where more than half of all rural households are subsistence producers. In all four countries, rural households without land depend primarily on salaries, both agricultural and non-agricultural, and remittances from internal and international migrants. Subsistence households produce basic grains on small holdings, principally for home consumption. Because they do not participate in markets, the implicit value of their grain output is given by shadow prices that are endogenously determined for each subsistence household group. In our DREMs as in the micro agricultural household models of Strauss and De Janvry, Fafchamps, and Sadoulet , these households are modeled as autarkic; basic grain production is equal to demand. A novelty of the DREM is its ability to represent differences in market articulation as well as in demands, production technologies, and activity mixes among different rural household groups. Production decisions in commercial households, which produce primarily for markets, are guided by market rather than shadow prices. Marketed surplus from these households is simply the difference between output and demand, as in the staple agricultural household model described by Singh, Squire, and Strauss . All household groups participate in markets for other agricultural and non-agricultural commodities and for factors, either as buyers or sellers . They differ with respect to incomes, activity mixes, demand patterns, and technologies. Average per-capita incomes, human capital and landholdings vary widely across countries as well as rural household groups. Landless households have an average annual income of US$347 per capita in Honduras and $877 in El Salvador, where we were unable to disaggregate landless households by schooling. Landless low-education households had an average per-capita income of $502 in Nicaragua and $576 in Guatemala. Average incomes of subsistence producer households range from $359 to $510 , and those of small commercial producers, from $409 to $479 . The highest incomes are found in large commercial households in El Salvador $1,909 and Nicaragua . With the exception of high-skilled landless households, rural household heads in all four countries have low levels of completed schooling, ranging from 1.3 years to 3.5 years .

We used a nested design and selected three clustered sites within a 1.5 km radius circle and repeated this design across the region . The sites exist along a landscape gradient of semi-natural habitat density and agricultural land use density within a 1.5 km radius. Organic farms sites were all certified organic and used less intensive practices than paired nearby conventional farms that used more intensive practices . Many farms grew a single crop variety, most commonly Brussel’s sprouts, strawberry, broccoli, or lettuce. Farms with multiple crop varieties included a mix of vegetables , beans, squash, tomatoes, herbs, and strawberries. Within each farm pair, we chose monitoring sites in the center of fields planted in annual crops with similar proximity to natural habitat. We used one detector for each site and placed detectors within fields and at the edge of woodland patches .We sampled bats at all sites with passive acoustic bat detectors from mid-June to early September 2014. Bat detectors were mounted on t-posts and microphones were elevated on 3 m PVC poles attached to the t-posts. We monitored bat activity levels and species richness at all sites. We did not compare feeding buzzes due to high subjectivity in distinguishing between a bat inspecting research equipment, a novel structure in their environment, and pursuing insect prey . We sampled each site for 6–7 nights during one sampling period from sunset to sunrise to account for high variability of bat activity across nights; the three sites clustered within each landscape were sampled simultaneously to reduce variability and increase sampling efficiency . Recorded calls were processed using Kaleidoscope V2.3.0 to filter noise files and split files to a max duration of 5 s,fodder system which we defined as a bat pass and used in subsequent analyses.

Files were automatically classified using Sonobat V3.1 West and then manually vetted by a team of trained technicians. To account for potential bias among technicians, we worked as a team until our classification decisions were at least 90% in agreement and used a decision key to finalize call identifications. Remaining calls that could not be positively identified to species were classified by characteristic frequency into three phonic groups, with species that comprise each phonic group listed in parenthesis: 50 kHz , 40 kHz , and 30 kHz . To account for differences in how bats perceive their environment, we grouped a subset of the species recorded in the study region based on their echolocation call structure, characteristic frequency, and foraging ecology into two functional guilds: clutter-adapted and open space bats. Of the 12 species recorded in the study region, two were classified as clutter-adapted bats and four were classified as open-space bats . These groups include the most common species in the study region and represent 97% of recorded calls. We used guidelines described in Schnitzler and Kalko and Buchalski et al. and echolocation call parameters described by the Humboldt State Bat Lab to partition species into functional guilds. Species in the open-space guild have call characteristic frequencies < 30 kHz and > 6 ms in duration, which experience less environmental attenuation and are therefore suited for foraging in uncluttered, open areas. Species in the clutter-adapted guild have calls with characteristic frequencies of > 45 kHz and duration < 6 ms. Bats in the clutter-adapted guild are able to forage in highly cluttered forest habitat by using short duration, high frequency calls to distinguish insect echoes from echoes produced by background clutter .We designed bucket style light traps with 12 W black light bulbs and clear plastic vanes and a brewer’s funnel with a mesh collecting bag containing a 2cm2 piece of pesticide strip .

Light traps were deployed simultaneously with acoustic detectors and were programmed to turn on at civil sunset for three hours during the first two nights that the detectors were deployed. Light traps were placed 10 m from bat detectors to prevent potential high-frequency interference from light traps from being recorded by bat detectors, either within fields or along linear habitat edges. Insects were later sorted and identified to order. We measured the length of each insect to estimate biomass using relationships described for terrestrial California insects in Sabo et al. .We surveyed local vegetation within concentric circles centered on acoustic monitoring sites. Within a 25 m radius, we measured the number of weed morphospecies and visually estimated the total number of flowers within the crop field. Within a 50 m radius, we measured the number of crop varieties, average crop height, and the percent of different ground cover types. For the percent of ground cover types, we focused on cover classes exceeding 5% of ground cover, and included bare ground, crops, non-crop herbaceous vegetation, and woody vegetation. Within both a 50 m and 100 m radius, we measured the number of trees > 30 cm circumference and the number of tree species. For all farms, we estimated the percent of field margins in insectaries , the percent cover of insectaries in crop fields, and the percent of weedy field margins. We gathered information about pesticide application on each farm . Most growers applied broad spectrum insecticides and/or fungicides, although a few smaller, organic operations reported that they had not applied pesticides in years. Some of these pesticides were widely used by organic and conventional growers; only conventional growers used organophosphates. For each farm, we categorized frequency of pesticide applications according to these categories: 1=pesticides applied every 1–10 days; 2=pesticides applied every 11–30 days; 3=pesticides applied less than once a month; 4=pesticides applied less than once a year.

We also gathered information about distance to habitat features that are important for bats, and that we could not standardize across the trio of clustered sites. We used Google Earth to calculate the shortest distance to water and distance to the nearest linear habitat element, such as a treeline, hedgerow, or forest edge .We created land cover maps from the National Agricultural Imagery Project 2014 using manual likelihood classification in ArcMap V10.3.1 . We categorized agriculture and semi-natural habitat, and smoothed and resampled maps to a resolution of 7 m2 to reflect ground-truthed land cover classes. We then calculated the land use density of agriculture and semi-natural habitat within a 1.5 km radius, an ecologically relevant scale for bats and insects .We used total bat activity, clutter-adapted bat activity, open-space bat activity, diversity, and species richness as response variables. Bat activity is a measure of relative abundance calculated for each site over a minimum of six nights of sampling, and thus not true count data. Therefore, we opted to log transform the average number of bat passes per night to meet assumptions of normality with a Gaussian error distribution,fodder system for sale instead of using the Poisson error distribution recommended for count data . We used the Chao1 species richness estimator to assess the completeness of species inventories and to compare species richness across site types . We calculated estimated species richness and diversity using all calls identified to species and the 40k phonic group with the package “vegan” in R software, version 3.3.1 To compare response variables between organic farms, conventional farms, and natural sites, we used a randomized block ANOVA, with sites blocked by landscape cluster, and conducted multiple comparison tests using Tukey contrasts as implemented in the “multcomp’’ package in R . We checked that assumptions of normality and homogeneity of variance were met using the Shapiro-Wilk test and the Brown-Forsyth test in the “HH” package in R . To compare community composition between organic farms, conventional farms, and natural sites, we used a one-way Analysis of Similarity test. We used the Bray-Curtis index to characterize species dissimilarity between habitat types using the “vegan” package in R . We used linear mixed models to compare differences in responses to local, on-farm management practices. We selected predictor variables that represent agroecological farming practices and/or practices characteristic of intensive agriculture that growers could potentially manipulate. We included the percent of weedy field margins, number of crop varieties , average height of herbaceous vegetation , distance from a linear element, and percent woody vegetation . We did not include the percent of field margins planted in insectaries or the percent of field planted in insectaries as covariates because many farms did not utilize either of these practices. Selected predictor variables were not strongly correlated , although they were somewhat correlated with a number of other farm characteristics . In addition, we included distance to water as a fixed effect and landscape cluster as a random effect to account for variation in the surrounding landscape, and to avoid spatial autocorrelation problems.

We used standardized model residuals obtained by the top model for total bat activity to create a variogram and verify spatial independence . We performed model selection using the dredge function in the package “MuMIn” after testing for normality . We log-transformed total bat activity, clutter-adapted bat activity, and crop diversity, and used a square root transformation for open-space bat activity to meet assumptions of normality. We tested all possible combinations of explanatory variables and selected the top model if the corrected Akaike’s Information Criterion score was at least two points less than the next best model . When the top models had similar AICc scores , we selected the top models within two points of the lowest AICc score and adopted a model averaging approach to obtain estimated coefficients and the relative importance of predictor variables from the top model set. We visually inspected the relationships between predictors in top models and responses, and noted an outlier site for crop diversity and weed morphospecies, with most sites ranging from 1 to 10 crop varieties, and one site with 39 crop varieties. We decided to remove the outlier after exploring its leverage on LMMs and Pearson correlation coefficients. The effect of the outlier was minimal in most cases, but it changed the significance of the effect of crop diversity on open-space bat activity, and the strength and significance of the relationship between crop diversity and weed morphospecies within 25 m. We asked if the same local management practices and farm characteristics that predicted bat activity would also predict the biomass of insect orders that are known to be consumed by bats and were commonly collected in light trap samples . We tested LMMs that contained the same set of predictors as bat models to assess if variables that predicted bat activity operated on bats via changes in abundance of insect prey. All models contained a random effect of landscape cluster. To meet assumptions of normality, we used a square root transformation for Diptera biomass, and a log transformation for Lepidoptera and Coleoptera biomass. We assessed Pearson correlations between bat activity and insect biomass for these common prey orders. We used LMMs to test for an interaction between local practices that significantly predicted bat responses and semi-natural habitat density using LMMs. We built a set of candidate models using the top model from model averaging and added an interaction with semi-natural habitat density , and compared models using AICc scores.Across 648 detector nights, we recorded 36,294 bat calls. Of these, we were able to confirm identification to species for 14,969 calls, and remaining calls were identified to phonic group. A total of 12 different species were recorded , and of those, Tadarida brasiliensis and Myotis yumanensis were the most common across all sites. Three recorded species are listed as species of special concern in California: Lasiurus blossevellii , Corynorhinus townsendii , and Antrozous pallidus . The species inventory appears to be complete for natural habitat, but not for farms, according to rarefaction analysis . We recorded fewer, high quality calls on farms compared to natural habitat. Bat calls recorded on farms had less noise interference than recordings from natural habitat, allowing us identify a greater number of species from fewer calls, resulting in steeper species accumulation curves that did not reach an asymptote.Categorical comparisons of lower- and higher-intensity agricultural systems have documented mixed effects on bat activity, diversity and species richness, and provide limited insight on the effects of specific, agricultural management practices.

Mineral phosphate solubilization by bacteria is often correlated with the release of organic anions and corresponding free protons, which lowers the pH in the surrounding soil water solution, and thereby induces chelation of the metal complexes Rodr g e and raga, 1999. If MPS bacterial populations are affected by biochar, this could have a significant impact on P availability from biosolid-derived biochars and plant P uptake. The abilities of the native soil bacteria to solubilize mineral phosphate in treatments prepared with biosoild-derrived biochars generated at 4 HTT’s were quantified using spectrophotometric assays and indicator media. Also, biochar could impact phytoremediation processes utilized in efforts to reduce concentrations of heavy metals and organochlorines pesticides in contaminated soils. Biochar has been shown to enhance root development in arsenic contaminated soils and influence sorption of heavy metals in soils . Some ferns have the ability to remove heavy metals from soils by translocating them into their biomass. Root development in contaminated soils can also stimulate the growth of soil microorganisms by release of root exudates that serve as substrates. Many soil microorganisms degrade organic pollutants, such as organochlorine pesticides. Also, survival of the accumulator plants is essential for successful soil remediation. In this study root-colonizing strains were isolated from soils contaminated with dichlorodiphenyltrichloroethane and arsenic and assayed for ACC deaminase activity and auxin production, microbial traits that play a major role in assisting survival of plants stressed by heavy metals . These PGPR activities were quantified across isolated cultures and mixed consortia taken from the rhizospheres of 2 fern species in contaminated soils amended with biochars prepared at 2 HTT’s. The ferns incl ded a New Zealand native species, Blechnum novaezelandiae,vertical hydroponic nft system and a species originally from China, Pteris cretica, which has been demonstrated to be an arsenic-hyperaccumulating species .

The main objective of these studies were to determine if PGPR communities were affected by different biochar materials and if this effect could be related to plant development in the given treatment soils. Changes in the expression of enzymes brought about by biochar will shed light on the physiochemical processes in the soil environment that shape the structure and function of microbial communities in the rhizosphere. Current strategies for sustainable soil management entail the use of methods that selectively enrich indigenous plant growth promoting bacteria , or carrier materials, such as biochar, that deliver beneficial soil inoculants to plant root zones. Many PGPR have the capacity to produce exogenous plant growth hormones, an activity that has been correlated with increasedtotal root length, branched root architecture, and root hair formation . Enterobacter cloacae UW5 serves as a well-studied strain for production of plant growth hormone, indole-3-acetic acid by the indole pyruvate pathway. Indole-3-pyruvate-decarboxylase is an enzyme essential for IAA generation via this pathway and the expression of the ipdC gene is induced by tryptophan . Another significant PGPR trait is the ability of some microorganisms to produce 1-aminocyclopropane-1-carboxylic acid deaminase. Under conditions of abiotic stress plants generate ethylene, which can accumulate in the rhizosphere and, in turn, elicit a stunting response in the plant, drastically reducing crop yields . Diverse soil bacteria have the enzyme ACC deaminase, which allows them to utilize the precursor to ethylene, ACC, as a nitrogen source, degrading the ACC into ammonia and α-ketobutyrate . PGPR with ACC deaminase activity have been shown to improve plant growth during flooding and drought conditions and in soils affected by salinity or heavy metals . ACC deaminase has been best studied in Pseudomonas putida UW4, and the expression of the gene encoding this enzyme is induced in the presence of ACC . The activities of each of these enzymes were determined to be essential to plant-growth-promotion by the given strains . Hence, any interference of biochar with the expression of these genes could result in loss of benefit associated with inoculum harboring these traits.

In previous work soil-microbial enzymatic activity was shown to be increased or decreased in the presence of biochar . Thus, it is important to better understand the influence of biochar on beneficial PGPR enzyme activity. Several methods were employed to analyze the expression of genes involved in ACC deaminase activity and IAA biosynthesis. Spectrophotometric assays provided initial insight into the PGPR activity of these strains as influenced by biochar in culturing media. The assays for PGPR traits among the native soil microbial communities indicated whether biochar amendment is influencing the microbial communities, possibly shaping the communities to select for more or less plant beneficial strains. For the most part, microorganisms isolated and mixed consortia cultured from the amended soils showed similar MPS bacteria proportions and activities to that of the unamended soil. However, the soils amended with BS250 had significantly lower percentages of MPS bacteria or MPS activity in mixed consortia. Of the amendment chemical properties analysed by Wang et al.the BS250 had notably higher volatile matter/ ratio and lower pH than did the other amendments. These properties may have had an influence on the soil MPS bacteria. In the case of the PGPR activities assayed in the phytoremediation study, bacteria with ACC deaminase were present in all rhizospheres and did not correlate significantly to the soil treatments. However, the W550 treatment had a positive influence on bacteria that produce IAA in the B. novae-zelandiae rhizosphere. This species of fern was found growing in the area from which the contaminated soil was extracted. The P. cretica fern species is not native to this area. Soil microbial communities may have been better adapted to the B. novae-zelandiae rhizosphere and this may exhibit a greater indication of response to biochar amendment. In other work using the same soil and biochars, microbial dehydrogense activity was significantly increased in the presence of W350 and even more so by W550 . This could indicate the benefit of using an indigenous plant species for phytoremediation of contaminated soils involving biochar.

The results of this research indicated that the biochar amendments did not affect population sizes of bacteria harboring the plant-growth promoting traits tested. During the course of this research, several PGPR strains were isolated and characterized based on PGPR activity. The use of these strains offers New Zealand organic farmers biological fertilizers composed of native species. Enzymes and their substrates could adsorb to char surfaces or be regulated by signaling molecules that interact with biochar. Recent studies generated concern over this phenomenon and showed that biochar had an effect on plant gene regulation and also interfered with microbial signaling . Figure 4.1 demonstrates that levels of indole production and ACC deaminase activity assayed from cells grown in the presence of 2% Pine600 biochar were not significantly different than those for cells grown in biochar-free medium. However,nft hydroponic system the spectrophotometric assay measures only the accumulation of these compounds in culturing medium. Hence, more sophisticated assays were developed to better monitor the expression of genes essential for these beneficial traits in aims to better resolve responses to biochar. In the in vitro gene expression studies conducted here, we did not see a biochar-induced change in the promoter activity or expression of genes involved in IAA production or ACC deaminase. The RFP reporters provided a qualitative assessment that promoter activities were positively regulated in the presence of biochar. Furthermore, the RT-qPCR provided quantitative verification that gene expression was not significantly impacted by the presence of 2% or 5% biochar. It appears that precursor compounds, such as tryptophan, were not irreversibly adsorbed to the biochars, which would have resulted in lower bacterial gene expression in the presence of biochar. This addresses the concern that biochar may interfere with PGPR activities and lower the efficacy of beneficial soil inoculants.Hunger in Africa has been central to discourses in aid organizations, NGOs, multilateral and unilateral government agencies, and billion-dollar multinational agribusiness entities for decades. Claims of concern for malnutrition on the continent are infused in initiatives for a range of issues, from economic policy to public health interventions. This phenomenon can perhaps be attributed to the visceral and immediate accessibility of the issue. The idea of hunger conjures a primal sense of urgency in the mind and hearts of donors and, as such, does not require the same degree of unpacking and validation as other equally-complex sociopolitical issues. That is, less effort is required to convey the gravity of starvation, the need to feed oneself palpable. However, that the importance of an issue is easily understood does not necessarily equate to correspondingly easy solutions. Despite this observation, many proposed hunger reduction strategies are packaged in consumable pithy slogans and oversimplified action plans, though the task requires thoughtful consideration for a number of interrelated factors, the most important of which is attaining of thorough understanding of root causes for the persistence of hunger. The continent became a more formalized “zone for agriculturalist expansion” in the last decade , as the recipient of grand gestures such as the Bill and Melinda Gates Foundation pledging to contribute 3.2 billion USD to African hunger efforts from 2006- 2011, alone .

The Bill and Melinda Gates Foundation’s Alliance for a Green Revolution in Africa as well as agrochemical company, Monsanto, feature prominently in contemporaneous campaigns that fly a banner of hunger alleviation. The surge of interest in food policy coalesced in the formation of the US-led G8 New Alliance for Food Security and Nutrition. Launched in 2012, the Alliance includes 21 African nations, 27 multinational organizations, and is fueled by corporate and AGRA donor interests. Rallying behind the premise that populations are merely undernourished because there is not enough food, the entities address caloric and nutritional deficiencies by promoting the adoption of proprietary genetically-modified and proprietary “improved” or high-yielding seed varieties, engineered to increase production of certain food staples. Thorough consideration for local nutrition ecologies, particularly ways in which trade relations can be threatened by a drastic change in agricultural output, is lacking. Thus, trials of improved and genetically-modified crops have met unsuccessful results, demonstrating that adoption of high-performing seed, alone, is insufficient. Continued implementation of failed approaches heightens risk for future populations, for it carries the potential of exacerbating the very poverty from which hunger results, while siphoning off funds that could be better used for infrastructural development and other more practical projects. Regarding GM and otherwise enhanced seed, there exists a disproportionate volume of critical research in two areas: prospective threats to environmental biodiversity and heirloom seed populations, and health risks associated with the consumption of modified foods and farm worker exposure to glyphosate. In response, multiple pro-GMO publications focus on countering those claims. Much of the research that professes the environmental and public safety of modified food crops are published by very institutions that own and produce said seed, a clear conflict of interest. Owners of the rights to proprietary seeds do not readily share their products for third party study so there is little opportunity for transparency, cross-referencing, or long term trials in controlled environments. Thus, many public health and bio-safety reports are ambiguous and inconclusive. The following paper will not directly address either of these two concerns. It is observed that proponents of Monsanto, for example, while comfortable debating human and environmental safety, fall relatively silent on the issue of financial concerns regarding the sale and use of proprietary plant species. Royalty payments and loan programs often go unmentioned, even as they threaten to burden peasant farmers or further strain government budgets. The issue of payments also implies that only certain groups will have opportunities to participate, and surplus distribution costs are not factored into foreign initiatives. Perhaps failure to address these matters is simply indicative of a failure to consider them. Or, conversely, perhaps it indicates the difficulty of providing a sound argument for proprietary seeds initiatives if evaluated strictly through the scope of financial responsibility. This paper will assess some of the glaring economic concerns related to the adoption of genetically-modified and improved seed on the continent. It will point to dilemmas which must be investigated in order for one to confidently propose the adoption of new seed varieties as a viable solution to hunger in East and Southern Africa. It will assess these matters independent of concerns related to super weeds and allergens, more narrowly focusing on implied costs, vulnerability, debt accumulation, and soft commodity trade as it relates to GM and hybrid seed adoption in Southern African Development Community member states. It is understood that undernourishment causes social problems that are antithetical to progress, but it is also true that hunger and malnutrition are the result of systemic inefficiencies.

Taken together, our results indicate sex-dependent protective effects associated with elevated tissue levels of ω-3 fatty acids in reducing the number of infiltrating immune cells into the lung, lower pro-inflammatory cytokine levels and reduced overall histopathology of the lung. The results identified herein model a long-term dietary intake of high ω-3 PUFA and reduced intake of ω-6 PUFA that achieves an ideal ω-6:ω-3 PUFA ratio throughout the body as reviewed before . This was achieved through the use of the Fat-1 transgenic mouse model; these mice express the Fat-1 gene from C. elegans encoding an ω-3 FA desaturase, converting ω-6 PUFA to ω-3 PUFA, leading to tissue ω-6:ω-3 PUFA ratios of ∼1:1 . This model is advantageous because it overcomes several issues that limit diet- and supplementation based experimental strategies; current clinical and preclinical studies have no standardization in terms of dose, duration, or source and quality of ω-3 PUFA, and each of these factors has implications on outcomes . These inconsistencies are considered leading factors for discrepancies in ω-3 PUFA study outcomes . The Fat-1 mouse thus provides a preclinical model for assessing how elevated tissue levels of ω-3 PUFA and reduced ω-6 PUFA can influence health outcomes by minimizing variation based on supplementation, intake and absorption and distribution of ω-3 rich fatty acids. Using this model, we have found genotype and sex-specific differences in infiltrating cells , proinflammatory cytokines and lung histopathology . The decreases in infiltrating PMNs and cytokines were consistent with each other within the Fat-1 male sex. Among the swine farm workers, sex-specific differences in lung function and TLR gene polymorphisms, which is a toll like receptor activated by swine farm dust, have been reported before . Gao et al. found that lung function is worse in males with the TLR9 gene polymorphism as compared to those males without the polymorphism,stackable planters and females with the TLR2 gene polymorphism exhibit better functioning lungs as compared to those females without the polymorphism in swine farm full-time workers .

Another study by Senthilselvan et al. found increased plasma levels of TNF-α in males without any TLR4 gene polymorphisms , and in females with the TLR4 gene polymorphism following 5 hours of swine farm exposure in naïve healthy subjects . We are not the first ones to report sex-specific differences in Fat-1 mice; a recent study investigating the role of elevated tissue levels of ω-3 fatty acids in obesity-associated post-traumatic osteoarthritis also reported sex-specific differences in Fat-1 transgenic mice . It appears that such sex-dependent differences are disease model-specific where one sex in the Fat-1 transgenic background exhibits a greater response than the other sex. Another study reported on sex-and age-specific differences of Resolvin D1 levels in the retina. This study found sex-dependent differences in retinal levels of RvD1 in aged mice as compared to young mice , with aged male mice showing a larger decrease in RvD1 levels . Sexdependent changes in the expression of genes involved in fatty acid synthesis, steroids and drug metabolizing enzymes have been identified before . Some of those genes encode for enzymes involved in the metabolism of ω-3 and ω-6 PUFA, thus identifying sex-dependent differences can inform pharmacokinetics, bio-availability and treatment options related to ω-3 and ω-6 PUFA-derived lipid mediators. The sEH inhibitor TPPU was used in this study as an indicator that to the inflammation resolving epoxide metabolites of ω-3 lipids might be a partial explanation for their beneficial effect. It is attractive to consider sEH inhibitors or mimics of ω-3 fatty acid epoxides as a prophylactic or therapeutic agent . Such mimics and sEH inhibitors are in clinical development by several companies but none are available on the market . However, there are a number of sEH inhibitors from natural sources that are commercially available such as Maca . Male sex in the Fat-1 transgenic mouse had lesser number of aggregates as compared to their corresponding WT controls, which was further reduced in the presence of TPPU .

While we observed a similar trend for the female mice these differences did not reach significance. Lymphoid aggregates, which can be composed of T cells, B cells and dendritic cells play different roles in different disease models such as COPD and tuberculosis. For example, in a chronic cigarette smoke-induced murine COPD model, lymphoid aggregates are associated with adverse outcomes and thus pathological, whereas in a tuberculosis model induced by the Mycobacterium tuberculosis, it is found to be a host defense mechanism . To our knowledge sex-differences in lymphoid aggregate formation in the lung has not been fully explored. A recent study found that females are more susceptible to lymphoid aggregate formation as compared to males, and this was further confirmed by ovariectomy in a smoke-induced COPD model . This is consistent with the previous reports indicating that women are more susceptible to develop COPD than men . Overall, our results are consistent with the previously published literature on the effects of agricultural dust in males; and the improved histopathological effects seen in the male sex are novel. We observed an elevated alveolar cellularity , in wild-type female mice as compared to male mice. A study investigated the differences in alveolar macrophage proteome between males and females, and found several proteins associated with inflammation and interact with estrogen receptor to be expressed higher in females than males . Another study looking at sex-related differences in lung inflammation showed a higher baseline for lung histology score and number of infiltrating cells into the lungs in females compared to males in sham-operated controls . Both studies are consistent with the histological finding we observed in female wild-type mouse lungs. Because males responded TPPU treatment better, this might be related to differences in fatty acid metabolism between males and females given fatty acid epoxides regulate alveolar cell influx, as shown in a study demonstrating that pharmacological modulation of fatty acid epoxides affect inflammatory cell influx to the lungs . In addition, SPMs also modulate macrophage chemotaxis, trans-endothelial migration and cytokine release from macrophages as reviewed by Haworth and Levy . More studies are needed to dissect differences in fatty acid metabolism between males and females. It is well accepted that sex-specific differences that result in different biological responses between males and females stem from sex hormones. These differences affect storage and distribution of lipids thereby affect free fatty acid availability between sexes.

Stable isotope studies report that ARA and DHA contribute more to blood lipids in women than in men and that there are differences in the conversion rate of fatty acids, for example conversion of ALA to omega-3 fatty acids is higher in women than in men . Also, preclinical studies show that reproductive hormones affect the enzymes involved in the biosynthesis of fatty acids. Another study found that sex-related differences in COPD might be related in part to the increased production of leukotoxin-diol by goblet cell P450 and sEH activities . Overall,stacking pots our results suggest a mechanism that 1) availability of free fatty acids from the elevated tissue levels of ω-3 acids in Fat-1 mice are sex-dependent and 2) females have different conversion rates of fatty acids as compared to males and this might lead to changes in gene expression of chemokines and cytokines, thereby affecting alveolar macrophage recruitment into the lung and thus creating sex-dependent host defense mechanism within the Fat-1 genotype. In addition to dietary strategies aimed at promoting the healthful benefits of ω-3 PUFA, therapeutic strategies leveraging the endogenous repair SPM pathways to promote inflammation resolution and repair hold great clinical promise. For example, many investigations have identified positive outcomes in ameliorating lung inflammation/disease via therapeutic administration of SPM , including our own previous studies identifying beneficial effects of the DHA-derived SPM maresin-1 in reducing the lung inflammatory effects of acute and repetitive organic dust exposure . While SPM can potently inhibit inflammation while promoting tissue repair, these bioactive metabolites are quickly deactivated by subsequent metabolism . Thus, another therapeutic strategy to leverage these endogenous inflammation resolution pathways is to combine ω-3 PUFA supplementation with pharmacologic inhibition of enzymes responsible for the deactivation of SPM. One such strategy has been the use of inhibitors of the sEH enzyme to prevent the deactivation of the cytochrome P450 family of SPM, thereby potentiating their protective effects . Previous studies have found enhanced protective effects of ω-3 PUFA when used in combination with inhibitors of sEH such as TPPU . This enzyme deactivates the epoxide SPM into less active diol forms – DiHDPA. A recent study in a model of metabolic disease identified that a sEH inhibitor enhanced the protective effects identified in Fat-1 mice vs. WT mice , while previous studies also identify beneficial effects of sEH inhibition in murine models of acute lung injury , pulmonary fibrosis , asthma , and COPD . Corroborating these previous reports, when we utilized TPPU in the experiments described herein, we found that addition of TPPU lowered all outcomes examined in the DE-exposed animals, suggesting that TPPU not only enhanced the effects of ω-3 fatty acids as in Fat-1 + DE + TPPU animals, but also showed efficacy independent of the Fat-1 genotype. In addition, we observed a better response in the Fat-1 male sex receiving the TPPU treatment and three-weeks DE exposure. Consistent with our results sex-specific differences have been reported in sEH null mice and sEH activity in other mouse disease models . While our results support a beneficial effect of maintaining a low omega6:omega3 ratio in response to agricultural dust, omega- 6 PUFAs and their metabolites also modulate inflammation and participate in inflammation resolution and tissue homeostasis.

The SPMs derived from arachidonic acid, such as LXA4 and metabolites generated by the P450 pathway have been repeatedly shown to have anti-inflammatory effects . Most surprisingly, the ARA metabolites generated by the COX-2 pathway, such as PGE2 have protective effects in the lung despite their infamous proinflammatory notion, as shown in asthma and allergicairway inflammation . Airway epithelial cells are the major source of PGE2 production in the lung, and PGE2 protects against airway hyperresponsiveness to allergens by inhibiting leukotriene and thromboxane synthesis that cause bronchoconstriction and by reducing eosinophil recruitment, both of which are antiinflammatory effects of PGE2. Similarly, in asthma, it has been shown that the homeostatic balance between the COX and LOX pathways metabolizing ARA are altered due to damaged epithelium in asthmatic airways. Given this, it has been proposed that the dysregulation of these pathways leads to an imbalance between PGE2 and PGD2/LT which is in part responsible for increased bronchoconstriction. Other roles attributed to PGE2 in the lung include inflammatory cell recruitment, eosinophil degranulation, bronchodilation, T-cell recruitment and differentiation and adhesion molecule expression as reviewed before . With regards to sex-related differences in response to environmental stimuli, a study examined changes in gene expression in the lung associated with inflammation and immunity after ozone exposure . This study found increased lung histological scores and increased infiltrating PMN in the female sex as compared to males after ozone exposure. Among control mice exposed to filtered air alone, females displayed about 5% difference in gene expression of genes related to chemokines and cytokines as compared to males. These genes included Cxcl2 and Ccl19 , Myd88 , and C4b , all of which were associated with immune cell adhesion and recruitment. Considering the sex- and genotype-dependent differences in our model, we examined changes in gene expression as well. Since the most significant changes we observed in our model was in the male sex , we focused our gene expression studies to male sex. NanoString gene expression analysis identified differentially regulated pathways consistent with our previous results indicating that immune cell activation, cell proliferation, wound healing and transport pathways were altered following 3-weeks DE exposure. In an In-depth analysis both using STRING database proteinprotein interaction and NanoString advanced analyses, we also identified changes in NFκBIA, response to macrophage colony stimulating factor, immune clearance, and neutrophil aggregation between the two genotypes . In addition, TPPU treatment affected distinct cellular processes such as T-cell differentiation in WT mice and regulation of neutrophil activation in the Fat-1 genotype. This observed effect of TPPU is consistent with a previous report showing modulation of the Th1/Th17 response while elevating regulatory T-cells by TPPU in an arthritis model .

To complement experimental work in nanoparticle therapies, mechanistic mathematical modeling and computer simulation can be used to better understand experimental results and provide quantitative guidance for more efficient design of nanotherapeutics. Optimizing carrier and drug penetration into the tumor tissue is critical to maximize the therapeutic effect. Toward this goal, I developed a mathematical model of nanoparticle diffusion and uptake in a spheroid approximation of a solid tumor segment without capillaries. Our model differs from other models that can be found in the literature by taking into account the effect of shape and size on the diffusion constant of nanoparticles. Our model also builds on the previous models by incorporating the rate of endocytosis and how it is affected by size, shape, and surface modification of nanoparticles. As the model nanoparticle, I used the nucleoprotein components of the tobacco mosaic virus . Virus-based plant nanoparticles, such as TMV, provide a unique platform for nanomedical engineering because their dimensions are known and tunable on the molecular level, which cannot readily be accomplished with synthetic nanoparticles. Native TMV particles form a cylindrical structure measuring 300 × 18 nm with a 4 nmwide hollow interior channel. TMV is composed of single-stranded RNA wrapped inside a hollow nanotube formed by 2130 identical coat proteins. TMV offers a programmable scaffold for both genetic engineering and chemical bio-conjugation to impart new functionalities, e.g. therapeutic payloads. TMV virion formation can be initiated by self-assembly of coat proteins from an RNA hairpin forming sequence. This origin of assembly site is the only sequence required to promote a bidirectional coat protein self-assembly along the template RNA. This principle has been exploited to produce TMV nanotubes with diverse shapes such as kinked nanoboomerangs or branched tetrapods.This RNA-templated self-assembly principle has also been used to produce TMV-like nanotubes with distinct longitudinal domains as well as materials of defined aspect ratio.In previous studies,nft channel we have shown that bio-distribution and tumor homing is a function of the carrier’s aspect ratio.

With higher aspect ratio, particles avoid clearance by the mononuclear phagocyte system, resulting in increased tumor homing.Nevertheless, a balance must be established between immune evasion, tumor homing, and tissue penetration. While higher aspect-ratio materials have enhanced tumor homing, the higher molecular weight particles have slower diffusion rates. The TMV platform technology provides a high precision platform with which to specify aspect ratio and surface chemistries that affect tissue penetration in tumorspheroids. I chose to study TMV diffusion in a spheroidal cell-culture system with different sizes and cell densities. This 3D cellular system mimics a small segment of a solid tumor between capillaries and bridges the gap between 2D tissue culture and in vivo mouse models for screening therapeutics. In tumor tissue, the combination of leaky vasculature and deficient lymphatic clearance leads to diffusion as the driving mode of nanoparticle transport and penetration into the tumor tissue.For this study, I focused on ‘stealth’ TMV formulations with reduced cell uptake rates produced by coating the particle surface with polyethylene glycol . Targeted TMV formulations with molecular specificity and increased cellular uptake rates were simulated by displaying the integrin specific peptide ligand RGD on their surface. PEG and RGD are surface modifiers frequently used in nanoparticle engineering to promote immune invasion and targeted endocytosis, respectively. These coatings serve as good model systems whose results can be translated to other nanoparticle formulations.I developed a mathematical model of TMV diffusion and uptake in a spheroid tumor model to evaluate the effect of particle aspect ratio . The input to this model was a bolus injection of a known TMV mass in the medium surrounding the tumor . The rate of diffusion in the interstitial space is much slower than in the surrounding medium so that the distribution of TMV in the surrounding medium is uniform . In addition, the volume of the surrounding medium is much greater than the volume of the spheroid so that the changes in TMV concentration in the surrounding medium are negligible Supporting Equations 6.1.

The tumor cell density within the spheroid segment is uniform and considered as a continuum. The rates of cell proliferation and death are assumed negligible relative to the other TMV rate processes so that the viable cell volume remains constant. From the interstitial space, I assume that TMV is taken up irreversibly by tumor cells at a constant rate that is dependent on the aspect ratio and surface chemistry of TMV nanorods . Furthermore, the TMV does not interact with extracellular matrix components and cannot bind to them. The model parameter values known from direct measurement are the mass of TMV injected, the volume of the surrounding medium , and the radius of the spheroid . The parameters that must be estimated indirectly are the cellular uptake rate coefficient and the diffusion coefficient . For each experiment, these coefficients are constants. This implies that free receptors are always available at the cell surface so that k is constant in any experiment. For different experiments, however, their values change depending on their surface area, shape and cell density within the spheroid . The uptake rate coefficient is directly proportional to the total cell surface area as indicated by the cell density, where k = k0. The diffusion coefficient is a complex function of the cell shape and cell density. Our tumor micro-environment system consists of a spheroidal cancer cell-culture whose diameter can vary between a few hundred micrometers to 1 mm, which corresponds to the heterogeneous spacing of capillary distribution within the tumor . Modeling the diffusion of nanoparticles in the tumor tissue and quantifying the time scales as a function of capillary and cell density could inform dosing and administration schedules. The physiological barriers and diffusion rates of nanoparticles also depend on nanoparticle shape, size and surface chemistry. The simulated effects of spheroid radius, cell density, and aspect ratio on the TMV concentration distributions without cellular uptake are shown in Figures 6.2, 6.3 and 6.4, respectively. The parameters used in each of these figures are summarized in Table 6.1. These results and their significance are discussed in the following sections.The spheroid segment radius represents the distance between capillaries.

The intercapillary distance is highly regulated by a fine balance between angiogenic factors that promote or inhibit vessel growth, as well as the oxygen and nutrient consumption by the surrounding cells.In healthy tissue, particle diffusion from the vessels to the cytoplasmic membrane of surrounding cells does not exceed 100 μm. In the tumor micro-environment, however,hydroponic nft the oxygen consumption is lowered and the tolerance of cancer cells to hypoxic conditions is increased. Tumors with a high rate of oxygen consumption have a higher microvascular density and, therefore, a smaller intercapillary distance. On the other hand, tumors with a low rate of oxygen consumption have a lower microvascular density and, therefore, a higher intercapillary distance.This phenomenon is currently being investigated for nanoparticle-based antiangiogenic tumor therapy.By reducing the oxygen supply to the tumor site, anti-angiogenic tumor therapies aim to prevent the growth and aggressiveness of the tumor. To quantify the effect of different intercapillary distances within the tumor micro-environment, I simulated the diffusion of TMV in a spheroid system without cellular uptake for a range of radii in the absence of cellular uptake . Within the tumor cell spheroid, the simulated concentration distributions at various times of TMV with different spheroid radii are shown in two and three dimensions. This poor tumor penetration correlates with increasing risks of survival of cancer cells and promotes drug resistance.When the tumor cell density increases, the cytotoxicity of chemotherapeutic drugs such as vincristine, bleomycin, and doxorubicin is impaired.Increasing the cancer cell density within the spheroid decreases the void volume through which nanoparticles can diffuse as represented by a smaller diffusion coefficient. With high cell density, the limitation of TMV nanoparticle penetration is a major barrier to chemotherapeutic drug delivery in the deep tissue, which also correlates with increasing risks of survival of cancer cells and promotes drug resistance.While smaller aspect-ratio rod-shaped nanoparticles have higher diffusion and accumulates more easily in the deep tumor tissue, the higher aspect-ratio nanoparticles have enhanced margination toward blood-vessel walls, increased transport across tissue membranes, and reduced clearance by phagocytosis.In other words, a “one-size-fits-all” nanoparticle does not exist and a compromise must be made to optimize the diffusion and accumulation of nanoparticles within the tumor without impairing their ability to extravasate , cross tissue membranes, and evade the immune system. With complementary data, this model can provide a basis for predicting the aspect ratio that promotes optimal accumulation of nanoparticles injected intravenously.Perhaps, a better approach would be to inject intravenously a cocktail of TMV nanoparticles with various aspect ratios. In this scenario, the lowest aspect-ratio TMV are less likely to reach the tumor site, but the fraction that do penetrate the tumor can diffuse more readily than the higher aspect ratio TMV in the deep tumor tissue. In the meantime, the higher aspect ratio nanoparticles can reach the tumor site more readily, but only accumulate in the peripheral tissue of the tumor. The net result would be to improve overall drug distribution and maximize efficacy. The simulations presented above do not include TMV uptake by cells so that the effects on diffusion are not obfuscated. While targeted nanoparticle formulations can increase delivery, endocytotic clearance of targeted nanoparticle can reduce drug distribution and tumor cell access.

To assess the effect of cell uptake on TMV distribution throughout the spheroid, I evaluated the cell uptake rates of TMV in cancer cells experimentally: fluorescently-labeled, RGDtargeted TMV formulations were obtained as described by Pitek et al.310 A fluorescence assay was developed to quantify TMV particle uptake cancer cells over time . I chose triple negative breast cancer cells as our model cell line for their relatively highexpression of v3 integrins.I determined that the targeted TMV formulation exhibits a cell uptake rate of 130 particles/h/cell. With this experimental value, we can extrapolate cell uptake rates of PEGylated and RGD-targeted TL, TM, and TS particles .These data and resulting cell uptake rates are summarized in Table 6.2. While RGD-targeted formulations are readily taken up by the cells, PEGylated formulations show negligible cell interactions. The PEGylated formulations with TS and TM aspect ratios have comparable effects on uptake. The targeted formulations with TL and TM have comparable effects on uptake, but the uptake with TS increases significantly . The experimental data shows that TMV-PEG formulations exhibit low uptake with time. The TMV-RGD formulations, however, display a biphasic behavior: rapid cell uptake within the first 3 h followed by a plateau region with little to no cellular uptake, most likely indicating saturation. This behavior is typical of particle internalization mediated by cell surface receptors.The rate of cellular uptake of TMV reported in this study is much smaller than the rates reported for synthetic nanoparticles. Doiron et al.320 reported that spherical polystyrene nanoparticles with diameters ranging from 20 nm to 500 nm had uptake rates ranging from 6.6×107 particles/h/cell to 12,000 particles/h/cell respectively within the first 3 h of incubation. In addition Huang et al.reported rod-shaped gold nanocrystals displaying RGD peptideson their surface had a rate of internalization in A549 lung carcinoma cells equivalent to 4500 particles/cell/h within the first 2 h of incubation at 37°C. However, the same nanoparticles coated with single-chain variable fragment peptide to target the epidermal growth factor receptor were internalized at a slower rate of 1,250 particles/cell/h. This demonstrates that the rate of cellular uptake is dependent on nanoparticle shape, surface chemistry, as well as the nature of the molecular receptor targeted. Using the evaluated cellular uptake of TMV formulations , I simulated TMV diffusion in a spheroid cell system with different rate coefficients of cell uptake and aspect ratios . This prevents deep tissue penetration because cell uptake occurs at a rate much higher than diffusion. Coating TMV with RGD peptides to target integrin receptors further decreases the TMV concentration within the spheroid. Active targeting of receptors overexpressed on cancer cells is commonly used to promote tissue specificity and accumulation. However, it is counterproductive for tissue penetration.For TM , the TMV concentration reached the center of the tumor within 3 h. At steady state, its concentration at the center was 4% of the concentration in the surrounding medium. For TS , the TMV concentration reached the center of the tumor within 3 h, but its steady-state concentration at the center was 12% of the concentration in the surrounding medium.

Each ferritin complex can sequester up to 4500 Fe2+ ions and convert them to Fe3+ to prevent oxidative stress in the cytosol, nucleus, and mitochondria. Ferritin has been investigated as an imaging reagent and vaccine platform as well as a nanocarrier.It has already been used to deliver cisplatin,doxorubicin,and curcumin,and the contrast agents gadolinium and Mn. There are few examples of proteinaceous nanocarriers used in agriculture, but nanocarriers based on maize storage proteins are being tested for the delivery of pesticides that protect soybean crops from defoliator parasites.The number of proteinaceous nanocarriers reaching the market will continue to grow as we learn more from nature and expand our bioengineering tools and processing capabilities, including the use of genome editing and directed evolution.Furthermore, rather than harnessing protein complexes from nature, advances in de novo protein design will allow us to select customized proteins with shapes that may be difficult to obtain via the directed evolution of natural proteins.Modular building concepts have been established to achieve the defined folding and programmed assembly of proteins into complex architectures.Accordingly, some synthetically designed protein-based nanoparticles have entered translational development. For example, the start-up company Tychon Bioscience is developing prosthetic antigen receptors that modulate protein dimerization to produce self-assembling nanoscale ring structures for applications in cancer immunotherapy. The entirety of my dissertation relied on the use of virus-based nanocarriers and their application in medicine and agriculture; they present many advantages over the other nanocarrier platforms,blueberry grow bag as described below and in all chapters of my dissertation. Viruses have evolved to deliver their genetic payload to host cells and can therefore be regarded as nature’s nanocarrier systems.

The structure of a virus capsid is genetically programmed so replication yields millions of identical particles, a level of monodispersity that cannot yet be achieved with synthetic nanoparticles. Viruses are proteinaceous structures, and are therefore similar to the protein cages discussed above in terms of biocompatibility. The capsids are highly symmetrical structures that come in various shapes and sizes, and they are amenable to both chemical and genetic modification to impart new functionalities, including the encapsulation or conjugation of active ingredients Given the natural function of viruses, it is unsurprising that one of the first applications of virus-based nanocarriers was the delivery of nucleic acids. Mammalian viruses such as Adenoassociated virus are established as gene delivery vectors.The first AAV-based gene therapy vector was approved by the EMA in 2012 for the treatment of lipoprotein lipase deficiency, but was not approved by the FDA, and UniQure subsequently announced its withdrawal from the European market in 2017 following the treatment of only 31 patients.The FDA has since approved two AAV-based vectors, namely Luxturna in 2017 for the treatment of patients with RPE65 mutation-associated retinal dystrophy, and Zolgensma in 2019 for the treatment of young infants with spinal muscular atrophy. One of the major drawbacks of AAV therapies is their high cost: Luxturna treatment is estimated to cost $850,000, whereas Zolgensma was priced at $2.125 million by Novartis as a one-time cure. In addition to AAV nanocarriers , other mammalian viruses have been developed for gene delivery including adenoviruses , herpesviruses , and lentiviruses and are undergoing clinical trials , whereas retroviruses and alphaviruses remain at the preclinical development stage.As an alternative to mammalian viruses, several plant viruses and bacteriophages have also been repurposed as nanocarriers or vaccines because they are non-infectious to humans and can be manufactured on a large scale as viral nanoparticles or virus-like particles .

For example, based on the immunostimulatory nature of VNPs/VLPs, several have been developed as in situ cancer vaccines, including Cowpea mosaic virus bacteriophage M13,Potato virus X ,Tobacco mosaic virus ,and Papaya mosaic virus.The CPMV system has already demonstrated efficacy in canine trials.The development of plant viruses or bacteriophages as vaccine candidates for infectious diseases, autoimmune disorders and cancer has been extensively reviewed.One of the key applications of VNP/VLP vaccine candidates is the display of heterologous epitopes.This protects the epitope from degradation, ensures delivery to antigen-presenting cells, provides an inbuilt adjuvant, and also generates cross stimulatory virus-based antigens to boost humoral and cellular immunity.Several VNPs/VLPs presenting heterologous epitopes have been tested in human clinical trials and veterinary tests.The use of VNPs and VLPs as nanocarriers for active ingredients can be achieved by passive infusion through pores in the capsid, encapsulation during assembly, as well as chemical conjugation and/or genetic fusion of active ingredients to the outer or inner surfaces. For example, doxorubicin has been conjugated to TMV,infused into Cucumber mosaic virus and Red clover necrotic mosaic virus ,and passively complexed with PVX.Virusbased nanocarriers have also been used to deliver bortezomib,cisplatin,5-fluorouracil,hygromycin,mitoxantrone,phenanthriplatin,and paclitaxel.Examples of protein delivery include TRAIL,40 TPA,and Herceptin. Filamentous phages have been developed to deliver antibiotics such as chloramphenicol and neomycin to prevent the growth of Escherichia coli, Streptococcus pyogenes, and Staphylococcus aureus.Finally, siRNA has been delivered using bacteriophage MS2 and Cowpea chlorotic mosaic virus ,and mRNA for the in situ expression of green fluorescent protein has been successfully encapsulated into CCMV and TMV, followed by the release of the mRNA cargo into the cytosol of mammalian cells and its subsequent translation.Plant VNPs have also been proposed as pesticide carriers because they are already part of the natural soil ecosystem and are harmless to humans and domestic animals.

Compared to synthetic nanocarriers, plant viruses are highly mobile in soil and can deliver pesticides to the roots, where many pests are concentrated. TMGMV was approved by the EPA in 2007 as a bioherbicide for the treatment of the invasive tropical soda apple weed in the state of Florida, thus paving the way for the development of nanocarriers based on plant viruses.Since then, RCNMV has been proposed for the delivery of abamectin to crops.The higher stability and superior soil mobility of abamectin encapsulated in RCNMV increased the efficacy of the nematicide in tomato seedlings infested with root knot nematodes compared to the free chemical. Similarly, TMGMV loaded with the anthelmintic drug crystal violet was highly toxic towards the nematode Caenorhabditis elegans in vitro. Rational design and size and shape engineering in plant virus-based carriers may enable multi-level targeting of different soil zones.Nanocarriers have revolutionized the medical, veterinary, and agricultural sectors through their ability to deliver active ingredients in a targeted and controlled manner to appropriate sites, such as cancer cells or plant roots, thereby maximizing efficacy while minimizing off-target effects. Based on the current landscape of research articles, patents, clinical trials, and approved nanocarriers, I have revealed a growth trend which predicts that more formulations will be commercially available over time, allowing the targeted delivery of small molecules, peptides and proteins, as well as nucleic acids to combat pests, pathogens and diseases in animals and plants. I observed a shift away from the development of nanocarriers for small-molecule reagents and toward the delivery of peptides, proteins and nucleic acids. Advances in bioengineering have also encouraged the development of bio-inspired nanocarriers that are friendly to the environment. Several challenges must be addressed to streamline the translation of nanocarriers from the bench to the market. In medicine, nanocarriers could greatly benefit from the incorporation of targeting ligands, aptamers, antibodies, or antibody fragments to promote their binding to receptors overexpressed on target cells or in the surrounding extracellular matrix. Additional targeted nanocarriers must undergo clinical trials before we can conclude that active targeting achieves greater therapeutic efficacy. In parallel,blueberry grow bag size the development of veterinary nanocarriers has intensified with the growing public interest in animal welfare and food safety and security. Companion animals with cancer have benefited the most from nanocarriers, whereas livestock require low-cost and prolonged treatments, such as the delivery of antibiotics. The future of veterinary nanocarriers will depend on our ability to manufacture products at a relatively low cost. Finally, precision agriculture is required to meet the growing demand for food. Nanocarriers provide the opportunity to increase crop yields in an environmentally friendly manner by delivering fertilizers and pesticides directly to plants while minimizing leaching. However, the translation of nanocarriers for agricultural applications is restricted by the lack of well-structured regulations for commercial approval. More research is therefore required to determine the fate and toxicity of nanocarriers applied in the field.Plant parasites are a major burden to the global agricultural industry.

Among them, the United States Department of Agriculture has highlighted several species of insects and worms as the most common and devastating parasites; they either directly injure crops by feeding on them or indirectly cause injury through the transmission of bacteria, viruses, and fungi. Specifically, crops infested by parasitic worms, including across the United States, results in an estimated $157 billion loss each year in crop production worldwide.In particular, endoparasitic plant nematodes feed on the crop roots, causing distinctive root swellings commonly referred to as galls. Gall formation impairs the root conduction of water and growth nutrients into the rest of the plant, resulting in lower crop yields. In addition, galls often promote crack damages in the roots and increase the plant vulnerability to secondary infections.The root-knot Meloidogyne spp, the potato cyst Globodera spp, and the soybean cyst Heterodera glycines are the most damaging and widely spread plant parasitic nematodes. Combined they can infect more than 3000 plant species, including bananas, corn, cotton, potatoes, lettuce, and tomatoes.While crop nematode infestation is relatively easy to diagnose , treatment options are limited. In most countries, crop rotation is frequently employed to selectively control plant parasitic nematode infestations.Nonetheless, the wide host-range of root-knot nematodes limits the choice of alternate crops to a few species yielding little to no revenue. Genetically modified crops resistant to nematodes are an economically and environmentally viable alternative.Unfortunately, genetic resistance to plant parasitic nematodes is selective to specific nematode species, limited to a few crops, and takes years to engineer.While these aforementioned control strategies can reduce the burden of plant parasitic nematodes on most crops, their efficacy and economic benefits are no match to the use of nematicides.The first generation of nematicides rely on highly toxic and volatile fumigants, such as methyl bromide, but their use has declined due to environmental and health concerns.Alternatively, non-fumigant nematicides, such as organophosphates, carbamates, and bio-nematicides, have been employed.Their efficacy, however, is limited by their ability to diffuse through soil, which is dependent on the amount of organic matter, moisture, and the soil structure . To be effective, non-fumigant nematicides must persist long enough and in concentrations equivalent to the nematode-lethal dose at the root level. Extended persistence in such doses increases the risk of chemical contamination of crops, soil, and groundwater. Therefore, there is a critical need to resolve soil mobility issues of nematicides to enhance their agrochemical efficacy, reduce their indiscriminate use, and ensure their safe application. To attack the problem at its roots, nanotechnology has led to the development of smart delivery systems that can be tailored to deliver pesticides in a controlled and targeted manner,similar to nanomedicine in humans.Nanomaterials used as carriers have advantages over commonly used pesticides, such as enhanced biodegradability, thermal stability, permeability, dispersibility, wettability, and stiffness.When pesticide-loaded nanoparticles are spread uniformly over the soil surface, their large surface areas increase their affinity to the target pest and reduce the dose of pesticide required to effectively eradicate the infestation.In addition, encapsulation of nematicides in nanoparticles protect the active compound from premature biodegradation and photolysis while isolating the toxic nature of the nematicide from the end-user. Liposomal formulations, as well as synthetic and natural polymer-based nanoparticle formulations have been employed as pesticide-delivery systems While synthetic nanomaterials overcome the various challenges associated with the use of nematicides, it still remains uncertain whether their high cost of manufacturing makes them economically viable.In this study, I turn toward using plant viral nanoparticles as an economically and environmentally viable alternative to synthetic nanoparticles. In addition, VNPs are exceptionally robust to the harsh environment of crop fields, yet they are biodegradable. From a human health perspective, VNPs are bio-compatible and non-infectious, making them safe to use on industrial crops. From an engineering perspective, VNPs are self-assembling systems that form highly symmetrical, monodisperse structures, amenable to both chemical and genetic modifications to impart new functionalities.Since plant viruses have naturally evolved to protect and efficiently deliver their payload , they can be regarded as naturally occurring nanocarriers. At first glance, applying VNPs onto crops might seem counterintuitive since their natural hosts for infections are plants. However, Cao et al. recently introduced the concept by utilizing the red clover necrotic mosaic virus to manage plant parasitic nematode infestation.

In Central and Northern Europe, where the cultural response to environmental stress involved the direct consumption of milk, this appears to buffer environmental stress and may have fueled the patterns of human growth and body size observed in the late Holocene. The trends observed in this paper may be a direct or indirect consequence of shifts in energy allocation to somatic growth associated with the digestion of lactose but may otherwise be influenced by patterns of disease load during growth, changes in weaning patterns, population density, migration, or genetic drift. A life-history framework may help to understand how the interaction of such factors influences somatic investment . We note that there are other regions where LP genetic variants are found in high frequencies, including the Mongolian Steppe , and convergent evolution of MCM6 in East Africa with what may be a stronger directional selection among the Maasai . At present, we do not have data of sufficient resolution to investigate whether ancient selection and dairying fueled phenotypic change in these regions. However, our results suggest that the transition to agriculture may have had regionally specific influences on human populations that can be elucidated through analyses of long-term diachronic trends in human-culture-environment interactions. Long-term trends are best investigated through broadscale integration of bio-archaeological and phenotypic data with aDNA, paleoecology, and archaeological data that account for the spatiotemporal complexity of Holocene cultural and dietary transitions.Waterborne zoonotic pathogens pose a public health risk due to their consistent point and non-point sources,plastic pot which can significantly impair the ecological quality of aquatic systems. Pathogens enter streams and rivers in a variety of processes including overland flow and groundwater fltration.

Viruses, bacteria, and parasites persist for varying amounts of time, especially within streambed sediments, leading to long-term disease transmission. Of particular concern is the protozoal parasite, Cryptosporidium, which can remain infective for weeks to months under cool and moist conditions, with the infectious state largely resistant to chlorination. Te 50% infectious dose for livestock-derived Cryptosporidium, specifcally C. parvum, for healthy humans ranges between 10–1,000 oocysts. Monitoring programs assess the microbiological quality of waters to minimize health risk associated with pathogenic microorganisms. However, as it is still unfeasible to experimentally monitor pathogen levels at the high spatiotemporal resolution ofen needed to assess risk, sampling is often complemented with a model. Both environmental and hydrological processes control the residence time and persistence of pathogens within a stream network. Current models consider stream flow conditions, but it is imperative to incorporate the wide variety of processes that control the transport and retention of Cryptosporidium in a dynamic stream environment. Commonly, hyporheic exchange – the two-way exchange of water with the underlying sediments induced by pressure variations associated with stream flow over stream channel topography – is ignored in surface water modeling of pathogen and microbial transport in streams. However, as the size and specific gravity of Cryptosporidium are low, it is mainly removed from the water column by hyporheic exchange and to a lesser extent by sedimentation via association with larger and denser suspended aggregates. Microbial interaction with the streambed and other stream transient storage areas has been greatly underestimated by only assuming gravitational settling without considering the key mechanism of hyporheic exchange.

Hyporheic exchange of particles differs from solutes because of strong particle deposition during porewater transport. Even though the settling velocities of fine particles are low, gravitational settling can be more important within porewaters, where porewater velocities are extremely small. Filtration in the bed leads to pathogen immobilization. However, filtered microbes and fne sediment are often remobilized, corresponding to reversible fltration. This slow release of microbes after initial deposition has been observed in streams. If models do not consider hyporheic exchange within the hyporheic region then pathogens will not be conceptualized as being in the nearbed or hyporheic region to experience these additional immobilization processes, thus underestimating pathogen immobilization and retention in streams. This underestimation of pathogen accumulation during base flow can lead to inaccurate predictions for pathogen resuspension during storm events, when the majority of pathogens are transmitted downstream. Te main objectives of this modeling study was to improve storm flow predictions of potential resuspended Cryptosporidium oocysts by appropriately characterizing the transport and retention of Cryptosporidium during base flow conditions through incorporating hyporheic exchange and immobilization processes, calculating residence times of Cryptosporidium in surface water and accumulation in immobile zones, such as streambed sediments, to estimate long-term persistence, and estimating Cryptosporidium accumulation during base flow conditions that can potentially be resuspended during a storm event. We apply a previously developed mobile-immobile model for microbes to Cryptosporidium, which accounts for hyporheic exchange and transport through pore water, reversible ifltration within the streambed, and inactivation of microbes, to accurately predict the long-term persistence of pathogenic microorganisms within stream storage areas.

The mobile-immobile model framework is convenient for river transport as the water column can be considered mobile and material retained in streambed sediments or slow-moving surface waters is comparatively immobile. This model framework, in contrast to previous work, was developed for microbial transport in streams to incorporate detailed measurements of transport and retention processes at multiple scales, which allows the use of lab-scale measurements to parameterize key transport and retention processes and apply them to reach-scale modeling. We used the model to assess the transport, retention, and inactivation of Cryptosporidium within stream environments, specifically under representative conditions of California’s Central Valley, where pathogen exposure can be at higher risk due to agricultural and wildlife non-point sources. Comparison of modeling results with and without immobilization processes provided novel insights into the significance of hyporheic exchange and subsequent immobilization processes on pathogen retention and long-term persistence within streams. This study provides new understanding of pathogen transport and retention dynamics in streams to help improve future risk assessment.Te study site is California’s Central Valley and the Sierra Nevada foothills , draining ~23,000 sq. miles of the western slope of the Sierra Nevada mountains down to the floor of the Central Valley. These streams originate in snow-fed lakes and streams surrounded by United States Forest Service and National Park lands where cattle and other livestock are grazed and descend through rolling foothills to the low-lying Central Valley, with food crop agriculture and animal feeding operations supported by a network of man-made canals. This site thus has potential inputs of fecal organisms from grazed allotments in the higher elevations and in animal feeding operations along the lower reaches and canals,grow bag in addition to inputs from wildlife such as striped skunks, coyotes, California ground squirrels, and yellow-bellied marmot. California’s Central Valley has a Mediterranean seasonal climate, with highly seasonal water inputs, with precipitation primarily in the winter and spring. Following the spring snow melt period, most of the Central Valley is relatively dry with occasional summertime precipitation at higher elevations.Approximately 1.7×105Cryptosporidium oocysts/animal/day are shed from a California adult beef cow and 6×105 oocysts/animal/day from California beef calf. An average beef herd size is approximately 100 adult cows and 150 calves, which equates to 1.1×108 oocysts/day/livestock operation. Cryptosporidium species include C. bovis, C. ryanae, and the more infectious C. parvum.

Oocysts deposited on the terrestrial portion of a watershed from beef cattle only reach streams through overland flow run of and direct deposition of feces. Oocysts remain trapped in the fecal matrix or are eluted and reach streams via groundwater or overland flow, with loads dependent on storm intensity, soil structure and infiltration rates. The high risk fecal pats are those deposited directly into the stream, less than 1–5% of total fecal loads, depending on cattle access to the stream via lack of fencing. Thus, a reasonable estimate of Cryptosporidium that could potentially reach a stream in the region, estimating that 20 beef lots may impact a single stream, from a combination of direct deposition, overland flow, and groundwater inputs is approximately 1–5% of the oocysts shed. Dairy lots are assumed to have minimal release of Cryptosporidium oocysts as the operations are confined and run of into stream is not permitted. Other non-point sources include wildlife, where the highest loads come from the California ground squirrel , averaging 1.13×105 C. parvum oocysts/animal/day. Ground squirrel populations result in loading rates of 9×105 oocysts/hectare/day for low density populations with 8 to 94 adults/hectare in California. Therefore, non-point sources could potentially be a large source of Cryptosporidium to streams, even larger than beef herds and dairy lots combined. To account for these variable inputs, the highest figure from beef herds was assumed to represent an upper boundary of the oocysts load, given the uncertainty in the number of oocysts shed by beef lots, the limited oocysts that may be released from dairy lots, and the additional contribution of non-point sources in the watershed from wildlife excretions.Stochastic theory predicts that the slowest mechanism will control the long-term tailing behavior and model parameterization of a tracer concentration vs. time surface water profile. This concept can link multiple scales of transport, as previously demonstrated by combining lab scale and field reach-scale studies on solute, particle, and microbial transport and retention in streams. We apply this scaling concept to this study by using the column Cryptosporidium model parameters from a published study to characterize the pathogen transport and retention within the immobile zone of the reach scale mobile-immobile model framework. Specifically, Cryptosporidium breakthrough curves in a sand column showed power-law behavior, with a particle immobilization rate within the immobile zone, ΛIMM =0.2 s−1 and a power-law slope of the pathogen residence time distribution within the immobile zone, βIMM =0.35 . We assume Cryptosporidium release under summer base flow conditions with an average flow of 60L/s and an average velocity, v, of 5 cm/s. This velocity within an agricultural stream was associated with a dispersion, D, of 0.095 m2 /s, an exchange rate between the mobile and immobile zone, Λ, of 6×10−2 s−1 , and a power-law slope within the immobile zone, β =0.7. These parameters are reasonable and are within the range of hydrologic model parameters for solute transport within streams during base flow conditions. Inactivation rates of Cryptosporidium in the mobile zone and immobile zone are estimated for summer conditions with water temperatures of approximately 20°C as 0.088/ day and 0.011/day, respectively. A summary of all parameters used within the model simulations is shown in Table 1. The model simulations were run with the 1-month scenario detailed in the previous section. The 1-month duration of the release was chosen as an arbitrary reference duration to assess the permanence of oocysts in the stream even after the release has stopped. A total count of Cryptosporidium oocysts immobilized and inactivated were determined at each sampling distance and at different time points of interest . A model output breakthrough curve with and without inactivation was produced. These model outputs were integrated to the different time points of interest using the trapezoidal method to determine a total number of oocysts that passed by the sampling point within the surface water with and without inactivation. The difference between with and without inactivation was used to calculate the number of oocysts inactivated vs. immobilized within the stream at each time point of interest. The # of oocysts immobilized at each downstream distance was estimated as the difference between the previous sampling point . The values for % Cryptosporidium immobilized were calculated by dividing the total # immobilized by the known model input of Cryptosporidium oocysts .Model simulations for a 1-month input of Cryptosporidium to an agricultural stream show in-stream pathogen counts at 100, 300, 500, and 700m downstream of the input . Cryptosporidium transmission is presented under two scenarios with only hyporheic exchange and inactivation and with hyporheic exchange, inactivation, and additional immobilization processes in transient storage areas . For scenario 1, a decrease in maximum in-stream concentrations from 2.1×10−2 #/mL at 100m to 2.0×10−2 #/mL at 700m downstream of the input demonstrates how hyporheic exchange delays downstream transport, but does not greatly reduce the maximum in-stream concentration. As described previously, a safe water supply is considered to have less than 10−5 oocysts/mL. This value assumes a typical human consumption of 2L/day and a safety/error factor of 300 to 1,000, which is typical for public health standards. In-stream concentrations remained above 10−5 oocysts/ mL for 1269 and 2357 hours for sites 100 and 700 m downstream of the input, respectively.