Tag: agriculture

The appropriate design of such products requires this kind of data. Our analysis shows that no one risk management tool fits all growers. Some risk-related patterns may be observed broadly in certain segments of farms. However, those patterns change when smaller subcategories of crop producers are analyzed because risks and the way growers manage them depend on many complex factors. One implication is that insurance products that are designed and targeted for individual crops may miss the whole farm interactions. In reality, an insurance product for a specific crop would work differently for different growers depending on their characteristics outside the specific crop. It is also vital to better understand the risk management tools that growers currently use when designing public policy to help farmers manage risk. In many cases, public policy for risk management can be effectively designed to accommodate and complement rather than substitute for or conflict with the risk tools that growers already value and use. Overall, the results of this survey suggest that one must proceed with caution when attempting to develop government-sponsored risk management programs. Programs may fail to meet objectives and may have serious unintended consequences unless the full set of opportunities and constraints facing farmers is well understood and the differences across farms are incorporated in the program design. This study shows the complexity of risk related costs and revenues associated with the fruit, nut, vegetable, blueberry grow bag and ornamental horticulture industries in California. The data summarized in this report also can be useful for further research.

These data, together with information on grower costs and returns, can help analysts better understand variations among horticultural crop industries in California and elsewhere. Researchers are also pursuing more detailed analyses of the data. For example, these data are ideal for measuring patterns of diversification and, in some cases, vertical integrations and for examining the multivariate patterns of these with alternative measures of farm size. Assessing other, more detailed relationships among the variables is also on the research agenda. This report does not attempt to disentangle the various causal relationships among the data. Such research is on the horizon. Finally, this survey provides a one-time cross-section on many important variables. Periodic re-surveys would allow researchers to track the path of adjustment and allow assessment of industry dynamics with rich, repeated cross-sectional information.Bunch grapes , notably European , are considered among the major fruit crops worldwide, producing roughly 70–80 million tons each year . Cultivars of V. vinifera L. are used for wine, juice, and table grape production. Grape berries are classified as non-climacteric fruits, exhibiting a double-sigmoid developmental pattern with two rapid growth phases: the berry formation and the ripening phase , separated by an intermediate lag phase called the green plateau . The exponential increase in berry size characterizes both growth stages , but not the lag one . During phases and , also known as immature stages, organic acids, mainly tartrate and malate, accumulate leading to induction of acidity levels . At the end of the lag phase, a step-change point takes place known as veraison, where acidity starts to decline while sugars, mostly glucose and fructose, as well as anthocyanins in colored varieties, increase.

Of particular interest are phenolic compounds, which are major and ubiquitous plant secondary metabolites derived from the shikimate/phenylpropanoid and polyketide pathways, with three utmost categories: proanthocyanidins , also known as condensed tannins, the gallo- and ellagitannins , and the phlorotannins . Such diversity of polyphenols, with more than 8000 structural variants, bestows them a wide range of biological functions ranging from growth, development, and protection inside the plant to, to some extent, human-related issues . In grapevines, the accumulation pattern of phenolic compounds, along with the aforementioned berry attributes, distinguishes each of the berry phases throughout berry development . Indeed, berry quality and sensory characteristics are notably defined by its polyphenol content . Remarkably, astringency is among the hardest sensory traits to depict and interpret as many intricate processes underpinning its perception . For instance, a sensory characterisation of the astringency of 11 varietals of Italian red wine revealed that neither total phenols nor PAs can predict how all astringency subtleties will be perceived . It is worth noting that the amounts, compositions, and proportions of polyphenols in a given species may vary widely depending on several factors, such as genotypic variations, developmental stages, and environmental circumstances . Scarlet Royal is a mid-season ripening table grape variety, producing seedless, red-skinned, oval-shaped, firm, and moderate to large berries with a sweet to neutral flavor . In the San Joaquin Valley, California, it typically ripens in mid to late August, filling the harvest window between Flame Seedless and Crimson Seedless, and has thus become a very popular red table grape variety in California. However, an undesirable astringent taste has been observed occasionally in some cases.

In fact, the economic value of grapevines depends substantially on the environmental conditions, including climate, soil, cultural practices, cultivar, and root stock. Hence, the term “terroir” is used in viticulture to describe the effect of such an interactive ecosystem on grapevine and wine quality . The current study aimed to understand the underlying mechanism of astringency development in Scarlet Royal berries at two contrasting vineyards . The first location produces well-colored, non-astringent berries; however, the second site yields astringent taste, poorly colored berries . The data showed a large variation in berry astringency within the same vineyard and from year to year. The data illustrated that the divergence in berry astringency stemmed from alterations in its polyphenol composition , most notably tannins. Additionally, the ripening stage was the most distinguishing platform for such variation between both vineyards. We were able to determine the tannins’ threshold level that causes the Scarlet Royal astringency taste to be ~ 400 mg/L. Given the changes in the levels of polyphenols during berry ripening, the question was raised: what is the mechanism governing the distinctive tannins accumulation pattern between V7-berries and V9-berries, and hence astringency diversity? To answer this question, RNA-seq data generated at one ripening time point was associated to the changes in polyphenolic levels using a systems biology approach, WGCNA . The module-trait association analysis positively correlated the key flavonoid/PAs biosynthetic genes with the accumulation of tannins, catechin, and quercetin glycosides exclusively in V9-berries. The modulation of the berry’s transcriptomic profile is concomitant with its polyphenols’ composition, which finally disturbs berry quality, including astringency levels.Five-year-old V. vinifera cv. Scarlet Royal grafted on Freedom rootstock was chosen for its berry astringency diversity at two commercial vineyards located in Delano, San Joaquin Valley, California, USA. Vineyards were located at a close distance of 10 km, and the local weather conditions during the two seasons were collected from the Delano CIMIS weather station . Both vineyards were planted at the spacing of 2.44 and 3.66 m in an open gable trellis supporting system with East-West row orientation. Vines were pruned in a Quadrilateral cordon training with 7–8 spurs left on each cordon during the winter pruning. In addition, general UC guidelines practices were applied in both vineyard. Random forty vines from different four rows from each vineyard were used in this study. Starting from veraison and until the end of the season, during two consecutive years . During the first year, sampling dates were July 8th , August 1st , August 10th , September 9th , September 15th , and October 19th ; and for the second year, sampling dates were: July 15th , August 10th , August 25th , September 10th , September 29th , and October 21st . Sampling dates varied from the first to the second year due to the vineyard’s accessibility. At each sampling point, two sets of fifty berries were collected periodically. The first set was used to measure the berry weight, and then these berries were macerated in an electric blender, filtered through a paper towel, blueberry grow bag size and an aliquot of juice was used to determine soluble solids , pH, and titratable acidity . The TA and pH were determined by titrating a 40 mL aliquot of juice with 0.1 N NaOH to a pH of 8.2 using an automatic titrator Excellence T5 . Another random 50 berries from each replicate were collected for color, tannins, and phenolic compounds and sent immediately in a cooler to EST laboratories.

At harvest, which was during the month of September, an extra set of samples was collected and promptly frozen in liquid nitrogen and stored at −80°C for subsequent analysis, including RNA extraction and gene expression studies. Harvest time was determined by the growers, and the marketable clusters were picked based on the color, and yield was determined from the three harvest dates.At bloom, fifty leaves from each replicate were collected, resulting in a total of 200 leaves from each vineyard, for nutrient analysis. The leaf positioned at the front of the cluster was specifically selected, and the petiole was immediately separated from the blade. The petioles were transported to the laboratory, where they were triple-washed with distilled water to remove any impurities before being sent to a private laboratory for nutrient analysis. In the winter, soil samples were collected at a depth of 30 cm and at a distance of 30 cm from the vine. These samples were transported immediately to the laboratory for analysis. The nutrient content was determined using the methods described in US Salinity Laboratory Staff .The taste panel evaluation of Scarlet Royal table grapes was conducted with the participation of twelve nonprofessional panelists. Astringent taste perception was assessed using a scale ranging from one, representing an extremely low level of astringency, to seven, indicating an extremely high level of astringency. The taste evaluation was performed on 24 clusters from each vineyard. Phenolic compounds analysis. Total phenolic analysis was performed on 250 grams of whole berries by ETS laboratory using a reversed-phase HPLC method adapted from Price et al. .Total RNA was isolated from whole berry samples following the protocol described by Boss et al. . To remove any residual DNA, RNase-free RQI treatment was performed according to the manufacturer’s instructions , and the samples were further purified using the RNeasy mini kit . For RNA-seq analysis, a total of 8 RNA-seq libraries were generated, comprising four biological replicates from each of the two vineyards . The libraries were constructed as previously described using the NEBNext Ultra II RNA Library Prep Kit for Illumina . Subsequently, these libraries were pooled in equal amounts and subjected to paired-end 150-base sequencing on two lanes of the NovaSeq 6000 platform at the Novogene Co., Ltd .Illumina sequencing of the multiplexed RNA-seq libraries resulted in 8 FASTQ files containing sequences, and the dataprocessing followed the methods described in our previous work . In summary, the quality of reads was assessed using FASTQ before and after trimming with Trimmomatic v0.39 . Subsequently, the trimmed reads were quantified using Salmon in non-alignment based mode to estimate transcript abundance . Co-expression network modules were constructed using the variance stabilizing transformation values and the R package WGCNA . Before analyzing the data, lowly expressed genes among all sample types were removed by DESeq2, and the remaining non-lowly expressed genes of the 8 samples were used in module construction. The co-expression modules were obtained using the default settings, except that the soft threshold power was set to 9, TOMType was set to signed, minModuleSize was set to 30, mergeCutHeight was set to 0.25, and scale-free topology fit index was set to 0.8 . A module eigengene value, which summarizes the expression profile of a given module as the first principal component, was calculated and used to evaluate the association of modules with berry biochemical characteristics of V7-berries and V9-berries at the fifth sampling time . The resultant final WGCNA matrix had 42 modules with 17,553 genes. The module membership and gene significance values were calculated, subsequently the intramodular hub genes were identified .Scarlet Royal table grape is one of the major red varieties in California. Despite the premium fruit quality of the variety, in some cases, an undesirable taste was observed under certain unknown circumstances. To gain comprehensive insights into the development of the occasional berry astringency of Scarlet Royal and understand the underlying mechanism of this phenomenon, berries were investigated at two contrasting vineyards , both following the same commercial cultural practices.

The economic sustainability of individual farming operations and the area’s berry industry in total will ultimately be impacted by and continue to evolve with the ever changing business environment, and by an array of risks and challenges.Angle-resolved photo emission spectroscopy is used to directly measure the band structure of solids and is an essential experimental tool for solid state physics research. In addition to the band structure, ARPES provides information on other aspects of the electronic structure. For example, ARPES with a spin detector can be used to obtain spin information of the initial states. Polarization dependent experiments can provide symmetry information on the initial states; initial states from, for example, px and py orbitals can show dramatically different ARPES intensities depending on the polarization of the incident light. In recent years, there has been much interest in using circular dichroism in ARPES as a way to measure some aspects of initial states, such as the orbital angular momentum or the Berry curvature. It is well understood that OAM plays an important role in spin-split phenomena in systems without inversion symmetry, such as surfaces of solids and monolayer transition metal dichalcogenides. CD-ARPES has been utilized to obtain the crucial information on the electronic structures of such systems. While the final state of the photoemission process certainly has an effect on the CD-ARPES intensities, plastic grow bag experimental results show that CD-ARPES is a rough measure of the OAM of the initial state if the photon energy is not too low.

Exploiting this feature in CD-ARPES measurements, information on the OAM and hidden Berry curvature of 2H-WSe2 was recently obtained using CD-ARPES. An important aspect of this research was that the Berry curvature contribution to the CD-ARPES intensity could be isolated by decomposing the CD-ARPES intensity map into symmetric and anti-symmetric components about the experimental mirror plane, which is perpendicular with respect to the crystal mirror plane of 2H-WSe2. The symmetric component was attributed to the OAM or Berry curvature contribution, since the electronic structure should be symmetric about the chosen experimental mirror plane set along K–Ŵ–K′ in momentum space.Experimental geometry, including single crystal orientation, is especially important in this experiment. The crystal structure of the top atomic layer or ML of 2H-WSe2 is a hexagonal lattice, as shown in Fig. 1a; there is a unique mirror plane in the crystal structure, as indicated in the figure. The experimental mirror plane is defined by the plane defined by the normal of the sample surface and the direction of incident light. Two experimental geometries are possible, according to the direction of incident light, as indicated by blue and red arrows in Fig. 1a. The experimental geometries using incident light described by blue and red arrows are regarded as geometry-A and geometry-B for convention, respectively. Notably, the signals from the top layer of bulk 2H-WSe2 dominate the CD-ARPES data due to the surface sensitivity of ARPES; the corresponding momentum space view is shown in Fig. 1b.

The mirror plane is oriented along the M–Ŵ–M direction, and the direction of incident light is indicated by blue and red arrows on the mirror plane in Fig. 1b. This experimental geometry differs from that used in previous work, in which the experimental mirror plane was rotated by 30° with respect to the crystal mirror plane, such that the experimental mirror plane is oriented along the K–Ŵ–K′ direction. We expanded on our previous CD-ARPES work on 2H-WSe2 by focusing on a different mirror plane. Here, we report our CD-ARPES studies on 2H-WSe2 with the experimental mirror plane parallel to the crystal mirror plane or along the M–Ŵ–M direction in momentum space . Within the experimental constraint, there are two possible experimental geometries based on the incident beam directions, as shown by the blue and red arrows in Fig. 1a,b. The CD-ARPES values for the two geometries are nearly opposite to each other near the Brillouin zone corner, whereas they are almost identical near the Ŵ point. These observations are well explained by accounting for the Berry curvature contribution to CD-ARPES. Our results thus indicate that the deviation from the median value between the two experimental geometries can be interpreted as the Berry curvature or OAM. Figure 1c,d present the constant energy ARPES maps taken by RCP and by LCP incident light in geometry-A, respectively. The binding energy of all maps shown in Fig. 1 is 0.5 eV lower than the valence band maximum energy . CD signals, in which the intensity corresponds to the difference in the intensity taken by RCP and that taken by LCP , are mapped in the momentum space .

The anti-symmetric function of the CD map for the experimental mirror plane is expected for this experimental geometry, given that the Berry curvature is also anti-symmetric with regard to the experimental geometry. Figure 1f–h present the ARPES maps taken with RCP and LCP incident light in geometry-B and the corresponding CD map, respectively; the upper left corner corresponds to the K′ point in Fig. 1f–h and the K point in Fig. 1c–e. Remarkably, the CD signals at each corner of the BZ in Fig. 1h are almost opposite to those in Fig. 1e, whereas the CD signals near the center of the BZ are nearly the same. This can be explained by taking the Berry curvatures into account, given that the Berry curvatures are opposite at the K point and K′ point, whereas the Berry curvatures are nearly zero around the Ŵ point. A detailed analysis of CD data was performed for ARPES cut data along the K–M–K′ and K′ –Ŵ–K directions in geometry-A and along the K′ –M–K and K–Ŵ–K′ directions in geometry-B . Figure 2a,b present ARPES spectra taken by RCP and LCP light, respectively, in geometry-A along K–M–K′ , as indicated by the dotted line in Fig. 1e. Figure 2d,e present ARPES spectra taken by RCP and LCP light, respectively, in geometry-B along the K′ –M–K direction, as indicated by the dotted line in Fig. 1h. Two parallel dispersive bands are evident in the spectra, of which the maxima are located at K and K′ . Te energy difference between the upper and lower bands originates from atomic spin–orbit coupling of the W atom. The spin directions of the two bands are opposite, but the Berry curvature and OAM are the same, as expected from the massive Dirac–Fermion model. ARPES intensity clearly depends on the polarization of the incident light. Figure 2c,f present CD-ARPES intensity distributions for geometry-A along K–M–K′ and for geometry-B along K′ –M–K, respectively. Te CD intensities of the two bands are similar at each momentum point, but the intensities are almost opposite between the CD for geometry-A and that for geometry-B; this is consistent with the constant energy maps shown in Fig. 1e,h.Normalized CD intensities as a function of momentum are shown in Fig. 3a for the upper band and in Fig. 3b for the lower band. INCD is obtained by /, where IR and IL correspond to the ARPES intensity taken with RCP and LCP, respectively. INCD for the upper band along K–M–K′ in geometry-A, as indicated by the filled squares in Fig. 3a, has a positive value toward the K point from the M point. INCD exhibits a slight sign change beyond K and K′ points, pe grow bag although it is difficulty to catch the fact in Fig. 2c due to very weak ARPES intensities. INCD for the upper band along K′ –M–K , indicated by the empty squares in Fig. 3a, exhibits a negative value toward the K′ point from the M point and a positive value toward the K point from the M point, except very close to the M point, as we can also notice in Fig. 2f; sign changes beyond K′ and K were also evident in the data. The INCDs in geometry-A and -B are roughly opposite, but not exactly. The INCD for the lower band in geometry-A and geometry-B are also similar to those of the upper band, but they are slightly weaker. INCD consists of symmetric and anti-symmetric functions about the experimental mirror plane . Figure 3c,d present the INCD S s for the upper and lower bands from two geometries, respectively. Figure 3e,f present the INCD A s for the upper and lower bands from two geometries, respectively. As shown in the figures, the INCD S s were close to zero, and INCD A s were dominant components, regardless of the geometry or band. An asymmetric CD-ARPES distribution about the experimental mirror plane is a usual feature from solids, as the inversion symmetry along the surface normal direction is lifted on the surface of solids, which is similar to an oriented CO molecule system.

The CD-ARPES contribution caused by the inversion symmetry breaking in the material surface can be called surface effects. However, it is surprising that the CD was nearly opposite between geometry-A and -B. Based on this finding, we believe that a substantial portion of INCD A originates from the Berry curvature , given that the CD signs follow the Berry curvature direction, as shown in Figs. 1e,h and 2c,f. It is important to isolate the Berry curvature contribution to INCD A from other contributions. The Berry curvature contribution to CD-ARPES should be exactly opposite between the normalized CD-intensities along K–M–K′ in geometry-A and along K′ –M–K in geometry-B, because the Berry curvatures themselves are exactly opposite for K and K′ points. We assume that other contributions, mainly the surface effects, are the same, regardless of the geometry. Ten, the median values of INCD A s from geometry-A and -B can be considered from the other contributions to INCD A s. Additionally, this assumption is experimentally justified by CD-ARPES data near the Ŵ point, as shown in Figs. 4 and 5. The difference in INCD A with respect to the median value is exactly opposite between the K–M–K′ cut in geometry-A and the K′ –M–K cut in geometry-B; this difference can be interpreted as the Berry curvature contribution to INCD A . Figure 3g presents the differences, along with the theoretical values of the Berry curvature and OAM. The differences are similar to the Berry curvature and OAM, except for the crossing at zero and the changing signs near 0.7 Å−1 . The sign change of the difference of INCD A from the median value is mainly due to the change in the final state character as the momentum of the photoelectron varies. We know that the wave function characters of the initial states near the K point change gradually and depend on the distance from the K point in the massive Dirac–Fermion model. The sign of CD-ARPES data can be reversed for the same initial states by only changing the final states, as indicated in the photon energy dependence of CD-ARPES. Figure 4 presents the ARPES cuts and CD-ARPES data along the K′ –Ŵ–K in geometry-A, and along K–Ŵ–K′ in geometry-B, as indicated in Fig. 1. These cuts are special, in terms of the Berry curvature and OAM of the electronic states near the Ŵ point being almost negligible, compared with those of states near the K point. Therefore, the Berry curvature contribution to CD-ARPES data is expected to be almost zero near the Ŵ point. The CD-ARPES signals in both geometries are quite strong near the Ŵ point and exhibit a clear node at Ŵ, indicating no symmetric component of the CD intensity. Te CD-ARPES intensities near the K point from both geometries are much weaker than those near the Ŵ point, and the CD-ARPES intensities near the K point from geometry-A are even weaker than those from geometry-B. Figure 5a–c present INCDs, INCD S s, and INCD A s, respectively. The symmetric components are negligible; the asymmetric components make up the majority of the INCDs . Remarkably, INCDs along K′ –Ŵ–K in geometry-A and along K–Ŵ–K′ in geometry-B are the same near the Ŵ point , and INCD A s are, in turn, the same near the Ŵ point . Figure 5d presents the deviations of INCD A s from the median value, along with the theoretical values of the Berry curvature and the OAM.

People’s Grocery had taken root. Ahmadi, an Iranian American from Los Angeles who studied Sociology at UC Santa Cruz, had been active in Oakland’s EJ movement for a couple years before starting People’s Grocery. Like the EJ movement, food justice shared an emphasis on environmental racism, economic and health disparities. Ahmadi felt that it was a logical progression from EJ to food justice, that food justice was in fact an “outgrowth of EJ” . The link between EJ and food justice made sense at multiple levels: “Nutrition, and land, and economic development. Those were really kind of the three things that started to triangulate for me” . Simultaneously reading up on the “social determinants of health” literature, and specifically interested in the relationship between malnutrition and resistance to toxins, Ahmadi turned to the work of Carl Anthony and Urban Habitat to guide his thinking about land use and structural racism. He continues, “[I was] craving something different, craving to be more entrepreneurial, craving to create alternative models. I connected the dots and saw this food security issue, and started learning about that.” Ahmadi found that food justice was a way to tackle multiple drivers of inequality in West Oakland, but only if it helped the community move away from a dependant “recipient” model towards a more economically self-sufficient one. Ahmadi’s story highlights the emphasis on growth and change, plastic square flower bucket on sustainability and community development that dominates the discourse employed by urban agriculture and food justice organizations.

For many activists, there is a sense of personal satisfaction or fulfillment that arises from developing creative strategies for changing the food system, from envisioning what a just sustainability might look like, and actively working to achieve this alternative vision. The material realization of this vision—a garden, a farm stand, a grub box—and the labor necessary to bring them to fruition, serve both the individual activist and the surrounding community. In East Oakland at the turn of the millennium, urban agriculture was mostly taking place in school gardens, community gardens, and people’s backyards, rather than through organizational garden projects. In terms of organized food justice-oriented urban agriculture activity, Grey Kolevzon’s work with Cycles of Change and EBAYC described in the previous section was concentrated primarily in San Antonio and Fruitvale. Few food justice organizations ventured into “Deep East Oakland”, the area east of Fruitvale, comprising a number of flatlands neighborhoods such as Elmhurst, Eastmont, and Melrose. Jason Harvey, founder of Oakland Food Connection, often tells the story of growing up in East Oakland where his mother supported him and his brother on food stamps. After a stint in the Air Force, Harvey returned to Oakland and got involved with the West Oakland Food Collaborative in 2003 . In early 2005 he began scouting out the work of the various organizations and noted that very little food justice work was happening in East Oakland where he had grown up.

Soon after he established Oakland Food Connection, formally establishing it as a 501 in 2007. Much of his work is concentrated in the area along MacArthur Boulevard in East Oakland, with a small farmer’s market, café, and bulk whole foods retail outlet in the Laurel neighborhood, a rooftop garden at E.C. Reems Academy, a charter school next to Castlemont High, his alma mater, as well as gardens at a handful of other schools . He focuses on both food production and culinary education, underscoring the linkages between “food, community, and culture” . Another East Oakland urban agriculture program grew out of Slide Ranch, an educational farm in Marin County where schoolchildren from San Francisco, Oakland, and Richmond learn about sustainable agriculture on one or two day field trips. Four of the garden-based educators working there were inspired by the way the children “blossomed” at Slide Ranch, but wanted to create a similar space within an urban area itself rather than busing them to a rural area. So they began searching for a space in Oakland and found an apartment with a large yard “perfect for a garden” advertised on Craigslist. They moved into the apartment on 23rd Avenue and International Blvd. in East Oakland’s San Antonio District . Shereen D’Souza, a South Asian American who grew up in New Jersey, had been working with hillside farmers and starting school farms in rural Honduras, before moving to SOL in 2004 on the invitation of one of the founders. She worked for Oakland Based Urban Gardens in West Oakland as a garden-based educator for several years before taking the helm of the California Food and Justice Coalition, a statewide food justice policy advocacy group. She describes SOL as “a living space, as well as a food justice project… We grow as much of our own food as possible, we have chickens and gardens, we buy bulk food from either Mandela Foods Coop or Rainbow and also if we need produce we go to the farmers markets” . SOL offers classes on sustainable agriculture and urban agriculture to neighborhood school groups, “and for older students, a critique of the industrial food system” . Mostly the youth come to SOL with other organizations that have included Bantaay Srei, an organization that helps Southeast Asian girls transition out of sex work; Street Level Health Project, an organization working with the children of jornaleros ; and Cycles of Change, a bicycle-oriented job training and education organization.

Their central program is a summer intern project for teens. She explains that SOL’s reach is limited due to meager funding. This was by choice, as their focus has primarily been on creating a sustainable living center rather than an NGO. Hayes’ Office of Sustainability focused primarily on reducing energy use and bringing hybrid and hydrogen vehicles into the public transit fleet. Under Hayes’ tenure, Oakland also joined the Chicago Climate Exchange, and teamed up with Greenpeace, Friends of the Earth, and the Cities of Boulder, Santa Monica, and Arcata in a lawsuit against several federal agencies for violating the National Environmental Policy Act by funding “certain overseas industries that exacerbate climate change” . In 2005 Mayor Jerry Brown, along with the mayors of 50 other cities around the world, signed the UN World Environment Day Urban Environmental Accords and pledged that Oakland would become a more ecologically sound, economically dynamic, and socially equitable city by 2012. As a result of steps taken toward this commitment, it ranked in the top ten sustainable cities in 2005, 2006, and 2008 . The high sustainability rankings were due in part to the city’s inclusion of the food system into its sustainability plan. In January 2006 on the recommendations of the Life Enrichment Committee, the Oakland City Council authorized the Mayor’s Office of Sustainability “to develop an Oakland food policy and plan for thirty percent local area production” . Building on a food assessment for Alameda County conducted in 1999, and inspired by similar assessments in Toronto, Vancouver, San Francisco, Portland, Chicago, and a number of other North American metropolises, two UC Berkeley graduate students in the Department of City and Regional Planning completed the Oakland Food Systems Assessment for the Mayor’s Office of Sustainability in May 2006 . The document has since served as a springboard for food systems change in Oakland. Upon the report’s recommendation, the City Council unanimously passed Resolution No. 80332, approving a seed grant for $50,000 to establish a municipal food policy council whose mission would be “to cultivate a sustainable food system by eliminating hunger, plastic plant pot increasing health, expanding a greener economy, and honoring diversity for all current and future generations of Oakland, especially the least served, by ensuring the availability and accessibility of a wide variety of local, safe, sustainably-grown, and nutritious food” . The Oakland Food Policy Council was seated in 2009 and has since developed an Action Plan that includes first steps towards “transforming Oakland’s food system,” including advocating for the protection and expansion of urban agriculture . 94 Arising from the same food systems vision, the Health for Oakland’s People and Environment Collaborative, an umbrella organization consisting of several community development organizations and spearheaded by the Alameda County Public Health Department, the Food Bank of Alameda County, and the Community Food Security & Nutrition Policy Program of Alameda County UC Cooperative Extension, competed for and won a two-year planning grant in 2007 for $495,200 from the W.K. Kellogg Foundation to develop a municipal program encompassing economic development, local food systems, green built environment, and public health education. HOPE was unique in the diversity of stakeholders it brought together: city officials, non-profit workers, food justice activists, students, homeless people, and homemakers. Teams of Collaborative members surveyed six “micro-zones”, # mile radius areas surrounding central intersections in the six poorest flatlands neighborhoods, interviewing community members and surveying food prices and availability in local stores.

They also conducted several community listening sessions and design charettes and funded an inventory of vacant land in Oakland with agricultural potential which has since been used by the OFPC and Oakland Climate Action Coalition to support their recommendations.95 HOPE continues to serve as the community engagement arm of the OFPC.While Oakland briefly seemed to be a national leader when it came to formally expanding urban agriculture thanks to the release of the Oakland Food System Assessment, the activity of the HOPE Collaborative, and the creation of the OFPC, municipal interest in urban agriculture briefly waned. The election of Ron Dellums as Oakland mayor saw the dissolution of the Mayor’s Office of Sustainability and the city’s entire sustainability program was shifted onto the shoulders of one man in the Public Works Department. Other cities soon took up the mantle, making strides in urban agriculture policy: Seattle, for example, declared 2010 as the “Year of Urban Agriculture” and passed a sweeping overhaul to allow the expansion of urban agriculture ; Cleveland legalized livestock ownership and committed $1.1 million to a pilot urban farm . In San Francisco, efforts to scale up urban agriculture through policy reform gained momentum, as well, ironically due to the visibility of urban agriculture across the Bay. Mayor Gavin Newsom actually announced his Healthy and Sustainable Food for San Francisco Directive in July 2009 standing in front of City Slicker Farms’ WOW Farm in West Oakland, “a junkyard-turned-farm in West Oakland that could serve as a model for how land could be converted in San Francisco” . The Directive signaled municipal commitment to improving the food system, and specifically addressed the importance of encouraging urban agriculture through “community, backyard, rooftop, and school gardens, edible landscaping, and agricultural incubator projects” and ordered all city departments “having jurisdiction over property [to] conduct an audit of land suitable for or actively used for food producing gardens or other agricultural purposes” , a response to public pressure to facilitate urban agriculture on the city’s more than 3,000 privately owned and 2,000 publicly owned vacant lots in the city . In the year and a half that followed, an umbrella organization of urban agriculture activists called the SF Urban Agriculture Alliance , working in conjunction with the SF Food Policy Council , pushed through one of the nation’s most comprehensive pieces of urban agriculture legislation: Ordinance 66-11. Passed by the City’s Board of Supervisors in April 2011, it greatly expanded the area where urban agriculture is permitted in San Francisco and allowed sales of produce by home gardeners . Back in Oakland, despite the dragging of feet by the Dellums administration, interest in urban agriculture is slowly managing to take root within City Hall. These changes were due to the activity of the OFPC whose recommendations received airtime during the 2010 mayor race. At-Large Council Member Rebecca Kaplan, during her bid for election in the 2009 mayoral race, included food issues in her platform and has consistently advocated for adopting the OFPC’s recommendations. While she did not win the election, she continues to advocate for progressive food system overhauls from her seat on the Council, including the expansion of urban agriculture in the city. At the January 2011 presentation of the OFPC’s Transforming the Oakland Food System report to a Council sub-committee, Kaplan lobbied the committee to support the OFPC’s recommendations for urban agriculture zoning changes.

Such coping mechanisms generally shift an additional burden onto the shoulders of urban women, in particular . In addition to expending her energy on food production and jobs in the informal economy, a female farmer may also divert income earned from sale of surplus produce towards the purchase of additional ingredients for a meal; as a Senegalese extensionist explains, “Whatever a woman earns [from her gardens] goes directly into the cooking pot” . A straightforward Marxian analysis of the combined impact of low wages and dispossession from the land can largely explain the rise of urban agriculture and its continued presence in the Global South. Indeed, primitive accumulation is ongoing as Southern countries integrate more fully into the global economy and communally managed property “enclosed” by titling arrangements and emerging land markets. In the North, however, such processes happened longer ago; it is therefore helpful to draw also on the work of Karl Polanyi in order to understand how social rift has produced urban agriculture in the North. Polanyi describes in detail how land, labor, and money are bought and sold as “fictitious commodities”, fictitious because they were not produced to be sold as a commodity. Under the expansion of laissez faire economic liberalism, they are increasingly subject to the whims of the free market . In times of economic crisis, when the market value of the fictitious commodities fluctuates dramatically, an “avalanche of social dislocation” tends to follow . Wages left to laissez faire or free market logic decline as surplus labor enters the market , round flower buckets depressing wages which lowers work and living standards .

Land—and by extension natural resources—valued only as a production input or commodity for exchange can be over-exploited for short-term gain with little consideration of its long-term productivity. In sum, “leaving the fate of soil and people to the market would be tantamount to annihilating them” . To protect people from extreme social dislocation, a “protective counter-movement” inevitably arises which ranges in form from communal networks of support to government intervention and regulation. With the rise of rapid urbanization during the industrial era, urban agriculture repeatedly arose as part of a counter-movement to protect the population from the social dislocation resulting from “leaving the fate of soil and people to the market.” Subsistence food production was part of the American and European urban landscapes well into the 20th century. As urban areas developed during industrialization, urban agriculture often served as a coping strategy, significantly subsidizing the social reproduction of workers as in the South today. In Britain, the Commons Act of 1876 and various Allotment Acts obliged local governments to provide citizens with space for food production . In the US subsistence production was actively practiced and encouraged well into 20th century in urban centers such as Los Angeles, where chickens, pigs, beans, and tomatoes were common sights in the small yards of worker housing . Community gardens in the US and allotment gardens in the UK grew in number during times of economic hardship and austerity, but not due to household coping alone. Governments often orchestrated the growth of urban agriculture during these crisis periods as a part of a coordinated protective measure. Urban food production served not only to buffer food security, but also to quell potential unrest .

As America industrialized in the late 19th century, a growing pool of unemployed gathered in urban areas. Municipal governments provided garden plots and seeds to stave off hunger and unrest. During the Depression of 1893, the mayor of Detroit launched a so-called Potato Patch plan—later adopted across the US—to provide the unemployed with vacant lots between # and 1 acre each. More than 1,500 families farmed small vacant lots between an eighth- to a half-hectare each on 455 acres . Gardens were intended not only to provide food and employment, but also to create self-respect and to help assimilate recent immigrants. During the Great Depression urban agriculture again provided food and jobs for the masses of unemployed. The New Deal Federal Emergency Relief Administration spent $3 billion on relief gardens between 1933 and 1935 alone. One gardening program in New York City transformed 5,000 vacant lots into highly profitable gardens by 1934 . Garden programs also exploded during wartime. Liberty gardens proliferated in the US during the First World War as a government response to the food riots gripping the nation. Under the guidance of the National War Garden Commission, more than 5 million gardeners cultivated “idle” land. During World War II, under the National Victory Garden Program 20 million gardens produced 40 percent of America’s food by 1944. During the economic recession of the 1970s, “inflation” gardens flourished in America’s inner-cities with a boost from the back-to-the land ideals of the environmental movement and the USDA’s $1.5 million Urban Gardening Program.

During this period community gardeners and activists took over thousands of vacant lots left fallow as industrial and residential capital abandoned US cities . The discourse of crisis driving these programs was used not only to justify urban agriculture, but also to denigrate it as an act of welfare for the poor once crises had passed. As such, crisis discourse helped to obscure the subsistence role that urban agriculture has always played in urban landscapes, as well as to devalue urban agriculture in times of prosperity . Indeed, when the economy improves and adjacent land values rise, urban agriculture is no longer seen as a public good but an obstacle to development. In New York’s Lower East Side during the 1970s, for example, municipal government promoted community gardens as “a productive use of land considered to be relatively useless.” The gentrification of nearby SoHo in the 1980s, however, led to rising land values and a growing interest in development, and eventually to a moratorium of leasing vacant land for gardens and the bulldozing of several squatter gardens. Tensions also arose within the community over whether to use vacant lots as space for gardens or for low-income housing . These tensions between development and urban agriculture are often racialized, as in the case of the South Central Farms. The 14-acre community garden was originally established in 1993 by the Los Angeles Regional Food Bank in an effort to bring healthy food to the impoverished neighborhood. In the now famous case, the gardens were bulldozedin 2006 following a long and nasty legal and political battle between Latino/a activists, a black city councilor, and a white Jewish land owner . 31 Urban agriculture’s relation to social rift does not lie with land alone. Food, even while produced as a commodity in the capitalist agri-food system, functions in a similar manner to Polanyi’s other fictitious commodities. Understanding food as a fictitious commodity like land further clarifies urban agriculture’s ability to mend social rift. Its treatment as a simple commodity to be bought and sold according to market logic effaces the complex weave of relations running through its production, distribution, preparation, and consumption. The rapid transformation of the agri-food system during the 20th century was due in large part to the expanded commodification of food, from patented seeds to artificial ingredients and fast food restaurants. As food has become increasingly processed and packaged, the culture and traditions surrounding food production and consumption have gradually been obscured by the market based ideology of cheap food . The socio-cultural significance of food and agriculture rarely factors into calculations of profit margins; certain social relations woven into the agri-food system—agricultural and culinary knowledge and its cultural significance, for example—are impossible to quantify and either resist commodification or are erased by a commodified agri-food system. Since the middle of the last century, plastic flower buckets wholesale the commodification of food has systematically unraveled many of these existing social relations and created new commodity-driven relations of production and consumption that “undermine the source of all wealth—the soil and the worker” at multiple scales . Farming has evolved into a highly-specialized industry based on inputs and outputs and which engages less than 2 percent of the U.S. population; over-application of agri-chemicals have poisoned farmworkers and created a massive “dead zone” in the Gulf of Mexico; agricultural and culinary knowledge have been lost; diabetes, heart disease, and obesity have followed on the heels of junk food consumption worldwide. As a protective counter-movement, urban agriculture attempts to mitigate social rift by de-commodifying land, labor, and food. Various case studies in North America have illustrated how gardens are a site of interaction between various ages and ethnic groups, where knowledge about food production and preparation is shared and community ties strengthened .

Urban agriculture produces new commons, by returning—at least partially—the means of production to urban populations. The verdure emerging from cities’ marginal spaces—road medians, infrastructure rights of way, vacant lots, wasteland—signals both a reclamation of what remains of the commons and the creation of new commons from the interstitial spaces skipped over by capital or left fallow in its retreat. While the forces giving rise to it differ between the Global North and South, urban agriculture joins together these tiny tesserae into a fertile mosaic in both places, where gardens grown along the abandoned railroad right of way in Detroit are not unlike those growing alongside rusted rails in Bamako. Goats and cattle graze weeds growing up amid the cement blocks and rebar of all-but-abandoned buildings. A bean patch is tucked in the 3-meter wide strip of road shoulder between the asphalt and the wall of a government building. An abandoned racetrack is a patchwork of vegetable gardens irrigated from a nearby drainage ditch. Industrial brown fields in the US and Europe are transformed into urban green space dotted with community gardens .Social and ecological dimension alone cannot fully explain the rise of urban agriculture in the North. For many, a certain lifestyle politics drives the attraction to the urban farming; “getting in touch with nature” or “learning where our food comes from” are common tropes. As a broader social rift is cleaved by the commodification of land and labor, people experience an internalized dimension of metabolic rift, which I refer to as “individual rift”. Essentially what Marx called alienation from labor and from nature, it manifests as the perception of self as external to the environment. While this dimension of metabolic rift is perhaps the most difficult to overcome due how deeply rooted it is in the social processes outlined above, individual rift can be addressed—and potentially overcome—through urban agriculture more easily than can other forms of rift precisely because it arises at the level of the individual consciousness. Two interrelated forms of alienation are central to individual rift: alienation from labor and alienation from nature. First, individual rift arises from our alienation from the fruits of our labor. As discussed above, the social rift in metabolism arises from the commodification of labor and the separation of the worker from the means of production . What this means is that under capitalist production a wage laborer no longer owns the finished product he or she creates. Rather than producing something for his or her own use, the worker produces it for the capitalist to sell as a commodity to earn profits used to fuel further accumulation. As Sohn-Rethel argues, the root of this alienation lies in the division of intellectual and manual labor, a long historical process cemented at the dawn of capitalism via the rationalization of labor and which intensified individual rift.33 The later “Balkanization of knowledge” into social and natural sciences encouraged the division of labor, further alienating humans from nature as a result of the “inadequate understanding of how these knowledges connect with one another in the process of producing the concrete outcomes in which we are interested” . Due to this division of manual and intellectual labor, the rationalization of production through technological advances and the de-skilling of labor has further alienated the worker from the product and the whole process of production. In short, the more that science enters into production, the less the worker understands about the process of production and the more his or her creative capacity is undermined . Second, the separation from land as discussed in the previous section is central to individual rift. From both ecological and Marxian perspectives, humans simultaneously shape and are shaped by the ecosystems to which we belong. More specifically, we are the nature around us. Nature is, Marx theorized, integral to human life and development .

Additionally, our study provides valuable insight into areas of greatest risk for dieback and mortality, which are predominantly in lower elevations. These are important factors to consider when predicting vulnerabilities and potential impacts of future extreme drought events . Mediterranean shrublands like those in southern California already considered high risk for global-change type drought, , and research suggests a general trend of upwards-shifting ranges in southern California chaparral species driven by changes in climate . Therefore, populations of A. glauca occurring at the lower edge of their natural range are at high risk for dieback and mortality, and should be the focus of management efforts. Lastly, while studies on the various physiological mechanisms for plant survival during drought are critical for predicting differential responses to stress, there is an increased emphasis on the importance of understanding the diverse role of pathogens in order to accurately model species vulnerabilities to climate change . Studies that incorporate the impact of pathogens help inform new integrative approaches to protecting plants against drought and biotic infection, rather than treating these influences separately. Examples include Jactel et al., , whose meta-analysis showed the significant effects of water stress on symptom severity in plants infected with latent pathogens like Bots, and experiments like Drake-Schultheis et al. , procona system who found interactive effects between drought stress and infection from N. australe in driving symptoms of stress and increasing mortality rates in A. glauca.

The results of our study align with these frameworks, and provide additional evidence that as climate change models are predicting more intense and frequent drought events, our need to understand the role of latent pathogens in at-risk natural systems is becoming more critical.Reports of large-scale, drought-associated mortality events in forest and woodland systems have been on the rise in recent decades . These reports have spanned across biomes, including in classically drought-tolerant species across Europe , Australia , Africa , and the United States . As a result, interest has been growing in understanding how species that are typically capable of withstanding periodic drought stress may become susceptible to drought and experience significant dieback and even large-scale mortality when exposed to acute or prolonged chronic drought . These droughts of unusual extremes are referred to as “globalchange-type drought” and are becoming more common as the climate warms . While the exact physiological mechanisms leading to dieback and mortality during such events are variable across species and conditions, drought is generally hypothesized to promote physiological decline either via loss of hydraulic functioning or carbon starvation or a combination of both . In the case of hydraulic failure, plants with insufficient soil water experience xylem cavitation , which can ultimately lead to cellular death. Alternatively, plants that avoid drought by closing their stomata to reduce water loss subsequently suffer insufficient carbon supply to meet other metabolic demands. In either scenario, the stress that drought places on a plant is likely to cause measurable decreases in physiological functions that may be irreversible .

An additional factor that can play a significant role in drought-related dieback and mortality is the presence or introduction of biotic agents. Indeed, introduced plant pathogens have been well documented to cause canopy dieback and dramatically alter community structure in a variety of forested systems . Some well-known examples in the United States include Dutch elm disease , chestnut blight , white pine blister rust , and sudden oak death . Significant pathogen events have also impacted the landscape in wild land shrub communities including sclerophyll shrub woodlands in Australia and salt desert scrub in the western United States . However, large-scale dieback of shrubs has been less documented than their arboreal counterparts, despite evidence of disease from fungal species being abundant in many scrubland systems including southern California chaparral , northern California foothill shrublands , and South African fynbos . Such studies, along with expectations of increasing threats from pathogens due to climate change and accelerating trade/movement of biological materials globally , have led scientists and land managers alike to anticipate introduced pathogens as important contributors to future changes in wild land communities.While both global-change-type drought and pathogens are likely important contributors to plant dieback and mortality, current research suggests that these two factors are not mutually exclusive . Rather, canopy dieback and mortality may result from the combined influences of environmental stress and biotic agents, and theoretical frameworks describing these influences have been put forth .

These frameworks incorporate biotic agents into the drought-hydraulics complex described above, whereby pathogens and insects may amplify or be amplified by drought-associated hydraulic failure or carbon starvation . Amplification can occur when biotic agents damage host tissue—by defoliation or blocking transportive vessels, for example—to the extent that the effects of drought are greatly exacerbated . Alternatively, physiological responses to extreme environmental stress can have negative effects on plant defense systems, rendering them susceptible to mortality through biotic infection . In both scenarios, the effects of biotic agents and drought stress are strongly linked, and these interactions have been well documented in drought-tolerant systems such as South African fynbos , red pine forests , eucalyptus forests , and California chaparral . Latent or secondary pathogens are particularly likely to be involved with dieback and mortality events in these systems, as they are known to increase damage in hosts experiencing drought stress . Therefore, while drought events alone are expected to play an important role in reshaping ecosystems as the climate changes, in some cases, synergies between environmental stress and biotic influences might lead to shifts in plant community structure and composition, and thus ecosystems as a whole. In the Santa Ynez Mountains in Santa Barbara County, California, United States, big berry manzanita began exhibiting dramatic canopy dieback during the 2011–2018 drought . Shrubs in the genus Arctostaphylos are common in Mediterranean shrub communities extending from southwest Oregon to northern Baja California . They may occur in monospecific stands or in alliances with other important community members like chamise and Ceanothus spp. . Within these alliances, Arctostaphylos spp. frequently occupy >50% average cover , which along with their nutritious and prolific fruits, and fire-induced regeneration strategies, make them one of the most important members of the chaparral community . In the southern California chaparral ecosystem where hot, dry summers with high vapor pressure deficit are the norm , seasonal drought tolerance has long been considered a common strategy among dominant plant species, including A. glauca. However, the severity of recent canopy dieback observed suggests that this species is reaching a threshold in its drought-resistance capability. Concurrent with observations of canopy dieback, visible symptoms of fungal infection were observed including wood cankers and leaf discoloration , both ofwhich progress during prolonged drought stress, suggesting that multiple driving forces contribute to manzanita dieback. Molecular sequencing identified the dominant fungal pathogen found on symptomatic A. glauca in this area to be Neofusicoccum australe, a member of the well-known pathogenic Botryosphaeriaceae family . Members of this family are most commonly associated with disease in plant species experiencing severe environmental stress , including Arctostaphylos spp. . They are also known to play a variety of functionally diverse roles, from asymptomatic endophytes to obligate pathogens . Yet, while N. australe has been described around the world , relatively few studies have been conducted on its specific interactions with host species, procona valencia buckets as it was only fairly recently described . Historically, Bot. pathogens have most frequently been studied in agricultural host species , and little is known regarding their ecological role in wildland ecosystems , especially with regards to chaparral shrubland systems . The present study was aimed at identifying the possible role of N. australe in A. glauca dieback in Santa Barbara County, particularly in combination with extreme drought. Because this pathogen has only recently been reported on wild shrub species in California and is thought to be an introduced species native to Western Australia , this outbreak represents a new and undescribed threat to these wild land plant assemblages. This study addresses the following questions: How does A. glauca respond physiologically to drought and fungal infection, separately and together? 

Are these responses correlated with visual signs of stress, specifically leaf health? Can drought and fungal presence interact to increase or accelerate plant mortality compared to drought or fungi alone in A. glauca? To address these questions, a greenhouse experiment was conducted in November 2016 through February 2017 manipulating both drought and fungal infection and observing trends in plant stress symptoms, physiological function, and mortality. We predicted that both drought stress and fungal infection would lead to declines in physiological function compared to the control and that these declines would be strongly correlated with increases in stress severity. Furthermore, we expected that those individuals experiencing both drought stress and fungal infection would die sooner than those in all other treatment groups. This experimental study elucidated the potential of the interaction between drought stress and introduced pathogens to significantly impact chaparral shrub health and important implications for the future of these shrubs faced with increasingly frequent globalchange-type droughts. A completely randomized full-factorial design was used to organize the individuals into four treatment groups: droughted and inoculated with N. australe , droughted and not inoculated , watered and inoculated with N. australe and a control; watered and not inoculated . Data were collected for ~90 days to track declines in health and mortality rates among the different treatments. Drought-treated plants received 1 L of water on the day of inoculation and another 0.5 L on day 38. Those with no drought treatment received 0.5 to 1.0 L of water by hand once per week depending on soil moisture, which was monitored regularly using a TDR machine from Soil Moisture Co. . Soil moisture for non-drought plants was maintained between 15–25% moisture for the entire experiment. Cultures for inoculations were made from re-isolations of field samples that were collected in January 2016 and positively identified to be N. australe . Inoculations took place on 3 November 2016 , using methods adapted from Michailides and Swiecki and Bernhardt . Mycelial plugs were made from 8-d-old cultures growing on half strength potato dextrose agar amended with streptomycin to prevent bacterial contamination. Plants were first sprayed with 70% isopropyl alcohol to sterilize the surfaces and surrounding areas. Mycelial plugs were taken from the advancing margin of N. australe cultures and placed on strips of Parafilm using sterile petroleum jelly for adhesion. Plugs were then placed to superficial wounds made on the main stem . The Parafilm strips were then gently wrapped 2–3 times around the stem to keep the plugs in place and prevent contamination. Those plants not receiving fungal inoculation received a control inoculation with uncultured potato dextrose agar using the same techniques. To confirm Koch’s postulates, the standard criteria to determine the agent causing a disease , we reisolated fungi from stem tissue at least 2-cm above the point of inoculation in harvested plants, amplified using primer pairs ITS1F/ITS4 for the ITS and EF1-728F/986R for alpha-elongation factor-1 . They were sequenced using the protocol described by Schultheis et al. . Greenhouse conditions were set to reflect summer conditions in Santa Barbara. Daily temperatures were maintained between 18–30°C during the day and 10–15°C at night. Humidity maintained at 50%. Photosynthetically active radiation lights were set to provide 14 h of daylight per day and a maximum of 2000 µmol. Plant positions were randomized weekly using a random number sequence generator to eliminate any microclimate effects in the greenhouse. Physiological stress due to drought and pathogen infection was inferred from weekly measurements of net photosynthesis and dark-adapted chlorophyll fluorescence using a LI-COR 6400XT and Hansatech FMS2 system fluorometer , respectively. Leaves were dark-adapted using leaf clips for 20–30 min before measuring fluorescence. One healthy , fully expanded leaf per plant, or on one healthy and one stressed/diseased leaf per plant if symptom onset had begun . All data were collected between 10:00 hours and 16:00 hours to capture peak values for the day, with the majority of measurements taken between 10:00 hours and 12:00 hours. Due to mechanical issues, chlorophyll fluorescence was not measured on 4 and 11 November and on 20 December 2016. Net photosynthesis and dark-adapted fluorescence were chosen as proxies for plant health, as lower values correlate strongly with higher levels of drought stress .

Future research projects could also benefit from a larger sample size to analyze farm-level differences and whole genome sequencing of positive isolates to ascertain any genetic relatedness between livestock species or between farms, as well as presence of antimicrobial resistance genes. In Chapter 2, the risk map determined regions at highest risk for contact between feral pigs and outdoor-raised pigs, and these areas will be important to target surveillance and outreach, in the case of future disease transmission between these two swine groups. This project can be expanded nationwide to create awareness of high-risk contact and potential disease transmission areas, to protect both public health and agriculture in the US. For example, this risk map could be used to plan surveillance programs to prevent transmission of imported diseases to the US, such as African Swine Fever that was recently detected in the Dominican Republic, or prevent the spread of reemerging diseases like pseudorabies, which was detected in feral pig populations in Mendocino County, CA in 2015. A 2015 report by the European Food Safety Authority concluded that surveillance programs will be key in preventing the introduction and spread of ASF in North America and other naïve countries. Additionally, if feral or outdoor-based domestic swine disease location data were readily accessible in the US, additional risk maps could predict the spread of specific pathogens. Disease risk maps are useful to support decision making for agencies focused on wildlife management and conservation as well as animal and public health.

Currently, USDA collects data through surveys for swine operations only in the top 16 producing pork states in the US, and California is not included, raspberry grow in pots which reduces available data for disease risk models. However, the swine NAHMS is due to be conducted again in 2021 with a larger focus on small-scale swine operators. Another avenue for future research entails using covariate rasters from specific years or decades to predict the distribution of a feral pigs. Few SDM or MaxEnt comparison projects have compared temporality of covariate rasters for model prediction accuracy. Shifts in weather patterns, as well as the dynamics of large fires, will most likely be exacerbated by climate change and will affect wildlife movements and locations in the future, which may indicate the importance of choosing temporally-specific variables for model building. Additionally, if climate change and wildfires accelerate in California, current static rasters may become inaccurate in predicting future suitable habitat. California’s annual precipitation levels fluctuate between drought and excessive precipitation associated with El Niño and La Niña events. Climatologists predict volatility of rainfall patterns and temperature for California, which may affect suitable habitat for wild mammals such as feral pigs, and emphasizes the need for dynamic climate rasters. Both the MaxEnt model and risk map in Chapter 2 are limited because they are static maps that used fixed layers as their foundation; consequently, they do not incorporate dynamic events. Future species distribution models could incorporate temporal environmental patterns into models, due to dynamic changes over time, especially in regions like California where climate change and large wildfires can affect the distribution of certain species.

For instance, Snow et al used temporally dynamic prediction models and examined three decades from 1982 to 2012 to report evidence of feral pig expansion due to climate change. Also, feral pigs in Canada build “pigloos” to be able to survive the harsh Canadian winters, expanding their habitat northward. A 2015 study on climate change affecting wild boars in Europe also reported that milder winters allow for expanded abundance of these mammals.. Additionally, feral pigs may migrate seasonally due to food and water availability in California, therefore future projects could incorporate migration patterns and develop risk maps for specific time periods as Lee et al conducted with waterfowl species, although these data are not available yet for most predictors in California. Building real time dynamic risk maps that incorporate remote sensing data, such as satellite information, could be the next step in predicting high-risk disease transmission areas, as built previously for avian influenza by the California Waterfowl tracker. However, tracking birds may be easier than collaring feral pigs. Chapter 3 combined aspects of Chapters 1 and 2, by determining the prevalence of STEC in feral pigs that reside near domestic swine raised outdoors and predicted possible areas of contact between these two swine populations. Both multilevel logistic models in Chapters 1 and 3 identified outdoor-raised livestock with access to wild areas, such as wetlands or forests, as a significant risk factor for the presence of STEC in samples. One possible pathway for shared pathogens in wild areas may be wildlife contaminating food or water, which are then consumed by livestock. Additionally, Chapter 3 results could be improved upon by using WGS to analyze relatedness between feral pig and domestic pig samples. Although the pathway for pathogen spillover can be bi-directional and temporality may be unclear, identifying clusters of shared indicator pathogens is an important next step in analyzing disease risks from feral pigs in California and nationwide. Chapters 2 and 3 analyzed feral pig populations and their risk to farms that raised domestic swine outdoors.

In Chapter 3, 45.45% of survey respondents observed feral pig presence on their farm, with 36.36% stating that feral pigs had direct contact with their domestic pigs in pastures, pens or barns. These results match the risk map from Chapter 2, which overlapped predicted suitable habitat for feral pigs and OPO locations and showed that 49.18% of the 305 OPO identified in California overlapped with suitable feral pig habitat, indicating that spillover of an emerging or transboundary disease is possible, given the correct drivers. We know human or livestock encroaching into tropical forests are drivers for zoonotic diseases such as COVID-19 or Nipah Virus, usually with an intermediate host such as bats. Although emerging zoonotic diseases in many cases originate at the interface of wildlife-livestock-humans, the US is not considered a hot spot for zoonotic disease outbreaks according to Daszak and the EcoHealth Alliance , yet zoonotic pathogen outbreaks can still occur. Possible drivers of disease spillover in the US between feral and domestic pigs raised outdoor include density of animals, shared natural areas between domestic and wildlife and increasing contact between these two growing swine populations. As the number of DSSF farms continues to grow, continued evaluation of risk factors and agricultural management practices that are unique to these small operations will identify additional risk mitigation strategies and develop extension outreach materials to keep food safe from farm to fork and protect California’s agricultural economy. Additionally, as the two parallel trends nationwide of expanding feral pig populations and outdoor-based domestic swine continues, disease surveillance of feral pigs located near outdoor-raised domestic swine is key in preventing transmission of emerging or reemerging pathogens in the future.Encouraged by consumer preference for local foods and willingness to pay more than double the price for local products , both large and small-scale farming is increasingly turning to direct markets through you-pick operations, farm stands, farmers’ markets, 30 planter pot and Community Supported Agriculture . Currently, nearly 7% of U.S. farms are involved with direct marketing with an 8% increase in sales since 2007 . The federal government began tracking the number of farmers markets in 1994 and CSAs in 2007. The number of farmers’ markets has more than doubled in the past decade, rising to 8284 in 2014 from 3706 in 2004 . Local food is also increasingly promoted through food hubs and sales to restaurants and grocery stores . Numerous practitioners of planning, land-use management, policy and economic development encourage local food programming . ‘Buy Local’ campaigns have been codified in every state with branding and are buoyed through formal and informal economic development support in comprehensive planning documents. With its growing popularity, the local food movement is expected to change both consumers and farmers. The movement often emphasizes ‘weak social ties’ created through food as bringing together novel constituents for political persuasion which combines purchasing power with the ‘soft power’ of a social movement. Where markets should emphasize the highest financial returns, economic sociologists have noted their non-economic logic , terming them ‘embedded’ in both geographies and social value systems . Hinrichs states that part of what direct marketing producers sell is “social connection. Local embeddedness itself then becomes some of the value added in the farmers’ market experience” .

Embeddedness describes the noneconomic logic of how markets yoke together two separate geographies through shared economies and social values . This research asks: what is the extent and orientation of embeddedness in the local food system? First, a literature review demonstrates the current understanding in the field and the need for new methodologies to help test theories of embeddedness within local food systems. Namely, the local food movement is expected to transmit values through proximate economic and social networks. But which communities are connected, and across which local marketing strategies? In response to this question, I pilot a method for mapping the local food system socially and spatially. Document review and program director interviews help to verify and explain the findings as well as their consequences for food systems planning and economic development.Local food activists have reconceptualized food supply chains as a means of spatially distributing social values by leveraging economic capital. The values encompassed by the food system are exemplified by the over 300 different labelling schemes which promote fair labor, sustainable land-use, and animal welfare practices to name a few . Yet, only a few global corporations control distribution, connecting consumers to producers . This bottleneck in supply chains reveals an important lever for altering geographies and financing shared value systems. Renting et al. asserts that shortening the supply chain by decreasing the number of intermediaries involved in production, distribution, processing and purchasing should clarify the values and geographies involved. In sum, geographically explicit, personal relationships between producers and consumers are expected to raise awareness about social, economic, and environmental effects of food consumption by tightening feedback loops which concentrate economic and social capital toward values-based goals . Hinrichs cautions that even the shortest supply chains, such as direct marketing from farms to consumers, can have varied power structures. Namely, farmers often travel to cities for farmers’ markets, while consumers travel to farms in which they own a share of the commodities produced in the CSA model. Hinrichs asserts that while both supply chain typologies emphasize direct, local consumer relationships with farmers, the resulting geo-social embeddedness of the network and the values it promotes will fundamentally differ. In addition, local values-based supply chains are not limited to direct-marketing. Nearly 50,000 farms in 2012 sold some or all of their products directly to retail outlets such as restaurants, grocery stores, schools, hospitals, or other businesses that in turn sold to consumers . Intermediaries between farms and consumers can also play important roles in food system-based social change. For example, chefs, like Alice Waters of Chez Panisse in California, are often seen as the forefront of the local food movement where they change consumer demand for certain types of local food. In the process, their search for ingredients resulted in direct contracts with farmers to grow specific products using agroecological methods . Similarly, farm-to-school programming is conceptualized as a means of encouraging healthy eating, transferring farming education to the next generation, and preserving local farming land-uses . Sonnino finds that school food reform in the UK gave small producers access to new income streams while offering students food that is more nutritious. Similar rationales underpin the motivations behind promoting regional food hubs . Planning practitioners have also noted that public procurement anti-hunger efforts that champion local food have had a successful track record of protecting farmland, spurring rural economic development and increasing urban food security in Canada and Belo Horizonte, Brazil . Most importantly, the geo-social embeddedness of food systems may not be driven solely by food purchases. In addition to supplying food, farms serve numerous socio-ecologic functions for urban users and nearby communities . In 2012, over 33,000 farms listed income from agritourism and recreational services such as farm tours, hayrides, school visits, and other activities . A review of the mission and vision statements from 130 nationally accredited farmland preservation agencies notes that ecosystem, social and cultural services are among the top reasons for preserving farmland, ranking far above food supply .

All these findings highlight the need for further investigation to identify high-risk areas for disease spread in the event of a future disease outbreak in California or nationwide. My overall thesis goal entailed evaluating the risk of STEC on DSSF and the risk of disease transmission in the spatial overlap of feral pigs and domestic swine raised outdoors in California. In Chapter 1, we collected fecal samples from cattle, goats, sheep and pigs raised on DSSF to estimate the prevalence of STEC on these unique operations. I used a multilevel logistic regression model to assess the association between risk factors and STEC presence in fecal samples. In Chapter 2, I used a species distribution modeling method Maximum Entropy to predict suitable habitat for feral pigs in California. Then I overlapped this MaxEnt model with the location of over 300 OPO in California to create a risk map that identified areas most at risk for disease transmission between these two growing swine populations. The increasing potential for contact between domestic swine raised outdoors and feral pigs provides an opportunity for the widespread transmission of diseases throughout California, as each pig could serve as a link in the transfer of pathogens between wildlife, livestock and humans. Additionally, the transmission of diseases to domestic pigs raised outside could negatively impact the sustainability of California’s agriculture economy. In Chapter 3, I designed a study to evaluate the prevalence of STEC in six counties at highest risk for contact between feral pigs and OPO, large plastic garden pots based on the risk map built in Chapter 2. I collected fecal samples from both feral pigs and domestic pigs raised outdoors and used a multilevel logistic regression model to assess risk factors associated with the presence of STEC in samples.

The results of these last two chapters fill critical information gaps regarding the epidemiology of STEC harbored in outdoor-raised pigs on DSSF located near suitable feral pig habitat. The increasing number of diversified small-scale farms that raise outdoor-based livestock in the United States , reflects growing consumer demand for sustainably-produced local foods, including animal products such as meat and eggs. California is the top producer of agricultural products in the US and also leads the country in organic food sales, which includes products from DSSF However, there is a lack of science-based information characterizing the risk factors associated with the prevalence of food borne pathogens, such as Shiga toxin-producing Escherichia coli , in livestock raised on DSSF. Diversified farms are most often small-scale and raise a combination of livestock and numerous types of produce or multiple livestock species, with the intent of selling specialized animal products directly to consumers. Some diversified farms integrate livestock and crop production by using their animals to graze crop residues or cover crops before planting a field to fresh produce. Grazing improves soil fertility and provides farm owners with another source of revenue through fiber or meat products. Many consumers perceive produce grown on small-scale farms and/or meat raised on pasture as more “natural” or safer than food grown on large-scale conventional farms or meat animals raised in confinement systems. However, livestock are asymptomatic reservoirs for food borne pathogens and without adequate mitigation strategies, these pathogenic microorganisms may enter into the food supply. Livestock are intermittent shedders of enteric pathogens and shedding may increase under certain conditions, such as during periods of stress , due to certain management practices or seasonally.

Foodborne pathogens survive in the soil for extended periods of time and can spread to humans directly through contact with livestock or indirectly via contaminated food or water.For instance, cattle grazing uphill from a produce field was likely the causative factor for the 2019 E. coli O157:H7 romaine lettuce outbreak. STEC remains one of the top enteric pathogens associated with food borne outbreaks in the US. The top seven STEC O-serogroups that cause the most severe illness in humans have been traced to consumption of produce consumed raw, such as spinach, tomatoes and melons. Fresh produce consumed raw , which has been contaminated by livestock or wildlife feces containing STEC, can become a vehicle for these pathogens to enter the food supply. The aim of this study is to a) describe the unique characteristics of DSSF, b) estimate the prevalence of STEC in livestock raised on DSSF and c) evaluate the association between risk factors and the presence of STEC in livestock raised on DSSF located in California. Farms were visited twice between May 2015 and June 2016, once during each of the following periods: summer/autumn or winter/spring, which reflect California growing seasons and the seasonality of STEC shedding. Livestock species sampled in this study included dairy and beef cattle, dairy and meat goats, pigs and sheep. Sample sizes were calculated using Epitools based on the total number of animals on each farm, with an assumed STEC prevalence of 5% and 10% precision error, stratified by each livestock species. Individual fresh fecal samples were collected from the ground. Samplers wore gloves and placed approximately 50- 100 grams of feces into each sterile whirl-pak bag . Bags were immediately placed into plastic coolers containing ice packs, transported to the laboratory at the end of the sampling day and most samples processed within 24 hrs.

STEC was isolated from fecal samples as described previously with modifications. In brief, 10 grams of fecal material was placed in 90 ml Tryptic Soy Broth and homogenized before and after. Samples were then incubated for 2 hrs at 25°C with 100 rpm agitation, followed by 8 hrs at 42°C with 100 rpm agitation, and held overnight at 6°C, using a Multitron programmable shaking incubator . For detecting E. coli O157:H7, immunomagnetic separation using Dynal anti-E. coli O157 beads was performed on TSB enrichment broths with the automated Dynal Bead Retriever per the manufacturer’s instructions. After incubation and washing, 50 µL of the resuspended beads were plated onto Rainbow agar O157 with novobiocin and tellurite . Fifty µL of the resuspended beads were also plated onto MacConkey II Agar using sorbitol supplemented with potassium tellurite and Cefixime ; plates were streaked for isolation and incubated for 24 hrs at 37°C. Suspect E. coli O157:H7 isolates were confirmed using traditional PCR for the rfbE gene. To detect non-O157 STEC, 1 mL of pre-enrichment broth was incubated in mEHEC selective media for 12 hrs at 42°C followed by plating and incubating on Chromagar STEC . Up to 8 presumptive STEC positive colonies were confirmed for the presence of stx1 and/or stx2 genes by real-time PCR. Confirmed STEC isolates were then characterized for virulence genes using conventional PCR. After PCR testing, one colony from each positive sample was submitted to the Pennsylvania State University E. coli Reference Center to confirm O-serogroups.A 41-question questionnaire, raspberry plant pot consisting of mostly closed-ended questions, was administered to farm owners at the end of the study period. The questionnaire included sections regarding farm demographics, animal health, farm management practices, and water sources . Variables analyzed for model building included risk factors from the farmer questionnaire, sample day factors and variables that were created using known information about each farm, for instance, whether a farm raised multiple types of livestock or if they integrated livestock within produce fields before planting. Variables from the questionnaire included whether farmers allowed different livestock species to share the same barn and if livestock had contact with wild areas . Weather data from the nearest California Irrigation Management Information System weather station within a similar microclimate, provided environmental factors for possible model inclusion . Also, USDA plant hardiness zones, which are based on the average annual minimum winter temperature, were included as a proxy for the many microclimates in California . Only three zones were necessary to categorize our participating farms: zone 7b , 9a and 9b .Descriptive statistics, were calculated for all data. STEC was estimated for the overall study and per livestock species . Generalized linear mixed models were used to assess the association between STEC presence in fecal samples and risk factors. The binary outcome of interest was whether each fecal sample was STEC positive or negative. Univariate analysis assessed the distribution of variables. During bivariate analysis, variables with low variability, small cell sizes , or large standard errors were either modified, collapsed if appropriate, or discarded from model building. Correlation of numeric variables was measured with Spearman’s rank correlation coefficient; those variables that were correlated 0.80 or more were highlighted during the model-building phase to evaluate for multicollinearity issues. To identify possible confounders, each variable was evaluated using a directed acyclic graph and then added to the model to determine whether the variable affected the odds ratios of the other variables by more than 10%. The glmer function was used from the lme4 package in R to build models, with farm added as a random effect to account for possible farm-level clustering effects when analyzing individual samples.

Variance inflation factors identified possible multicollinearity and variables in the model that had a VIF over 5 were assessed for removal. Top models were compared, and a final model chosen based on the lowest Akaike Information Criterion , smallest deviance, relative to the other models. Intraclass correlation . Diagnostic plots from the DHARMa package in R were used to assess the final model and included fitted vs binned residuals, a Q-Q plot and the Kolmogorov-Smirnov test statistic. Odds ratios and 95% confidence intervals were calculated for variables in the final model. All data analysis was performed using R Statistical Software version 1.4.1036 ©.Of the 16 participating farms, two were not included in model building, as their questionnaires were not completed, leaving a total of 502 fecal samples for model building. The mean, median and range of selected numeric variables assessed for inclusion during model building are shown in Table 1.4. Farms in this study ranged from two to 500 acres and had been farming two to 30 years. Stocking rate was calculated by dividing the total number of livestock, excluding poultry, by the total number of farm acres . Selected categorial variables, stratified by whether they were STEC positive or negative are presented in Table 1.5.P -values were reported for chi-square test or Fisher’s Exact test if cell sizes were less than five. For instance, 28.99% of positive samples came from farms that mixed livestock species within a barn, whilst only 15.70% of negative samples came from farms with shared barns . Moreover, 72.46% of positive samples were from farms that allow livestock to have contact with bordering wild areas .This is one of the first studies to describe the unique characteristics of diversified small scale farms in California, while ascertaining significant associations between risk factors and the prevalence of STEC. This study detected STEC on more than half of the enrolled farms and in all the livestock species sampled. Moreover, O-serogroups isolated in this study included ones that cause serve illness in humans, including O157:H7, O26, O103 and O111. Significant risk factors associated with the presence of STEC included the daily maximum temperature, whether multiple livestock species shared a barn, the livestock source of the collected fecal sample, and whether livestock had contact with wild areas.Overall STEC prevalence measured for the 16 farms in this study was 13.62%. Six of the 16 farms had 0% STEC prevalence; however, due to the intermittent shedding of STEC which may be affected by many factors, this result does not necessarily indicate that they are free from STEC. Although STEC prevalence in livestock raised on large farms has been measured frequently in past studies, evaluation of STEC prevalence and associated risk factors estimated on DSSF is less common. However, a study conducted by USDA-APHIS collected fecal samples from dairy cows in 21 states and stratified E. coli O157:H7 prevalence between large dairies and small dairies and reported that small ranches had 29.4% E. coli O157:H7 and large dairies had 53.9% prevalence. Although this USDA-APHIS study indicated that small farms have less E. coli O157:H7 than large farms, the 29.4% prevalence they detected on small dairies is still larger than the 18.18% we identified in dairy cattle. Risk factors for the transmission of food borne pathogens on large farms may be different, especially if they only raise one crop or livestock type, instead of a diversity of species. One of our studies published in 2018 measured a 4.17% STEC prevalence in sheep raised on a mixed crop-livestock organic farm in California, which was lower than the 13.4% prevalence in sheep identified in this current study.

Reliable markers could aid in the decision of when to harvest the grapes. “Optimum” maturity is a judgement call and will ultimately depend on the winemaker’s or grower’s specific goals or preferences. A combination of empirical factors can be utilized including °Brix, total acidity, berry tasting in the mouth for aroma and tannins, seed color, etc. °Brix or total soluble solids by itself may not be the best marker for berry ripening as it appears to be uncoupled from berry maturity by temperature. Phenylpropanoid metabolism, including anthocyanin metabolism, is also highly sensitive to both abiotic and biotic stresses and may not be a good indicator of full maturity. Thus, color may not be a good indicator either. Specific developmental signals from the seed or embryo, such as those involved with auxin and ABA signaling, may provide more reliable markers for berry ripening in diverse environments, but will not be useful in seedless grapes. Aromatic compounds may also be reliable markers but they will need to be generic, developmental markers that are not influenced by the environment. This study revealed many genes that are not reliable markers because they were expressed differently in different environments. One candidate marker that is noteworthy is ATG18G . Its transcript abundance increased and was relatively linear with increasing °Brix and these trends were offset at the two locations relative to their level of putative fruit maturity . ATG18G is required for the autophagy process and maybe important during the fruit ripening phase.

It was found to be a hub gene in a gene subnetwork associated with fruit ripening and chloroplast degradation. Further testing will be required to know if it is essential for fruit ripening and whether its transcript abundanceis influenced by abiotic and biotic stresses in grape berry skins.The ultimate function of a fruit is to produce fully mature seeds in order to reproduce another generation of plants. The ripe berry exhibits multiple traits that signal to other organisms when the fruit is ready for consumption and seed dispersal. In this study, we show that there were large differences in transcript abundance in grape skins in two different locations with different environments, plastic seedling pots confirming our original hypothesis. We also identified a set of DEGs with common profiles in the two locations. The observations made in this study provide lists of such genes and generated a large number of hypotheses to be tested in the future. WGCNA was particularly powerful and enhanced our analyses. The transcript abundance during the late stages of berry ripening was very dynamic and may respond to many of the environmental and developmental factors identified in this study. Functional analysis of the genes and GO enrichment analysis were very useful tools to elucidate these factors. Some of the factors identified were temperature, moisture, light and biotic stress. The results of this study indicated that berries still have a “sense of place” during the late stages of berry ripening. Future studies are required to follow up on these observations. It appears that fruit ripening is very malleable. Manipulation of the canopy may offer a powerful lever to adjust gene expression and berry composition, since these parameters are strongly affected by light and temperature.

The ability of a genotype to produce different phenotypes as a function of environmental cues is known as phenotypic plasticity . Phenotypic plasticity is considered one of the main processes by which plants, as sessile organisms, can face and adapt to the spatio-temporal variation of environmental factors . Grapevine berries are characterized by high phenotypic plasticity and a genotype can present variability within berries, among berriesin a cluster, and among vines . Berry phenotypic traits, such as the content of sugars, acids, phenolic, anthocyanins, and flavor compounds, are the result of cultivar and environmental influences , and often strong G × E interactions . Although grapevine plasticity in response to environmental conditions and viticulture practices may provide advantages related to the adaptation of a cultivar to specific growing conditions, it may also cause irregular ripening and large inter-seasonal fluctuations , which are undesirable characteristics for wine making . Due to its complex nature, the study of phenotypic plasticity is challenging and the mechanisms by which the genes affecting plastic responses operate are poorly characterized . In fact it is often difficult to assess the performance of different phenotypes in different environments . It has been suggested that genetic and epigenetic regulation of gene expression might be at the basis of phenotypic plasticity through the activation of alternative gene pathways or multiple genes . Epigenetics has been proposed as crucial in shaping plant phenotypic plasticity, putatively explaining the rapid and reversible alterations in gene expression in response to environmental changes. This fine-tuning of gene expression can be achieved through DNA methylation, histone modifications and chromatin remodeling . Small non-coding RNAs are ubiquitous and adjustable repressors of gene expression across a broad group of eukaryotic species and are directly involved in controlling, in a sequence specific manner, multiple epigenetic phenomena such as RNA-directed DNA methylation and chromatin remodeling and might play a role in genotype by environment interactions.

In plants, small ncRNAs are typically 20–24 nt long RNA molecules and participate in a wide series of biological processes controlling gene expression via transcriptional and post-transcriptional regulation . Moreover, small RNAs have been recently shown to play an important role in plants environmental plasticity . Fruit maturation, the process that starts with fruit-set and ends with fruit ripening , has been largely investigated in fleshy fruits such as tomato and grapevine. These studies highlighted, among others, the vast transcriptomic reprogramming underlying the berry ripening process , the extensive plasticity of berry maturation in the context of a changing environment , and the epigenetic regulatory network which contributes to adjust gene expression to internal and external stimuli . In particular, small RNAs, and especially microRNAs , are involved, among others, in those biological processes governing fruit ripening . In this work, we assessed the role of small ncRNAs in the plasticity of grapevine berries development, by employing next-generation sequencing. We focused on two cultivars of Vitis vinifera, Cabernet Sauvignon, and Sangiovese, collecting berries at four different developmental stages in three Italian vineyards, diversely located. First, we described the general landscape of small RNAs originated from hotspots present along the genome, examining their accumulation according to cultivars, environments and developmental stages. Subsequently, we analyzed miRNAs, identifying known and novel miRNA candidates and their distribution profiles in the various samples. Based on the in silico prediction of their targets, we suggest the potential involvement of this class of small RNAs in GxE interactions. The results obtained provide insights into the complex molecular machinery that connects the genotype and the environment.RNA extraction was performed as described in Kullan et al. . Briefly, total RNA was extracted from 200 mg of ground berries pericarp tissue using 1 ml of Plant RNA Isolation Reagent following manufacturer’s recommendations. The small RNA fraction was isolated from the total RNA using the mirPremier R microRNA Isolation kit and dissolved in DEPC water. All the steps suggested in the technical bulletin for small RNA isolation of plant tissues were followed except the “Filter Lysate” step, which was omitted. The quality and quantity of small RNAs were evaluated by a NanoDrop 1000 spectrometer , and their integrity assessed by an Agilent 2100 Bioanalyzer using a small RNA chip according to the manufacturer’s instructions. Small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit , following all manufacturers’ instructions. Forty-eight bar-coded small RNA libraries were constructed starting from 50 ng of small RNAs. The quality of each library was assessed using an Agilent DNA 1000 chip for the Agilent 2100 Bioanalyzer. Libraries were grouped in pools with six libraries each . The pools of libraries were sequenced on an Illumina Hiseq 2000 at IGA Technology Services . The sequencing data were submitted to GEO–NCBI under the accession number GSE85611. A miRNA was considered as “expressed” only when the values of both biological replicates were greater than or equal to the threshold set at 10 TP4M. We defined a miRNA as “vineyard-, cultivar-, or stage-specific” when it was expressed only in a given vineyard, cultivar or one specific developmental stage. Differentially expressed miRNAs were identified using the CLCbio Genomics Workbench using multiple comparison analysis. We loaded the total raw redundant reads from our 48 libraries in the CLCbio package and trimmed the adaptors, considering only reads between 18 and 34 nt.

We annotated miRNAs against the user defined database, comprehending our set of 122 MIRNA loci and their corresponding mature sequences. For each library, container size for raspberries the total counts of read perfectly mapping to the miRNA precursors was considered as the input of the expression analysis. Given the main focus of our work, we aimed at identifying miRNAs differentially expressed between the two cultivars in the same environment and developmental stage , or between the three vineyards in the same cultivar and in the same developmental stage . For this reason, we considered each developmental stage and we performed the Empirical Analysis of digital gene expression , an implementation of the “Exact Test” present in the EdgeR Bioconductor package, as implemented in CLCbio software and estimating tagwise dispersion with pairwise comparisons and setting the significance threshold to FDR-adjusted p ≤ 0.05. The normalized reads of all miRNAs identified in this study and also the cluster abundances obtained from the static clustering analysis were submitted to another adhoc normalization [log10 or log10 ] for correlation analysis. This normalization was chosen because of the enormous range of abundance values that produced a logunimodal distribution and may cause significant biases in the correlation analysis when performed using TP4M or HNA values. A unity was then added to the abundance value due to the presence of zero entries. After this addition, a value of zero still corresponds to zero of the log10 function, thus making consistent the comparisons among profiles. The dendrogram was generated using the function hclust and the Pearson correlation was calculated using the function cor in R, based on the log10 or log10 values for miRNAs and sRNA-generating loci respectively. Pearson’s correlation coefficients were converted into distance coefficients to define the height of the dendrogram. Heat maps were produced using MeV based on TP4M values of miRNAs abundance. The Venn diagrams were produced using the function vennDiagram in R, based on the miRNA list for each cultivar, environment and developmental stage.Small RNA libraries were constructed and sequenced for 48 samples of grapevine berries . We obtained a total of 752,020,195 raw redundant reads . After adaptors trimming, 415,910,891 raw clean reads were recovered, ranging from 18 to 34 nt in length . Eliminating the reads mapping to rRNA, tRNA, snRNA, and snoRNA sequences, 199,952,950 reads represented by 20,318,708 distinct sequences, i.e., non-redundant sequences found in the 48 libraries , were perfectly mapped to the V. vinifera PN40024 reference genome . The libraries were analyzed to assess the size distributions of mapped reads. Distinct peaks at 21- and 24-nt were observed in all the libraries. Consistent with previous reports in grapevine and other plant species , the 21- nt peak was the highest, comprising a higher proportion of redundant reads, whereas the 24-nt peak was less abundant. A few exceptions regarding the highest peak in the small RNA size profile were observed: Ric_SG_ps had the highest peak at 24- nt whereas Mont_CS_ps and Mont_SG_bc did not show a clear difference between the 21- and the 24-nt peak. Using the Pearson coefficients we observed a strong association between the replicates as indicated by the high coefficients . To facilitate access and utilization of these data, we have incorporated the small RNAs into a website . This website provides a summary of the library information, including samples metadata, mapped reads, and GEO accession numbers. It also includes pages for data analysis, such as quick summary of the abundances of annotated microRNAs from grapevine or other species. Small RNA-related tools are available, for example target prediction for user-specified small RNA sequences and matching criteria. Finally, and perhaps most importantly, a customized browser allows users to examine specific loci for the position, abundance, length, and genomic context of matched small RNAs; with this information, coupled with the target prediction output, users can develop and assess hypotheses about whether there is evidence for small RNA-mediated regulation of grapevine loci of interest.

Using k-means clustering, VviERF6L1 fell within Cluster 8 with 369 transcripts, including five additional VviERF6 paralogs. The top GO categories associated with Cluster 8 were genes associated with terpenoid metabolism and pigment biosynthesis . Other interesting flavor associated categories included fatty acid and alcohol metabolism . Representative transcripts from Cluster 8 that were correlated with the transcript abundance profile of VviERF6L1 can be seen in Figure 4. These are ACC oxidase, which is involved in ethylene biosynthesis; a lipoxygenase, part of a fatty acid degradation pathway giving rise to flavor alcohols such as hexenol; α-expansin 1, a cell wall loosening enzyme involved in fruit softening, and two terpene synthases, which produce important terpenes that contribute to Cabernet Sauvignon flavor and aroma. The high similarity of these transcript profiles indicates that ethylene biosynthesis and signaling may be involved in the production of grape aroma. Supporting this argument, two recent studies have shown that a tomato ERF TF , falling in the same ERF IX subfamily, has a strong effect on ethylene signaling and fruit ripening. The transcript abundance of AtERF6 in Arabidopsis is strongly increased by ethylene, which is triggered by the MKK9/MPK3/MPK6 pathway. The transcript abundance of VviMKK9 in the Cabernet Sauvignon berries was higher in the skin than the pulp, but there were no significant differences for VviMPK3 or VviMPK6 . This is not too surprising since AtMKK9 activates AtMPK3 and AtMPK6 by phosphorylation. In addition, planting blueberries in a pot the transcript abundance of AtERF6 in Arabidopsis increases with ROS, SA, cold, pathogens, and water deficit.

Additional circumstantial evidence for ethylene signaling in the late stages of berry ripening was that the transcript abundance of many VviERF TFs was significantly affected by berry ripening and/or tissue . The transcript abundance of 129 members from the berries was determined to be above background noise levels on the microarray . The expression profiles of the 92 significantly affected AP2/ERF super-family members were separated into six distinct clusters by hierarchical clustering and indicated that this super-family had a complex response during berry ripening . The 12 members of Cluster 1 responded similarly in both the skin and pulp, gradually decreasing with increasing °Brix with a large decrease in transcript abundance at the 36.7 °Brix level. Cluster 2 with 14 members, including 8 members of the VviERF6 clade, had much higher transcript abundance in the skin with a sharp peak at 23.2 °Brix. Cluster 3 had similar profiles in both the skin and pulp with a peak abundance at 25° Brix. Cluster 4 with 7 members was a near mirror image of cluster 2, with a sharp valley for transcript abundance in the skin between 23 and 25 °Brix. Cluster 5 had 36 members with a steady increase in transcript abundance in the pulp but no substantial increase in the skin until 36.7 °Brix. Finally, in Cluster 6, there were 13 members with a higher transcript abundance in skins compared to pulp. Their transcript abundance increased with increasing °Brix level, but decreased in the skin. The transcript abundance of important components of the ethylene signaling pathway characterized in Arabidopsis and presumed to be functional in grape were also affected by °Brix level and tissue . Three different ethylene receptors, VviETR1, VviETR2, and VviEIN4 decreased with °Brix level in the skin, however there was very little or no change in the pulp. Likewise, VviCTR1, another negative regulator of ethylene signaling that interacts with the ethylene receptors, decreased between 22.6 and 23.2 °Brix in both the skin and the pulp. The transcript abundance of the positive regulator, VviEIN2, peaked at 25 °Brix in both the skin and the pulp.

AtEIN2 is negatively regulated by AtCTR1 and when it is released from repression, turns on AtEIN3 and the ethylene signaling pathway downstream. The transcript abundance of VviEIN3 increased with °Brix level, peaking at 25 °Brix in the skin, and was much higher than in the pulp. Although more subtle, its profile was very similar to VviERF6L1. Derepression of the negative regulators and the increase in positive regulators indicated that ethylene signaling was stimulated during this late stage of berry ripening.The transcript abundance of many of the genes involved in the isoprenoid biosynthesis pathway peaked between 23 and 25 °Brix level, particularly in the skin; this stimulation of transcript abundance continued in both the carotenoid and terpenoid biosynthesis pathways . DXP synthase is a key regulatory step in isoprenoid biosynthesis and its profile was similar to VviERF6L1; its transcript abundance was correlated with the transcript abundance of several terpene synthases in the terpenoid biosynthesis pathway . About 50% of the putative 69 functional terpene synthases in the Pinot Noir reference genome have been functionally characterized. Another 20 genes may be functional but need further functional validation or checking for sequencing and assembly errors. On the NimbleGen Grape Whole-Genome array there are 110 probe sets representing transcripts of functional, partial and psuedo terpene synthases in Pinot Noir . It is uncertain how many may be functional in Cabernet Sauvignon. There were 34 probe sets that significantly changed with °Brix or the °Brix and Tissue interaction effect; 20 of these are considered functional genes in Pinot Noir. Terpene synthases are separated into 4 subfamilies in the Pinot Noir reference genome; they use a variety of substrates and produce a variety of terpenes. Many of these enzymes produce more than one terpene. The top 8 transcripts that peaked in the skin at the 23.2 to 25 °Brix stages were also much higher in the skin relative to pulp .

Five of the eight probesets match four functionally-classified genes in Pinot Noir ; these terpene synthases clustered very closely with VviTPS54, a functionally annotated – Linalool/- Nerolidol synthase. VviTPS58, a -geranyl linalool synthase, was also in the cluster. The other two probesets match partial terpene synthase sequences in the Pinot Noir reference genome. The transcript abundance of genes involved with carotenoid metabolism also changed at different °Brix levels and with tissue type . CCDs are carotenoid cleavage dioxgenases and are involved in norisoprenoid biosynthesis. The transcript abundance of VviCCD1 changed significantly with °Brix level and was higher in skin than pulp, except at 36.7 °Brix. Likewise, the transcript abundance of VviCCD4a and VviCCD4b changed signficantly with °Brix level, but was higher in the pulp than the skin. The transcript abundance of VviCCD4c significantly increased with °Brix level, but there were no significant differences between tissues. VviCCD1 and VviCCD4 produce β- and α-ionone , geranylacetone , and 6-methyl-5-hepten-2-one in grapes. There were no significant effects on the transcript abundance of VviCCD7. The transcript abundance of VviCCD8 significantly increased with°Brix level and was higher in pulp than skin. Phytoene synthase, raspberries in pots which was also increased in the skin compared to the pulp , and VviCCD1, have been associated with β-ionone and β-damascenone biosynthesis. Other important grape flavors are derived from the fatty acid metabolism pathway and lead to the production of aromatic alcohols and esters. The transcript abundance of many genes associated with fatty acid biosynthesis and catabolism changed with °Brix level . In particular the transcript abundance of a number of genes were correlated with the transcript abundance of VviERF6L1 including VviACCase, Acetyl-CoA carboxylase; KAS III ; VviOAT, ; VviFAD8; ; VviLOX2 and VviHPL . The transcript abundance of alcohol dehydrogenases was affected by tissue and °Brix level . Some ADHs are associated with the production of hexenol and benzyl alcohol.Methoxypyrazines give herbaceous/bell pepper aromas. They are synthesized early in berry development and gradually diminish to very low levels at maturity. Nevertheless, humans can detect very low concentrations of these aroma compounds. Four enzymes, VviOMT1, VviOMT2, VviOMT3 and VviOMT4 , synthesize methoxypyrazines. The transcript abundance of VviOMT1 was higher in the pulp than the skin . In addition, the transcript abundance of VviOMT1 decreased significantly with °Brix level in the pulp. There were no significant differences in the trancript abundance in the skin or pulp for VviOMT2, VviOMT3 or VviOMT4 . There was a high correlation of the transcript abundance of VviOMT1 in the pulp with 2-isobutyl-3-methoxypyrazine concentrations in the berries . The transcript abundance of VviOMT2, VviOMT3, or VviOMT4 in either skin or pulp was not correlated with IBMP concentrations . This is consistent with the suggestion that the pulp is the main contributor of IBMP in the berry. Our data indicated that VviOMT1 in the pulp may contribute to the IBMP concentration in these berries.Orthologs of RIN and SPL tomato transcription factors, which are known to be very important fruit ripening trancription factors, were at much higher transcript levels in the skin and decline with °Brix level . The transcript abundance of the VviNOR ortholog in grape was higher in the pulp and increased slightly to peak at 25 °Brix. In addition, the transcript abundance of VviRAP2.3, an inhibitor of ripening in tomato , decreased in the skin with a valley at 23.2 °Brix; it belongs to Cluster 4 of the AP2/ERF super-family . Of particular interest was VviWRKY53 [UniProt: F6I6B1], which had a very similar transcript profile as VviERF6L1 .

AtWRKY53 is a TF that promotes leaf senescence and is induced by hydrogen peroxide. This is the first report we know of implicating WRKY53 in fruit ripening . AtERF4 induces AtWRKY53 and leaf senescence, so the interactions between WRKY and ERF TFs are complex. WRKY TFs bind to the WBOX elements in promoters and VviERF6L1 has a number of WBOX elements in its promoter . In addition, AtMEKK1 regulates AtWRKY53 and the transcript abundance of VviMEKK1 peaked at 23.2 °Brix in the skin as well. Interestingly, the transcript abundance of both VviERF4 and VviERF8, whose orthologs in Arabidopsis promote leaf senescence, were at their highest level of transcript abundance at the lowest °Brix levels examined in this study .This study focused on the very late stages of the mature Cabernet Sauvignon berry when fruit flavors are known to develop. Cabernet Sauvignon is an important red wine cultivar, originating from the Bordeaux region of France. It is now grown in many countries. Wines made from Cabernet Sauvignon are dark red with flavors of dark fruit and berries. They also can contain herbaceous characters such as green bell pepper flavor that are particulary prevalent in under ripe grapes. Grape flavor is complex consisting not only of many different fruit descriptors, but descriptors that are frequently made up of a complex mixture of aromatic compounds. For example, black currant flavor, in part, can be attributed to 1,8-cineole, 3-methyl-1-butanol, ethyl hexanoate, 2- methoxy-3-isopropylpyrazine, linalool, 4-terpineol, and β- damascenone and major components of raspberry flavor can be attributed to α- and β-ionone, α- and β- phellandrene, linalool, β-damascenone, geraniol, nerol and raspberry ketone. Some common volatile compounds found in the aroma profiles of these dark fruits and berries include benzaldehyde, 1-hexanol, 2-heptanol, hexyl acetate, β-ionone, β-damascenone, linalool, and α-pinene. In a study of Cabernet Sauvignon grapes and wines in Australia, Cabernet Sauvignon berry aromas were associated with trans-geraniol and 2-pentyl furan and Cabernet Sauvignon flavor was associated with 3-hexenol, 2-heptanol, heptadienol and octanal. In another comprehensive study of 350 volatiles of Cabernet Sauvignon wines from all over Australia, the factors influencing sensory attributes were found to be complex; in part, norisoprenoids and δ − and γ-lactones were associated with sweet and fruity characteristics and red berry and dried fruit aromas were correlated with ethyl and acetate esters. In Cabernet Sauvignon wines from the USA, sensory attributes were complex also and significantly affected by alcohol level of the wine. Linalool and hexyl acetate were postitively associated with berry aroma and IBMP was positively correlated with green bell pepper aroma. In France, β-damascenone was found to contribute to Cabernet Sauvignon wine aroma. Thus, flavor development in berries and wines is very complex, being affected by a large number of factors including genetics, chemistry, time and environment. In this paper we begin to examine the changes in transcript abundance that may contribute to flavor development. We show that the transcript abundance of many genes involved in fatty acid, carotenoid, isoprenoid and terpenoid metabolism was increased in the skin and peaked at the °Brix levels known to have the highest fruit flavors . Many of these are involved in the production of dark fruit flavors such as linalool synthases, carotenoid dioxygenases and lipoxygenases. These genes serve as good candidates for berry development and flavor markers during ripening.

This was widely assumed to be the case at the time of the system’s discovery. There is now substantial evidence that this system instead forms a valley coherent state stabilized by its spin order, which would require a new mechanism for generating the Berry curvature necessary to produce a Chern magnet. In general I think it is fair to say that the details of the microscopic mechanism responsible for producing the Chern magnet in this system are not yet well understood. In light of the differences between these two systems, there was no particular reason to expect the same phenomena in MoTe2/WSe2 as in tBLG/hBN. As will shortly be explained, current-switching of the magnetic order was indeed found in MoTe2/WSe2. The fact that we find current-switching of magnetic order in both the tBLG/hBN Chern magnet and the AB-MoTe2/WSe2 Chern magnet is interesting. It may suggest that the phenomenon is a simple consequence of the presence of a finite Chern number; i.e., that it is a consequence of a local torque exerted by the spin/valley Hall effect, which is itself a simple consequence of the spin Hall effect and finite Berry curvature. These ideas will be discussed in the following sections. In spin torque magnetic memories, electrically actuated spin currents are used to switch a magnetic bit. Typically, these require a multi-layer geometry including both a free ferromagnetic layer and a second layer providing spin injection. For example, spin may be injected by a nonmagnetic layer exhibiting a large spin Hall effect, a phenomenon known as spin-orbit torque. Here, we demonstrate a spin-orbit torque magnetic bit in a single two-dimensional system with intrinsic magnetism and strong Berry curvature. We study AB-stacked MoTe2/WSe2, plant pots with drainage which hosts a magnetic Chern insulator at a carrier density of one hole per moir´e superlattice site. We observe hysteretic switching of the resistivity as a function of applied current.

The real space pattern of domain reversals aligns with spin accumulation measured near the high Berry curvature Hubbard band edges. This suggests that intrinsic spin or valley Hall torques drive the observed current-driven magnetic switching in both MoTe2/WSe2 and other moir´e materials. The switching current density is significantly less than those reported in other platforms, suggesting moir´e heterostructures are a suitable platform for efficient control of magnetic order. To support a magnetic Chern insulator and thus exhibit a quantized anomalous Hall effect, a two dimensional electron system must host both spontaneously broken time-reversal symmetry and bands with finite Chern numbers. This makes Chern magnets ideal substrates upon which to engineer low-current magnetic switches, because the same Berry curvature responsible for the finite Chern number also produces spin or valley Hall effects that may be used to effect magnetic switching. Recently, moir´e heterostructures emerged as a versatile platform for realizing intrinsic Chern magnets. In these systems, two layers with mismatched lattices are combined, producing a long-wavelength moir´e pattern that reconstructs the single particle band structure within a reduced superlattice Brillouin zone. In certain cases, moir´e heterostructures host superlattice minibands with narrow bandwidth, placing them in a strongly interacting regime whereCoulomb repulsion may lead to one or more broken symmetries. In several such systems, the underlying bands have finite Chern numbers, setting the stage for the appearance of anomalous Hall effects when combined with time-reversal symmetry breaking. Notably, in twisted bilayer graphene low current magnetic switching has been observed, though consensus does not exist on the underlying mechanism. Current switching may be correlated precisely with magnetic structure.

To examine the metastable magnetic domain structure of the system under applied current, we use tuning-fork based gradient magnetometry where a magnetic signal is produced by modulating the tip position. Figure 6.5c shows the change in magnetization relative to the zero current state for ISD = 670 nA, well above the threshold current. The images in Figs. 6.5c-d are acquired over the scan range depicted by the dashed box in Fig. 6.4f. Above the threshold, a magnetic do- main a few µm2 in size is inverted relative to the ground state on one side of the device. Reversing the current flips the side hosting the reversed domain . We conclude that the current switching corresponds to the reversal of magnetic domains, with the inverted domains appearing on opposite edges for opposing directions of applied DC current. This is confirmed by the fact that the required switching current increases dramatically as a function of the applied magnetic field, which increases the energy cost of an inverted magnetic domain. The correspondence between magnetic dynamics and resistivity may be probed in detail using current modulation magnetometry, which examines the magnetic response, δBI to a small AC current. Figs. 6.5e and f show δBI , measured near the right and left edges of the device, respectively, for the same range of VBG, VT G, and VSD as Fig. 6.5a-b. The local δBI signal shows a single sharp dip feature on the right side of the device for ISD > 0 and on the left side for ISD < 0, but no signal for the opposite signs. These features correlate precisely with the current switching features observed in transport, as evidenced by overlaying a fit to the local δBI dip on the transport data in Fig. 6.5a-b. The δBI dips may be understood as a consequence of current-driven domain wall motion. As established above, applied current drives nucleation of minority magnetization domains.

Once these domains are nucleated, increasing the current magnitude is expected to enlarge them through domain wall motion. Where domain walls are weakly pinned, a small increase in the current δI drives a correspondingly small motion δx of the domain wall, producing a change in the local magnetic field δBI characterized by a sharp negative peak at the domain wall position . We may then use this mechanism to map out the microscopic evolution of domains with current. Fig. 6.5h shows a spatial map of δBI , measured at three different values of ISD corresponding to distinct features in the transport data. Evidently, the domain wall moves from its nucleation site on the device boundary towards the device bulk. Local measurements of δBI as a function of ISD show that this motion is itself characterized by threshold behavior, corresponding to the domain wall rapidly moving between stable pinning sites. A full correspondence of transport features and local domain dynamics is presented in the associated publication. The symmetry of the observed magnetic switching is suggestive of a spin or valley Hall effect driven mechanism. The bulk nature of the spin Hall torque mechanism means that similar phenomena should manifest not only in the growing class of intrinsic Chern magnets, but in all metals combining strong Berry curvature and broken time-reversal symmetry, including crystalline graphite multi-layers. Research into charge-to-spin current transduction has identified a set of specific issues restricting the efficiency of spin torque switching of magnetic order. Spin current is not necessarily conserved, and as a result a wide variety of spin current sinks exist within typical spin torque devices. Extensive evidence indicates that in many spin torque systems a significant fraction of the spin current is destroyed or reflected at the spin-orbit material/magnet boundary. In addition, the transition metals used as magnetic bits in traditional spin-orbit torque devices are electrically quite conductive, and can thus shunt current around the spin-orbit material, preventing it from generating spin current. These issues are entirely circumvented here through the use of a material that combines a spin Hall effect with magnetism, plastic plants pots and as a result of these effects this spin Hall torque device has better current-switching efficiency than any known spin torque device. We started this discussion with a favorable comparison of the impact of disorder on the ABMoTe2/WSe2 Chern magnet to graphene-based Chern magnets. I’m sure the reader was just as disappointed as we were to see the dramatic disorder landscape on display in Fig. 6.4E, which presents a map of the magnetization in the AB-MoTe2/WSe2 Chern magnet. This is not a refutation of our original claims; it remains true that the repeatability of the fabrication protocol of the AB-MoTe2/WSe2 Chern magnet is unambiguously much better than that of tBLG/hBN, or even tMBG. It is also easy to lose track of the scale of these images- the tBLG/hBN Chern magnet was only a few square microns, whereas this sample supports a Chern magnet that is almost a hundred square microns in area.

The presence of these ‘holes’ in the magnetization of this Chern magnet is not a result of strong twist angle disorder. We have so far discussed a variety of phenomena realized in gate-tunable exfoliated heterostructures. In all cases, these phenomena were accessible experimentally because of the presence of a moir´e superlattice, which gave us access to electronic bands that could be completely filled or depleted at will using an electrostatic gate. We will next be discussing an atomic crystal without a moir´e superlattice. This material does not have flat bands, and we will have no hope of completely filling or depleting any of the bands in the system. Instead, it has features in its band structure that lend themselves to interaction-driven phenomena, specifically flat-bottomed bands satisfying the Stoner criterion. The material we will be studying is an allotrope of three-layer graphene called ABC trilayer graphene. In addition to a variety of other interesting phases, this material supports both spin and orbital magnetism. We will discuss why this is the case, and we will study the ABC trilayer magnets using the nanoSQUID microscope. As in three dimensional crystals, many two dimensional crystals have multiple allotropes that are stable under different conditions. Trilayer graphene is such a material. We label multilayer graphene allotropes using letters that refer to the relative positions of atoms of different layers, projected onto the two dimensional plane. We have already encountered ABA trilayer graphene in the introduction, and this material has atoms in the third layer aligned to atoms in the first layer. At room temperature and pressure the ABA stacking order is preferred, but trilayer graphene has a metastable allotrope, ABC trilayer graphene, that can either be prepared or found naturally occurring. In ABC trilayer graphene atoms in the third layer are aligned neither with the first nor with the second layer. ABC trilayer graphene has band structure that differs significantly from ABA trilayer graphene, and these differences have important consequences for its properties. The band structure of ABC trilayer graphene at two different displacement fields is illustrated in Fig. 7.1. In the absence of a displacement field, the system is metallic at all electron densities. When a large displacement field is applied to the system, it becomes a band insulator when the Fermi level is tuned between the two resulting bands. This is the regime of displacement field that we will be discussing. ABC trilayer graphene has extremely weak spin-orbit coupling, so the spin degree of freedom is present and more or less completely orthogonal to electronic degrees of freedom, contributing only a twofold degeneracy to the band structure. Just like most other allotropes of graphene, ABC trilayer graphene has valley degeneracy, and this produces an overall fourfold energetic degeneracy of its band structure. This is illustrated in Fig. 7.2. As is abundantly clear from these plots, the bandspresent in ABC trilayer graphene are not flat; they have extremely large bandwidths. However, the bands do satisfy the flat-bottomed band condition, and as a result we can expect these systems to be able to spin- and valley-polarize without paying significant kinetic energy costs. A schematic of the device we will discuss is presented in Fig. 7.3A. This device allows us to perform several different experiments: we can tune the electron density and displacement field in the ABC trilayer graphene layer, we can measure in-plane electronic transport , and we can measure the out-of-plane capacitive conductivity as a function of electron density and displacement field. Data extracted from this contrast mechanism is presented in Fig. 7.3B. This dataset is restricted to the hole band; i.e., the bottom band in all of the plots we have so far encountered. Sharp features in this dataset correspond to spontaneous symmetry breaking; these features are marked with the numbers and .