Month: May 2024

Other authors have explored whether ethanol refineries have an effect on land use. Fatal and Thurman use county-level data to estimate the corn acreage effect of ethanol re- fineries. They find that a typical ethanol refinery increases corn acreage in its home county by over 500 acres and has effects that can persist for up to 300 miles. Miao also uses county-level data and finds a significant effect of ethanol refineries on corn acreage, as well as a differential effect between locally-owned and non-locally-owned refineries. Turnquist et al. , in contrast to more recent studies, fail to find any significant agricultural land conversion in areas near Wisconsin ethanol refineries. Finally, Feng and Babcock explore the full general equilibrium effect of increased ethanol production and find an unambiguous increase in corn acreage. Several researchers have focused on how ethanol production affects water quality and nitrate runoff. Donner and Kucharik highlight how the aggregate impact of the EISA will likely make achieving nitrate level goals in the Mississippi impossible. Thomas et al. use hydrologic models to estimate the water quality impacts of corn production caused by increased demand due to bio-fuel mandates. They find significant negative results. While it is likely true that “refineries cause corn,” it is also likely true that “corn causes refineries.” Ethanol refineries are not located at random,blueberries in pots and several researchers have explored the topic of ethanol refinery placement.

A series of papers have shown, unsurprisingly, that ethanol refineries are more likely to locate near areas with large corn production, near transportation infrastructure, and not near existing ethanol refineries . This finding is important because it highlights that ethanol refinery placement cannot be treated as truly random in econometric analyses without accounting for the underlying drivers of this placement. In my analysis, I argue that field-level fixed effects appropriately account for the major determinants of refinery placement. In particular, I study how distance-to-nearest-refinery affects the probability of a field being planted to corn. Whenever a new refinery is built, its presence differentially affects fields close to it relative to fields slightly farther away. However, due to the spatial characteristics of soil quality and topology, “more-treated” and “less-treated” fields are qualitatively comparable. My project improves upon previous work by leveraging new sources of field-level land use data and exploiting a finer-scaled panel of observations than previous authors. I exploit both the Cropland Data Layer and Common Land Unit to create annual observations of field-level land use. These agricultural micro-data allow for much more nuanced econometric estimation than in previous studies. Other authors have exploited similar micro-data in agricultural research to great effect . I also highlight the locality effect of ethanol refineries rather than the general equilibrium effect, focusing on small-scale heterogeneous effects that have not been well identified in previous work. The remainder of this paper is divided into a theoretical framework , a summary of my data, an overview of my econometric methods, a discussion of my results, and a conclusion. According to the Farm Service Agency of the USDA, a Common Land Unit is “an individual contiguous farming parcel, which is the smallest unit of land that has a permanent, contiguous boundary, common land cover and land management, a common owner, and/or a common producer association” .

Practically, a CLU represents a single agricultural field. Polygon shapefiles of CLUs are maintained by the FSA, but are not currently publicly available. I obtain CLU data for Illinois, Indiana, Iowa, and Nebraska from the website Geo Community . These data contain shapefiles from the mid 2000s, before CLU data were removed from the public domain. In this research, I implicitly assume that individual CLUs do not change over time: a reasonable assumption given the FSA definition. In reality, the FSA does adjust individual CLU definitions on a case-by-case basis if necessary, but I assume these adjustments to be negligible as in previous similar studies . Using the geospatial software ArcGIS, I overlay the CDL raster data with CLU polygons as shown in Figure 3.4. Upon visual inspection, the fit is quite good: CLU boundaries line up with crop changes in the CDL, roads appear clearly in both datasets, and geographical features such as waterways and elevation changes are visible. One concern is that many CLUs are quite small and appear to outline geographical features such as gullies, rather than larger constituent fields. This is particularly pronounced in areas near urban sprawl. Therefore, to maintain confidence that the fields I study are actually “fields” in the way we think of them, I drop all CLUs from my dataset with areas of less than 10 acres. I also drop CLUs with areas of greater than 10,000 acres, based on an assumption that these CLUs are incorrect.4 To assign each CLU a single crop cover, I calculate the modal value of the raster pixels contained within each CLU polygon. I then assign that modal value to the entire CLU. This procedure enforces the assumption that each field is planted to a single crop – an assumption strongly supported by a visual examination of the data. To my knowledge, this is the first instance of using modal statistics to interact the CDL and CLU datasets.

Previous research has used an off-center centroid to sample a single point of the underlying raster data. My procedure is preferable in that it reduces the chance of idiosyncratic mis-measurement of the field’s true land cover.In this paper, I have demonstrated that ethanol refineries exert a statistically significant effect on the land use of surrounding fields. Increases in corn acreage and nitrogen application occur within 30 miles of ethanol refineries, suggesting a highly localized effect. These findings are consistent with a model of ethanol refineries lowering corn basis for nearby farmers. Within a sample of almost 114 million acres, I find nearly 300,000 acres of the corn grown in 2014 can be attributed to ethanol placement effects accumulated over the years between 2002 and 2014. This project makes several important contributions to the existing literature and improves upon previous research. Most importantly, I leverage field-level observations of land use to create a thirteen year panel of over two million observations. This allows me to estimate a highly nonlinear relationship between distance to a field’s nearest ethanol refinery and that field’s probability of growing corn. My panel also allows me to include field-level fixed effects that control for time-invariant characteristics of each field such as soil type. In three econometric specifications that condition on the previous year’s land use, I find interesting patterns. Ethanol refineries seem to strongly incentivize nearby fields to grow corn-after-corn, while the effect appears opposite for corn-after-soy. The result for cornafter-soy is puzzling and is not predicted by my model. Future work may attempt to better understand this result. Nonetheless, the net effect of these two individual effects is that farmers appear to be growing more corn near ethanol refineries in the way the most stresses crop rotations and most exacerbates the use of nitrate-producing fertilizer. There is considerable room for further work on these questions. First, this analysis treats all refineries as identical. In reality, different refineries have different production capacities and ownership structures, and may have heterogeneous effects on surrounding land. Second, there is room to explore a wider range of econometric specifications beyond the linear probability model estimated in this paper. Finally, future work should explore data from the US Geological Survey to test whether water nitrate levels directly reflect the effect derived in the current project. While the findings of this paper appear relatively small in the context of the entire US Corn Belt, they are strongly statistically significant and demonstrate a real and important localized effect of ethanol refinery placement. My results are useful for anyone interested in a fuller understanding of the spatial forces driving land use change and nitrogen application in agriculture. Managing urban runoff and its associated pollutants is one of the most challenging environmental issues facing urban landscape management. The conversion of naturally pervious land surfaces to buildings, roads, parking lots,growing berries in containers and other impervious surfaces results in a rapid surface runoff response for both time of concentration and peak flow. Impervious land surfaces adversely impact the quantity and quality of surface runoff because of their effects on surface water retention, infiltration, and contaminant fate and transport. Large volumes of storm runoff from urbanized areas cause flooding, sewer system overflows, water pollution, groundwater recharge deficits, habitat destruction, beach closures, toxicity to aquatic organisms, and groundwater contamination.

Traditional urban runoff management focuses on removing the surface runoff from urban areas as soon as possible to protect public safety. However, as excess surface water is quickly drained from urban areas, it is no longer available for recharging groundwater, irrigating urban landscapes, sustaining wildlife habitat and other uses. Green infrastructure uses natural or engineered systems that mimic natural processes to control storm water runoff . For example, traditional detention ponds have been widely used to treat storm runoff and permeable paving promotes infiltration of rain where it falls. Importantly, decentralized green infrastructure strategies control runoff and contaminants at their source . Vegetation is a green infrastructure strategy that can play an important role in surface runoff management. Large-scale tree planting programs have been established in many cities to mitigate the urban heatis land effect, improve urban air quality, and reduce and treat urban runoff . There are municipal storm water credit programs in a growing number of cities that promote retaining existing tree canopy, as well as planting new trees. Although these programs encourage planning and management of urban forests to reduce runoff impacts, fertilizer is required to promote plant growth, and these added nutrients may contribute to contamination of surface runoff. Thus, reducing nutrients in storm runoff is a challenging task for landscape and water managers. Bioswales are shallow drainage courses that are filled with vegetation, compost, and/or riprap. As a part of the surface runoff flow path, they are designed to maximize the time water spends in the swale, which aids in the trapping and breakdown of certain pollutants. Bioswales have been widely recognized as an effective decentralized storm water BMP to control urban runoff. Their effects are threefold; vegetation intercepts rainfall reducing net precipitation; plant uptake of water via transpiration reduces soil moisture, thereby increasing subsurface water storage capacity, and root channels improve infiltration. Traditional bioswales are designed to remove silt and other pollutants from surface runoff waters. New bioswales are being developed for harvesting surface runoff and supporting urban tree growth . Bioswales that integrate engineered soil mixes and vegetation are being used to enhance treatment and storage of surface runoff . The composition of ESMs varies widely, from simple mixtures of stones and native soil to patented commercial products. Highly porous ESM mixes provide ample infiltration and pore space for temporary storage of surface runoff. Also, they support tree growth by providing more water and aeration to roots than compacted native soil alone. ESMs can reduce conflicts between surface roots and sidewalks by promoting deeper rooting systems. In California alone, over $70 million is spent annually to remediate damage by shallow tree roots to sidewalks, curbs and gutters, and street pavement. In Davis, California, a bioswale installed next to a parking lot reduced runoff from the parking lot by 88.8% and the total pollutant loading by 95.4% during the nearly two year monitoring period. Furthermore, a bioswale installed next to a turf grass patch at the University of California-Davis campus eliminated dry weather runoff from an irrigated urban landscape The ESM used in these studies offered several advantages over other ESMs because the main structural element was locally quarried and relatively inexpensive lava rock . This ESM had a high porosity, high infiltration rate, and a high water storage capacity . It effectively fostered the growth of biofilms that retain nutrients and degrade organic pollutants. Because vegetated bioswale research is in its infancy, very few studies have monitored vegetation growth and its impacts on bioswale performance. Moreover, evaluation of system performance is generally conducted before vegetation is fully established. In contrast, this study evaluated the effectiveness of two bioswales on surface runoff reduction, pollutant reduction, and tree growth eight years after construction.

This strategy is being employed by members of a European initiative, Meta Explore, who are screening fosmid clones from a variety of environmental samples to access enzymes of interest to industry, including chitinases and dehalogenases: . Another approach is to sequence subsets of the metagenome, such as collections of ribosomal RNA signature sequences. For example, based on 16S rRNA gene sequence data, we have developed a relatively good understanding of the species diversity and distribution of specific bacterial and archaeal phyla in different soils. Further, based on work from Noah Fierer, Rob Knight, and their colleagues at the University of Colorado, Boulder, we know that pH and salinity are major drivers of microbial biogeography. From these and other studies, we also know that soils contain high abundances of Acidobacteria, whose 26 subgroups vary in abundance from one soil type to another. Also, some phyla are more prevalent in a given soil type than in others. More generally, databases of 16S sequences are yielding insights into how chemical and physical parameters correlate with microbial distributions in soils. Here, I use the term metagenome to refer to sequencing of total community DNA, including both phylogenetic and functional genes, while taking a shotgun-sequencing approach. Although few shotgun soil metagenome studies are published, more are anticipated during the next year as investigators take advantage of recent advances in sequencing instruments, for example, using 454 pyrosequencing and Illumina technologies. These 2nd-generation sequencing approaches generate megabases to gigabases of sequence data, respectively,blueberry pot in single runs with relatively short read lengths of approximately 400 to 100 bp, respectively.

Other sequencing technologies recently developed, including the Pacific Biosciences platform for sequencing single molecules of DNA, holdpromise for generating longer sequencing read lengths.In a project involving my group at the Lawrence Berkeley National Laboratory, James Tiedje and his colleagues at Michigan State University, and the Joint Genome Institute , we are using a combination of second-generation platforms to sequence DNA from microbes in soil samples from the Great Prairie of the United States, including native prairie and adjacent cultivated soils from Wisconsin, Iowa, and Kansas . This project aims to determine the impact of land management on soil microbial communities and their functions, including cycling of carbon and nitrogen. One of the sites, Kansas native prairie, is also the focus of another project that is specifically addressing the impact of altered rainfall patterns due to climate change on carbon cycling processes in the Great Prairie . The Kansas prairie metagenome that was sequenced at JGI currently has the largest amount of sequence data of any soil metagenome to date, approaching 400 Gb of Illumina sequence, and will serve as a resource for this project. Also in collaboration with JGI, we sequenced DNA extracted from Alaskan permafrost soil samples collected by Mark Waldrop from the U.S. Geological Survey . The aim is to use metagenomics to gain an understanding of the impact of climate warming-induced thaw on the microbial degradation of carbon reserves that have been trapped in permafrost for thousands of years and that have potential to contribute large amounts of greenhouse gases to the atmosphere. Other ongoing soil metagenome sequencing projects include several that focus on field sites for which there is substantial temporal environmental and climate data. For example, the UK Rothamsted Field Station is one of the longest running field stations in the world and has served as the site for several metagenome sequencing projects.

One of these projects, “DeepSoil” , is sequencing DNA from a longterm grassland and an adjacent fallow site at Rothamsted. The overarching goal of this sequencing effort is to establish the long-term impact of plants on the soil microbiota. Another project at Rothamsted is a French metagenome sequencing project, Metasoil, coordinated by Tim Vogel and Pascal Simonet of the Ecole Centrale de Lyon, France. The Metasoil project is sequencing DNA from the Park Grass site at Rothamsted that was established in 1856. Their strategy relies on constructing and sequencing a fosmid library in addition to shotgun metagenome sequencing. Cheryl Kuske and coworkers at the Department of Energy Los Alamos National Laboratory, in collaboration with JGI, are sequencing soils from selected free air-carbon dioxide enrichment sites in the United States. These sites were established to determine the influence of increases in atmospheric CO2 levels due to climate change on terrestrial ecosystems. In addition, Folker Meyer and coworkers at the DOE Argonne National Laboratory are sequencing metagenomes from several different U.S. soils that were collected across a range of habitats to determine which microorganisms and functional processes predominate in different soil ecosystems. Together these soil metagenomics projects will be a tremendous resource to the scientific community and will provide a much greater understanding of microbial diversity and functions in soil.Although the sequencing of DNA is no longer a bottleneck, large amounts of sequence data generated from analyzing highly diverse soil communities are proving a challenge to accommodate. This issue is exacerbated by the need to cope with short reads—for example, 75–125 bp—that arise from analyses using the Illumina instrument. Thus, better algorithms, new bio-informatics tools, and “terabytes” of computer storage are required. Increased access to supercomputers, such as the National Energy Research Scientific Computing Center at the Lawrence Berkeley National Laboratory, can help.

For instance, we used NERSC to perform BLASTX of our permafrost metagenome data . This analysis took approximately 800,000 core hours, or the equivalent of more than 85 computer years, which lasted 2 weeks using the NERSC supercomputer and nodes at JGI. Cloud computing will further help to reduce this bottleneck. Another challenge is the large numbers of errors that different sequencing platforms generate. How can we differentiate sequencing errors from microheterogeneity within DNA samples from soil microbial communities? Also, there can be difficulties with different steps in sample processing. For example, each DNA extraction procedure can introduce its own bias with respect to sample loss or preferential lysis of some members of the microbial community over others. The most commonly used extraction procedures rely on beating with microscopic beads to lyse cells, although pressure lysis is another attractive option. Ideally, different laboratories should each use the same extraction protocol. However, despite the availability of commercial kits, laboratories typically follow their own favorite DNA extraction methods. Another problem lies with soil samples that have low biomass or high levels of contaminants such as humic acids that result in low DNA yields. For example, permafrost soils yield relatively little DNA in our experience. However, amplifying DNA before preparing a library might help. Two DNA-amplifying methods are used: multiple displacement amplification and emulsion PCR . Of the two, the MDA approach is subject to considerable bias, whereas emPCR should be less biased because each template is separately amplified. However, to my knowledge, no one has directly compared the two methods. Sometimes the volume of data falls short for conducting a metagenome analysis. For instance, when Susannah Tringe and coworkers at JGI first assembled soil metagenome data, their efforts failed because the 100 Mbp of sequence data that they collected proved insufficient. They estimated that they would need 2–5 Gbp to obtain draft genome assemblies of the most dominant organisms in soil, and current estimates from analysis of the Great Prairie metagenome data suggest that probably closer to 2 Tbp of data are needed! However, even a relatively low level of coverage was sufficient for some initial comparisons of the soil metagenome from a Minnesota farm to other available metagenome sequence datasets. Recently Etienne Yergeau and colleagues at the National Research Council of Canada produced 1 Gbp of sequence data from permafrost soil after amplifying their sample via MDA, which introduced considerable bias. Nevertheless,nursery pots when these data were compared to other metagenome data, DNA extracts from Minnesota farm soil—but not data from marine or other habitats—proved to be most closely related to the permafrost sample.Although we are learning a great deal about dominant bacteria and archaea in soils based on 16S rRNA gene sequence data, many of the dominant operational taxonomic units that we detect in soil have no close representatives in culture collections. Researchers are addressing these deficiencies through initiatives such as the Genomic Encyclopedia for Bacteria and Archaea project that Jonathan Eisen of the University of California, Davis and JGI coordinates. The long-term goal is to fill in the phylogenetic tree of life by sequencing genomes from underrepresented phyla. Another project, “Microbial Earth,” being coordinated by Nikos Kyrpides at JGI, calls for sequencing microbial type strains in culture collections. Meanwhile, the Earth Microbiome Project is an initiative that aims to sequence what some call the “dark matter” of biology, the full microbial diversity on Earth . The EMP will begin sequencing 10,000 metagenomes from various collections and habitats, and eventually will cover hundreds of thousands of such samples, pending dedicated support.

The soil microbial ecology research community has established an international consortium, the International TerraGenome Consortium . The consortium recognizes the high complexity of the soil environment and is focused on determining “the soil metagenome.” TerraGenome is a clearinghouse for information about funding for soil metagenomics research, for development and provision of bioinformatics tools, for metadata standards, and for workshops and meetings on these topics. For example, TerraGenome set forth criteria for metadata obtained from analyzing soil samples that researchers must meet before their sequence data may be deposited into centrally held databases. This effort to set the minimum information about an environmental marker sequence was coordinated through the Genome Standards Consortium .Through soil metagenomics research, we can address fundamental questions about soil microbial ecology. For example, is there functional microbial redundancy in soil? Soil microbial community compositions differ in different soils in terms of dominant populations, according to 16S rRNA gene surveys. Although soil pH is a Table 1. Examples of ongoing soil metagenome sequencing projects Sequencing project Strategy Status Principal Investigators Funding “Metasoil”: Rothamsted Park Grass permanent grassland, started 1856 454–FLX and Titanium 24 Gigabases Pascal Simonet & Tim Vogel France “DeepSoil”: Rothamsted Highfield permanent grassland and permanent bare-fallow plots, started 1959 Illumina paired end sequencing 80 Gigabases Dirk Evers , Tim Vogel, , Janet Jansson , James Tiedje Illumina Great Prairie Grand Challenge pilot study. Native prairie and adjacent cultivated corn sites in Wisconsin, Iowa and Kansas 454 Titanium and Illumina paired end sequencing  1.6 Terabase James Tiedje ; Janet Jansson, Susannah Tringe & Eddy Rubin DOE-JGI Alaskan permafrost, thermokarst bog and active layer samples Illumina paired end sequencing  80 Gigabases Janet Jansson, Eddy Rubin, Rachel Mackelprang & Jenni Hultman , Mark Waldrop DOE-JGI 24 Sites across continental US 454-FLX & Titanium 1.2 Gigabases Folker Meyer DOE-Argonne laboratory DOE FACE sites- impact of elevated CO2–5 sites 454–FLX & Titanium 5 Gigabases Cheryl Kuske DOE-JGI 314 Y Microbe / Volume 6, Number 7, 2011 6key driver of soil community composition, biogeography also plays a role. As an illustration, we can compare soil microbial diversity to the diversity of microbial communities in the human gut. The gut microbiota from one individual to another differs at the 16S rRNA gene level, but at the broad functional level the communities are rather homogenous in healthy individuals. This pattern suggests that several different bacterial species can carry out the same functional roles in the human intestine. The situation in soil might be similar, but we have yet to explore and compare many soil metagenomes in depth to determine whether that possibility holds. Metagenomics can help us determine whether microorganisms in soils embody a specialized cache of gene functions. Available metagenome sequence datasets are already providing clues as to what functions are predominant in soils. For example, genes for cellobiose phosphorylase, an enzyme that degrades plant carbohydrates, were identified in a Minnesota farm soil metagenome, but not in one from the Sargasso Sea. When we screened permafrost for other functional genes specifically involved in cycling carbon and nitrogen, the samples included several genes that were more or less prevalent after thaw. For example, although methanogens may not be numerically dominant in permafrost, they play a key role in producing methane, which is 21 times more potent as a greenhouse gas than carbon dioxide. With deep sequencing, it should be possible to obtain genomes of some of the dominant species in soil and even some species of relatively low abundance, provided that they do not have large amounts of strain heterogeneities.

Given that the full word meaning remains activated, the picture is thus judged as being less related to the full word. To a first approximation, it seems that cascading processes cannot account for the preferential access of the first “constituent” over the second. However, the activation of embedded constituents can be triggered by initially identifying the leftmost constituent . Thus, the meaning of the first followed by the second “constituent” can be quickly accessed and integrated with the full word meaning resulting in an inhibition for semantically unrelated “constituents”. Our results seem to be at odds with the predictions of models positing a prelexical parser that is entirely blind to the semantics of morpho-orthographic segments. A semantically blind system wouldn’t distinguish between compounds and pseudocompounds, not at least when scanning one of its constituents. If the system reads left-to-right, a semantically blind morpho-orthographic mechanism should treat both compounds and pseudocompounds as yielding potential morphemes. If the system is morphologically savvy and a “head hunter” it should treat the second morpho-orthographic sequence as a potential morpheme. But our results show significant differences in RTs and accuracy between compounds and pseudocompounds at both segments. However, it is possible that the lexical parsing mechanism first identifies the leftmost constituent but with semantic information quickly ruling out misparses. That would be the case of a pseudocompound whose “constituent” fan is accessed but quickly ruled-out upon accessing the full word fanfare. The whole word meaning can be accessed via a postlexical route or following a semantically anomalous composition of parsed “constituents”.

This in effect would reflect in faster and more accurate judgements for compounds given that the full word meaning is related to the meaning of the head,plant pot with drainage even if the referent picture stands for the head only . It is clear that the time-course of visual word recognition is faster than the time it takes to make a semantic judgement about a word and a picture. With our method, we aimed to capture the early moments of visual word recognition and lexical access by relying on a short presentation of words and pictures dichoptically, that is, without foveation. So, it is possible that the lexical targets—and thus their morpho-orthographic parsing—were degraded, limiting the scope of our results. However, it is important to note that the judgement accuracy for single constituents at the same spatial position as their embedded counterparts yielded high accuracy suggesting that parafoveal viewing was sufficiently clear to enable morpho-orthographic parsing. Taken together, our findings support a model whereby the visual word recognition system produces left-to-right constituent recognition, with these constituents accessing their lexical entries, but with morpho-semantic processes rapidly ruling out misparses. In other words, “constituent” meanings are accessed, though only the representation of semantically related “constituents” remain active. Our suggestion is that both constituents and full words token their concepts; but while the concept BED is compatible with the complex word bedroom , the concept FAN is incompatible with the monomorphemic word fanfare and is rapidly suppressed. This view is compatible with a model of visual word recognition that produces multiple parses that are initially insensitive to the semantics of morpho-orthographic sequences, but which are quickly evaluated by semanticcomposition processes.

With innovations and advancements in analytical instruments and computer technology, omics studies based on statistical analysis, such as phytochemical omics, oilomics/lipidomics, proteomics, metabolomics, and glycomics, are increasingly popular in the areas of food chemistry and nutrition science. Clear graphical representation and visual communication are effective ways to present large datasets and dense information to learners. Heatmaps with hierarchical clustering analysis and principal component analysis are commonly used cluster analysis methods for omics studies. Wang et al. investigated the interaction of fruity aromas with polyphenols by the use of heatmap cluster analysis by Origin Pro 9.0; Varunjikar et al. analyzed proteomics from tandem mass spectrometry by the use of heatmap cluster analysis through Omics Explorer V 3.6 software for food-grade insect protein analysis; Lin et al. analyzed the glycome profile of blueberry using a heatmap via R software. Yang et al. combined head space-gas chromatography-ion mobility spectrometry with PCA to detect the flavor compounds of fermented soybean products by the use of a software package with a dynamic PCA plug-in. Green & Selina employed both PCA and hierarchal cluster analysis without a heatmap to classify fatty acid and sterol profiles for analyzing avocado oil quality by the use of OriginPro2016 software. Zhao et al. implemented PCA in R software and machine learning algorithms in Python to classify up to ten types of major edible oils based on fatty acid profiles and Raman spectra datasets; Zhao et al. also applied PCA based on R software to analyze phenolic compound profiles of different cultivars of the US midwestern grapes with selenium and lithium fertilizer treatments. Richter et al. used PCA and heatmap cluster analysis to analyze inductively coupled plasma mass spectrometry data in R software for identifying food authentication of German asparagus. Zou et al. analyzed a multidimensional dataset of HS-SPMEGC×GC-TOFMS of coffee using ChromaTOF® , ChromaTOF Tile , R version 4.0.2, and MATLAB® .

However, processing high-dimensional data from raw food omics datasets is time consuming and remains a challenging task for data mining and untargeted foodomics studies. To achieve multiple data analysis methods, different software or code packages may be needed. For instance, by the use of R software, packages ‘ggbiplot’ and ‘ggplot’ are usually used for PCA analysis, while another package ‘heatmap20 is usually applied for heatmap cluster analysis. However, it takes time for researchers to learn and operate different software and code packages with confidence. The objective of the study is to develop an integrated code basis program based on MATLAB® software to give a 3D heatmap, heatmap hierarchical clustering analysis, and PCA all at once by directly reading datasets from Excel® files. The code has been optimized for figure qualities such as resolution, color code, and label font size. The code also adjusts the size of the 3D bars of the heatmap in accordance with the values, which gives readers better data visualization and differentiation. In addition, we have provided proper code annotations and completed user guidance in the supplementary materials for future learning and educational proposes. The original dataset of our previous publication about the US California olive pomace phenolics was used as an example dataset in this study. As can be seen from Table S1, the data matrix contained 7 extracts * 22 olive pomace phenolic compounds. Data were saved in an ‘.xlsx’ file format by the use of Microsoft® Excel; in this case, the full file name was ‘olive phenolics.xlsx’. Here, Hadley Wickham’s ‘Tidy Data’ conceptwas referred, where each variable was a column and each sample observation was a row, because the input data must be tidy for the best results. It can be seen from Figure S1a that the names of 7 olive pomace extracts were listed in the first column from A2 to A8,growing blueberries in pots and the names of 22 olive pomace phenolic compounds were listed in the first row from B1 to W1. The text ‘NAME’ was placed in cell A1. The file was saved as ‘olive phenolics.xlsx’ in a MATLAB work folder. The data area in the excel file can be expanded in both rows and columns; however, there should be no blank cells in any places in the data area. The sample observation name should also be listed in the first column and the compound variables names should be listed in the first row. Omics data of each sample must be listed in each row, and variables/compounds must be listed in columns; otherwise, the program will still run, but output meaningless results. The excel data file and ‘.m’ code in the MATLAB files have been uploaded to the file exchange website as a secondary way to obtain the dataset and code. Readers can download from there in the MATLAB software, as shown in the ‘screenshot’ in Figure S1b, or via the MATLAB file exchange website.In perennial plants, masting marks one extreme end of the spectrum of population-level variation, and constant yield marks the opposite end. To date, much of the research on synchronous seed production has been focused on mast-seeding by wind-pollinated trees in temperate regions. It may be that mast-seeding is more common in wind-pollinated taxa; theory suggests selection for enhanced pollination efficiency through synchronous flowering with conspecifics is more likely in wind-pollinated species .

In insect-pollinated species, synchronous flowering may saturate insect pollinators and high pollination efficiency at low flowering density may select for a more constant production of flowers . An alternative explanation of the over representation of wind-pollinated species in the synchronous seeding literature is that much of the masting work, and indeed the bulk of ecological and evolutionary research, has been done in temperate regions where wind is the predominant pollination syndrome among forest trees. Early reviews on whether pollination syndrome predicts the tendency for masting had difficulty gathering sufficient data on insect pollinated and animal-dispersed taxa. A recent meta-analysis included data with approximately equal numbers of animal- and wind pollinated species, but there were more time series per species for the wind- than animal-pollinated ones . To help to fill this gap, we make use of an analogous pattern of highly variable reproduction in perennial crop plants which, unlike mast-seeding forest trees, are biased toward insect-pollinated taxa and span tropical, Mediterranean and temperate climates . Alternate bearing in fruit and nut crops is an intermediate pattern of perennial reproductive variability in which a year of high reproduction is followed by a year of low reproduction. While media and trade reports have cited alternate bearing in discussions of national crop yield, literature on the extent and drivers of synchrony among alternate-bearing individuals is scarce. Despite evidence of similar plant-level mechanisms in masting and alternate bearing, ecological research on the synchrony of mast-seeding has largely ignored, or explicitly excluded, alternate-bearing crops . This may be because breeding and management actions are generally assumed to outweigh any natural conditions that could result in alternate bearing at farm-, region- or nationwide scales. Similarly, agricultural research on yield and alternate bearing rarely integrates insights from masting literature. Such insights include the possibility that factors which increase yield in one year may result in a more severe reduction in the following year and the expectation that wind-pollinated taxa may be more prone to synchronous fluctuations in yield at larger spatial scales than insect-pollinated taxa . Here, we use global crop production data for plants known to be alternate bearing at an individual level to evaluate patterns of seed production at the national level. Specifically, we assess whether these crops are alternate bearing at national scales and whether patterns differ across pollination syndromes and are consistent with findings in masting systems. For this analysis, we use data from the Food and Agriculture Organization of the United Nations. The global, long-term nature of the FAO data offers a unique opportunity to study reproductive patterns in perennial plants, but also poses some limitations that could mask a signal of alternate bearing even if one exists. First, the FAO reports data at the national level, and while the total area under production is included, it is not spatially explicit and thus cannot serve as a proxy for the extent of cultivation. As such, we cannot directly test for synchrony among individuals or populations using these data. While a signal of alternate bearing in national-scale data would require synchrony at smaller scales, a lack of a signal does not preclude synchrony at the farm or regional level. Studies of synchrony in mast-seeding species suggest that we might expect signals of alternate bearing to be weaker in data at national compared to local scales. In that sense, our analysis is likely to underestimate the magnitude of alternate bearing at more local scales and thus their potential impact on farmer livelihoods. Furthermore, multiple crops are sometimes grouped together into a single FAO crop category , which could mask a species-specific signal. Finally, there is no information on the genetic variety or cultivation practices employed in each country that could influence the tendency toward alternate bearing within taxa. These features make any observed patterns in these data particularly salient. The presence of alternate bearing at national scales would highlight its ecological and socio-ecological importance.

The ruling, which overturned lower court decisions, stated that the beef promotion messages were government speech that is not subject to certain First Amendment challenges. This newest ruling is expected to settle pending litigation for several generic promotion programs and increase producer interest in promotional programs. Issues still remain; for example, in 2005 Paramount Farms, California’s largest pistachio producer, filed a lawsuit against the California Pistachio Commission charging that its generic promotion program is ineffective. Then in 2007, the California Pistachio Commission was terminated by a referendum vote of the growers. Program expenditures increasing Budgeted expenditures for California marketing programs have increased significantly over time. Lee et al. estimated total budgets of $71.35 million in 1985 and $112.94 million in 1992. The estimated total for 2002–2003 was just over $208 million , increasing to over $226 million for 2004–2005 . A number of factors have contributed to the observed increase, including participation by more crops , the effects of inflation, and growth in the importance of individual crops. Tables 2A, 2B and 2C provide details on California mandated marketing programs and expenditures in the broad categories of administration, promotion, inspection and research. These are the most recent budget data available, covering annual budget periods that include months in 2004 in the case of federal marketing orders, to fiscal years that begin in 2005 and early 2006 for some state programs. Note that most programs include only the direct costs attributable to promotion, inspection or research in each of these three categories, with all other expenses in the administration cost category. Overall, the 63 California programs allocated 68.1% of their total budgets for advertising and promotion, 11.0% for research, 3.9% for inspection programs and the remainder for administration. California marketing orders and agreements accounted for 44.6% of total expenditures,gallon pot followed by state commodity commissions , federal marketing orders and councils .

California commodity producer groups spent over $154 million on generic advertising and promotion programs during 2004–2005 . These programs ranged from high-profile TV advertising such as “Real California Cheese” and “Got Milk?” to more common media messages in magazines, newspapers, radio and billboards, and public relations campaigns. Research has documented significant increases in product demand and prices as a result of commodity advertising and promotion programs, with the net monetary benefits to producers being much greater than costs . For example, promotions led to statistically significant increases in demand and price in case studies for eight California crops and benefit-cost estimates for four national check-off programs . Kaiser et al. wrote that “the overwhelming conclusion . . . is that mandated commodity marketing programs have been very profitable for California’s agricultural producers. In every case, the evidence suggests that one can be reasonably confident that the benefits have well exceeded the costs and that it would have been profitable for producers to have increased expenditures on the programs.” Tables 2A, 2B and 2C do not include all funding for California commodity promotion or assessments paid by California producers. For example, USDA’s Market Access Program awarded $23.95 million to California trade organizations and marketing programs in 2005. These federal dollar-for-dollar matching funds are used for market development activities in export markets. California producers also contribute to the majority of the 17 national check-off promotion programs, including those for blueberries, beef, cotton, dairy, eggs, fluid milk, honey, lamb, mushrooms, pork, potatoes and watermelons. None of the assessments for national check-off programs, which totaled an estimated $765 million for all U.S. producers for 2005 , are included in tables 2A and 2B. There were 28 California programs with research expenditures totaling almost $8.5 million in 1992 ; this increased to 45 programs with expenditures of over $21.2 million in 2003–2004 , and further to 48 programs with expenditures over $25 million in 2004–2005 .

The share of total program expenditures dedicated to research increased from about 7.5% in 1992 to about 11% in 2004–2005. Historically, research funded by California marketing programs was focused on production problems and issues. A sampling of research topics includes new variety development, insect and pest management, irrigation and water management, disease control, pollination, harvest methods/machinery, crop management and post harvest quality control. More recently, California marketing programs have also funded nutrition and health research. There are numerous examples of the benefits to producers from research expenditures by mandated marketing programs. Research has resulted in cost savings from the reduced use of inputs and changes in the input mix, yield increases, reductions in post harvest losses, improved crop characteristics and new management techniques. Several California commodity groups have funded research at UC that has helped them become the most efficient producers in the United States and world. Included are almonds, walnuts, pistachios, strawberries, lettuce and grapes . California producers have gained a short- to intermediate-term competitive edge from these research-enabling improvements and, over time, benefits have flowed to consumers in the form of increased supply and availability, improved quality and lower prices.The purpose of minimum quality standards is to maintain or enhance demand for a commodity by keeping inferior products off the market. They are used to prevent a market failure known as the “lemons” problem, which occurs when a product has unobservable characteristics for which the seller has much better information than the buyer. The best example is early-season sales of immature fruit, which can look good but taste sour. While the individual producer obtains a high price for this fruit, consumer dissatisfaction can adversely affect prices and subsequent sales of high-quality product by other producers later in the season. Provisions for grades and minimum quality standards are included in all 11 current federal marketing orders for California fruits, vegetables and nuts.

However, only 11 of the 29 California state marketing orders and agreements include quality standards and inspection provisions, and just seven of them actively use the provisions. Minimum quality standards typically include a minimum size, to keep small product off the market. Depending on the commodity, they may also specify minimum sweetness , a minimum degree of maturity , acceptable color and/or amount of discoloration, shape, amount of insect damage or cosmetic defects allowable, and maximum mechanical damage such as bruises, cuts or missing stems. While empirical analyses of the economic impact of such standards are limited, those available indicate that it is probably relatively small . However, some minimum quality standards have been controversial, with charges that they: are an inefficient form of supply control because they divert product to nonfood uses such as animal feed; are defacto price discrimination because they divert product to the less-price-sensitive processing market outlet; waste edible fruit with the primary impact being on the poorest consumers; and are sometimes inequitable because of regional variations in production conditions.A group that controls all or most production of a commodity can gain a measure of monopoly power and enhance short-run returns through restricting the supply placed on the market or practicing price discrimination between markets. However, such monopoly pricing reduces consumer welfare by increasing prices for a smaller amount of product and distorts resource allocation decisions, while producers face all of the problems of maintaining a cartel. A key feature of marketing orders is that volume controls apply only to the quantity placed on the market — they do not control the amount of product produced. Thus, reduced risk from price stabilization and improved average returns from effective price discrimination can be expected to shift the long-run supply curve to the right, increasing production of the marketing order commodity and increasing required product diversions. Over time, producers discover that they are subject to onerous controls and that returns are no better than before the program. The use of quantity control provisions has decreased significantly over time as longer-run economic impacts and administrative problems became evident. Six federal marketing orders for California commodities and two state marketing orders have quantity control provisions but, among these eight, only the federal marketing order for raisins has used these provisions during the last 5 years. In addition,gallon nursery pot government approval of a new marketing program with supply control provisions is now difficult to obtain. Assuring food safety is the newest use of minimum quality standards and inspection in marketing programs. The purpose of these standards is to enhance product demand by reducing the chances of a food safety incident, thereby increasing consumer confidence and preventing the costs of product recall or rejection. There are three California marketing programs currently stressing food safety: the Leafy Greens Products Handler Marketing Agreement, and the federal marketing orders for pistachios and almonds. The main provisions of the federal marketing order for pistachios set standards and require testing for quality and aflatoxin, a cancer-causing mold that can contaminate many nuts and grains. Producers’ concerns about the possible negative effects of an aflatoxin poisoning event were the major factor leading to the creation and adoption of the marketing order for pistachios, with support by more than 90% of the growers in a 2004 vote . Similarly, the California almond industry is currently developing treatment standards and plans for the pasteurization of all raw, natural almonds as a result of two similar food safety events. In 2001, a Salmonella outbreak in Canada was traced back to raw almonds from three orchards in California.

Then in spring 2004, food borne illnesses in Oregon from Salmonella were traced to raw almonds purchased from a retailer who obtained all supplies from one handler. The handler initiated a voluntary recall that involved approximately 15 million pounds of almonds. The California almond industry determined that additional steps were required to ensure that a third such incident does not occur. In summer 2004, the Almond Board of California’s board of directors unanimously approved an action plan calling for the pasteurization of 100% raw, natural almonds entering the food distribution system. The proposed new quality standard submitted to USDA will be effective when it has been determined that pasteurization technologies and capacity are sufficient to process all California production. The almond board’s target dates for voluntary implementation are during the 2006–2007 production/marketing year, with mandatory implementation for all North American shipments on Aug. 1, 2007, and mandatory implementation for 100% of almond shipments, including exports, on Aug. 1, 2008. Several California commodity groups are funding health and nutrition research on their products and using promotion programs to disseminate the results. During the last 5 years, more than $8.1 million was spent on research concerning the health and nutrition benefits of almonds, avocados, strawberries and walnuts; these four commodity groups also spent more than $19 million during the 2004–2005 marketing year on promotion using nutrition/health messages. Other commodity groups funding such programs include apples, blueberries, cranberries, kiwifruit, milk and table grapes. In 1990, the California Walnut Commission became the first California mandated marketing program to specifically fund health and nutrition research, when it contracted with Loma Linda University for research on the protective effects of walnut consumption on the risk of coronary heart disease. The motivation for walnut nutrition research was to counter the popular perception that walnut consumption was unhealthy because of their high oil content. Likewise, the Almond Board of California initiated a Nutrition Research Program and established a Nutrition Subcommittee in 1995. In 1997, the California Avocado Commission made a strategic change to proactively communicate the nutritional benefits of avocados through national public relations and outreach efforts. In 2003, the California Strawberry Commission began funding nutrition research proposals. These four commodities each have developed analyses detailing their chemical and nutritional composition, including the amount and type of fat, calories, vitamins, phytochemicals, antioxidants and minerals. The presence of particular components, already associated with favorable health outcomes, has helped focus research on important health topics. Each commodity group has or is seeking evidence that consuming their product may reduce the risk of heart disease and all have evidence that product components may help to lower the risk of certain cancers. In addition, each of the commodities contains antioxidants known to slow the aging process and protect against heart disease and various forms of cancer. Almonds, avocados and walnuts can be a component of diets to control weight gain and each can be part of a healthy diet for managing and controlling diabetes .

Blueberry phenolic compounds and more broadly, phytochemicals, exert regulatory effects including a decrease in proinflammatory gene expression/production in part through the modulation of the NF-κB pathway. A modulation of the MAPK pathway by blueberry phytochemicals is less evident with contradictory observations reported but may also play a role. Blueberry phytochemicals decreased DNA damage in cells in vitro, via the reduction of ROS production, lipid peroxidation, and an increase in antioxidant enzyme activities. Despite many in vitro studies on blueberry extracts, no specific compounds have emerged as singly responsiblefor the regulatory effects on inflammation and oxidative stress. Virtually all studies have focused on blueberry phenolic extracts or fractions, with a large emphasis on anthocyanins. Health effects of dietary anthocyanins have been extensively reported and discussed , and berries provide an excellent vector for anthocyanin consumption. Blueberries have a complex anthocyanin profile and both major anthocyanidin derivatives, malvidin and delphinidin, have demonstrated a reduction of inflammatory markers in different in vitro models of intestinal inflammation and endothelial dysfunction . Although it is highly likely that anthocyanins largely contribute to the health benefits provided by blueberries, as supported by the number of studies focusing on those compounds, it is doubtful that they are entirely responsible for the bio-activities. Several in vitro studies compared different fractions of blueberry phytochemicals,black plastic pots for plants with reports of similar or better effects by other phenolic fractions and/or whole blueberry extract compared with anthocyanins .

These different studies highlight that mechanisms of action of individual blueberry compounds and fractions are context and/or model specific. More studies comparing the effect on individual compounds and well-defined combinations of molecules in different systems are needed to investigate the impact of a system’s environment or system-specific regulation on the bio-activity of blueberries. Although the amplitude of the effect of individual compounds appears to be widely specific to the model studied, the use of whole fractions of the fruits seems to alleviate inflammation and/or oxidative stress more consistently across models, despite not always demonstrating the strongest effects compared with specific blueberry fractions. As the health effects of polyphenols have been extensively described, more data on other phytochemicals should be gathered as they may also exert health benefits. Other notable phytochemicals in blueberries include ascorbic acid , polysaccharides , and volatile compounds and could contribute to inflammatory or oxidative responses of cells to stimuli. A blueberry volatile extract, high in monoterpenes , modulated the inflammatory response in LPS-induced RAW 264.7 cells through inhibition of the NF-κB pathway . Phenolic compounds, although carrying anti-inflammatory and antioxidant modulatory effects, may not be solely responsible for the health benefits of blueberries. Whether the phytochemicals act in synergy or target different molecular pathways remains to be elucidated.Although the scope of this review is limited to blueberries, the anti-inflammatory and antioxidant effects and mechanisms are likely applicable to other commonly consumed berries. Berries are generally rich in polyphenols, particularly anthocyanins, flavonols, and proanthocyanidins, but the profile of each berry species, and even within varieties, harbors differences in terms of the individual compounds present and their respective concentration .

Gasparrini et al. reviewed in detail the anti-inflammatory effects of several berries in cellular models using LPSinduced inflammation, and consistently report alleviation of inflammation by berry phytochemicals through inhibition of NF-κB and MAPK pathways. Other reviews also discuss and compare the anti-inflammatory properties of berries, in preclinical and human models . Moore et al. and Gu et al. have reported similar anti-inflammatory effects of berry volatiles compared with phenolic extracts for cranberries, blackberries, blueberries, red and black raspberries, and strawberries. Notably, the bio-activities of berry polyphenol extracts do not always explain the overall anti-inflammatory effects observed with whole berries , highlighting that potential health effects of berries as a group derived from highly diverse phytomolecules. After consumption, blueberries and their phytochemicals undergo metabolism through phase II enzymatic reactions in the enterocytes and hepatocytes or microbial metabolism in the gut . Metabolites are more likely to reach target sites inside the body and exert health benefits than their parent compounds . Evidence of the role of blueberry metabolites in the modulation of inflammation and/or oxidative stress has also been established . Metabolites of elderberry were tested in RAW 264.7 and dendritic cells, and p-coumaric, homovanillic, 4- hydroxybenzoic, ferulic, protocatechuic, caffeic, and vanillic acids [also reported to be blueberry metabolites ], exerted a dose-response inhibitory effect on NO . Studies regarding berry catabolites are less abundant than studies on berry parent phytochemicals but have gained interest in more recent literature. These studies of microbeand host-modified phytochemicals are extremely important to fully understand the potential anti-inflammatory effects of blueberry consumption. Although most of the evidence focuses on the effect of individual compounds, it is essential to consider the potency of these metabolites in profiles similar to what occurs physiologically.

To take the compound profile and physiologically available doses into account, Rutledge et al. treated LPS-induced rat microglial cells with serum from subjects having regularly consumed blueberry, strawberry, or a placebo powder blends over 90 d. The blueberry consumption decreased NO production, TNF-α secretion, iNOS expression, and moderately modulated COX-2 protein expression in the cells . This type of design allows the integration of a more realistic profile of parent compounds and metabolites from blueberry consumption, at physiological doses, within a cell-culturebased model. The current review summarizes the extensive amount of literature available on blueberry phytochemicals and inflammation using cell-based models. This choice comes with limitations, since it can be challenging to interpret results using specific concentrations of berry-derived molecules on cells when concentrations of these metabolites at the site of the target organs may not be established. There have been major differences in concentrations used to treat the cells, ranging anywhere from tens of μg/mL to mg/mL for total polyphenols and from tens of ng/mL to ≤1.2 mg/mL for anthocyanin fractions. Some of these concentrations are much higher than the blood concentrations that would be present in the body after consumption, as bioavailability of anthocyanins in the body is estimated to be lower than 2%, and peaking at 100 nmol/L after consumption of grape/blueberry juice . The relevance of the findings of cell-culture-based studies in complex human systems needs further investigation. These studies should comprise of well-controlled clinical trials, with the relevant choice of placebo controls and inclusion criteria depending on the specific blueberry phytochemical and physiological condition investigated. Future studies should also quantify the entire suite of berry-derived molecules and derivatives in key pools such as the blood, concurrently with physiologic indices of inflammation and oxidative stress.Fruit, nut, and berry crops are commonly grouped into one of three categories: temperate, subtropical, and tropical. Temperate zone crops include almond, apple, apricot, peach, grape, blueberry, and strawberry . Avocado, citrus, and guava are considered to be subtropical, while banana, cashew, and pineapple are tropical . Generally, temperate and subtropical crops can be grown in San Mateo and San Francisco Counties ,drainage pot but tropical crops are rarely successful. This publication focuses on temperate and subtropical crops. Temperate zone crops generally require a period of cold temperature during the winter months for successful flower and fruit development. This cold temperature period is measured in “chill hours” . Some crops require many chill hours, while others require few. This is called the crop’s “chill requirement.” When selecting temperate zone crops, it is important to choose only those crops that have a chill requirement that will be met at your location. Subtropical crops, such as citrus, loquat, and guava, require little or no chilling. Native to warm-climate regions, these crops can be injured by cold temperatures during winter and spring months, and they require heat during the growing season for fruit maturation and flavor.There are a growing number of examples of a positive relationship between diversity and ecosystem services. As an ecosystem service, pollination can increase the fruit or seed quality or quantity of 39 of the world’s 57 major crops, and a more diverse pollinator community has been found to improve pollination service. For some crops, wild bees are more effective pollinators on a per visit basis than honey bees and/or can functionally complement the dominant visitor. A less explored reason is that in diverse communities, interspecific interactions potentially alter behaviour in ways that increase pollination effectiveness. Little is known about how community composition affects pollinator behaviour and the role such species interactions play in determining diversity–ecosystem service relationships. Interspecific interactions can result in non-additive impacts of diversity on ecosystem functions.

Examples include the facilitation of resource capture in diverse groups of aquatic arthropods, and non-additive increases in pest suppression and alfalfa production in enclosures with diverse natural enemy guilds. In diverse communities, one mechanism by which species interactions may augment function is the potential to modify the behaviour and the resulting effectiveness of the ecosystem service providers. Interactions with non-Apis bees cause Apis mellifera L. to move more often between rows of sunflower, increasing their pollination efficiency. Such changes in pollinator movement are particularly important in crop species with separate male and female flowers, and those with self-incompatibility . As well as direct interaction and disturbance, avoidance of interspecific chemical cues and resource competition have the potential to alter pollinator foraging movements. Global human population growth is putting greater pressure on agricultural production. There is concern over how to meet the increasing demand for food, while at the same time safeguarding ecosystems and biodiversity. In the future, land currently under agricultural production will have to be more intensively managed to increase yields and/or more land will have to be converted to agriculture. Given the negative impact agriculture has already had on biodiversity, it is important that future steps to increase production be made environmentally sustainable. In the last 50 years, the fraction of agricultural production requiring biotic pollination has more than tripled. When compared with crops that are not pollinator-dependent, those that are moderately pollinator-dependent have shown slower growth in yield and faster expansion in area from 1961 to 2006. Almond is a mass-flowering, varietally self-incompatible crop species, highly dependent on biotic pollination. Almond orchards are generally planted with alternating rows of two or more varieties. Planting a single variety per row facilitates harvest, but complicates pollination because pollen must be transferred between rows to achieve fruit set. To allow for management activities, trees between rows are further apart than those within the same row . Apis mellifera tend to forage within a tree and then move down the same row, probably because less effort is required to move to the next tree in the same row or because the rows act as visual markers that influence movement. This foraging pattern means A. mellifera tend to move more incompatible pollen, limiting their pollination effectiveness. In almond, we investigated whether the presence of nonApis bees affected the behaviour and pollination service of the dominant pollinator species, A. mellifera. Often almond orchards are isolated from natural habitat and non-Apis bees can be completely absent. Therefore, we were able to compare A. mellifera behaviour and pollination effectiveness in diverse bee communities with orchards lacking non-Apis bees. Here, we refer to pollinator effectiveness as the probability an ovule is fertilized following a single visit. We complemented our intensive field sampling with observations in a controlled cage environment, where A. mellifera were introduced along with the blue orchard bee Osmia lignaria Say. We hypothesized that where non-Apis bees were present, such as in sunflower , interspecific interactions would cause A. mellifera to more frequently move between rows. We further hypothesized that an increase in between-row movements by A. mellifera would increase their pollination effectiveness and increase fruit set .In 2011, A. mellifera movements were observed in five orchards isolated from natural habitat, where non-Apis bees were not present. The number of movements by A. mellifera was counted between two trees of different varieties across the orchard row for 1 min. This was repeated a minimum of four times, counting movements between the same two rows, between different adjacent trees. The number of movements by A. mellifera was also counted between two adjacent trees of the same variety within the same orchard row. These two counts were repeated a minimum of eight times down a row along adjacent trees .

To further examine the antioxidant capacity in ”Draper” during fruit development, fruits from the seven aforementioned fruit developmental stages were assayed for antioxidant levels . The highest level of antioxidants was observed at the earliest ”petal fall” stage after which, the level of antioxidants declined during the middle and late developmental stages. This is consistent with previous reports on the antioxidant activity in blueberry during fruit maturation and similar to observations in blackberry and strawberry, wherein green fruit have the highest ORAC values. Using the same fruit development series, we quantified anthocyanin and flavonol aglycones in ”Draper” using liquid chromatography-mass spectrometry . Overall, as the fruit changed its exocarp color from pink to dark blue during ripening, delphinidine-type anthocyanins started to accumulate and were the most abundant compound in ripe fruit followed by cyanidin, malvidin, and petuni-din . Flavonols were also detected in all developmental stages, with quercetin glycoside being the most abundant , while myricetin glycoside and rutin were present at very low levels. Blueberry also has high levels of phenolic acids; among phenolics, chlorogenic acid was the most abundant. High levels of CGA were observed throughout fruit development, with the highest accumulation detected in young fruits . This correlates with the pattern of antioxidant capacity across different fruit stages, 10 liter pot suggesting that CGA is one of the major metabolites contributing to high ORAC values in young developing fruit.

CGA is derived from caffeic acid and quinic acid and has vicinal hydroxyl groups that are associated with scavenging reactive oxygen species. The antioxidant properties of CGA have been associated with preventing various chronic diseases.To better understand the biosynthesis of antioxidants in blueberry fruit, we identified homologs of previously characterized genes in other species involved in ascorbate, flavonols, chlorogenic acid, and anthocyanin biosynthesis. The key bio-synthetic genes for these compounds exhibited a distinct developmental-specific pattern of expression . For example, genes involved in the conversion of leucoanthocyanidins to proanthocyanidins are highly expressed in the earliest and middle developmental fruit stages but not in ripening fruit . Conversely, genes involved in the conversion of leucoanthocyanidins to anthocyanins were highly expressed in mature and ripe fruit but not during early fruit developmental stages . Additionally, paralogs encoding the same anthocyanin pathway enzymes and genes involved in vacuolar localization of proanthcyanidins exhibited similar developmental stage-specific expression patterns. The expression of these bio-synthetic genes is regulated by specific transcription factors. For example, the transcription factor complex MYB-bHLH-WD regulates expression of anthocyanin biosynthetic genes in eudicots. Using the Plant Transcription Factor Database v.4.0, we identified homologs of transcription factors belonging to 55 gene families, and members of some of these gene families were predicted to be involved in the developmental regulation of flavonoid biosynthesis during blueberry fruit growth , including R2- R3-MYBs, R3-MYBs, bHLHs, and WDRs . These transcription factors also exhibit fruit development-specific expression patterns. In addition, we performed a gene co-expression network analysis to identify metamodules of genes that appear coregulated during fruit development, specifically genes that are associated with phytonutrient biosynthesis. Our analysis identified 1,988 meta modules of co-expressed genes, of which 428 metamodules contained at least one of the 57 Pfam domains that have been previously categorized as associated with specialized metabolic pathways in plants.

Our analysis revealed that 142 of 428 meta modules were more highly expressed in developing fruit compared to other plant tissues. Some meta modules showed clear trends of being highly expressed during either early or late fruit development. For example, METAMOD00377 is expressed early in fruit development and contains homologs to known anthocyanin genes OMT, HCT, PAL, and HQT as well as 31 homologs to known transcription factors. In contrast, METAMOD01221 is expressed late in fruit development and contains homologs of HCT, TT19, UFGT, and OMT and contains 10 homologs to known transcription factors. Moreover, we also examined meta modules for genes associated with other bio-synthetic pathways that impart unique blueberry fruit characteristics. We identified two meta modules where genes appear to be co-regulated. Meta module METAMOD00377, which contains Pfam domains associated with terpene, saccharide, and alkaloid specialized metabolism, and METAMOD01221, which contains terpene and saccharide metabolism. These meta modules contained genes that are differentially expressed during fruit development. Overall, the developmental-specific expression patterns of key biosynthetic genes and their putative transcriptional regulators emphasize the tight regulation of production, conversion, and transport of precursor compounds that lead to the accumulation of antioxidant-related metabolites in blueberry.The coregulation of genes involved in the biosynthesis of terpenes and saccharides during early and late fruit development described above reflects a coordinated interplay between these metabolites during fruit growth. Both terpenes and sugars contribute to the characteristic flavor of ripened fruit . In blueberry, two components play a central role in flavor perception: taste, which is a balance of sweetness and acidity, and aroma. Blueberry aroma is a complex blend of volatiles that include aldehydes, esters, terpenes, ketones, and alcohols. Previous reports in blueberry showed that the aroma profile varies greatly across different blueberry ecotypes and cultivars.

For example, the aroma of high bush blueberry is primarily driven by terpene hydrocarbons and aldehydes -2-hexenal, -2-hexenol, -3-hexenol. Both linalool and geraniol are associated with sweet floral flavor. However, linalool was reported to largely impart the characteristic blueberry flavor when combined with certain aldehydes . Here, we also identified and examined the expression of genes involved in the biosynthesis of linalool. Four of the linalool synthase homologs in tetraploid blueberry are highly expressed during late fruit development . This pattern of expression coincides with previous reports of linalool accumulation in ripened blueberry fruit. On the other hand, one homolog of linalool synthase, although it was expressed during fruit growth, did not show a clear fruit development-specific pattern. Investigating the underlying factors regulating these enzymes will facilitate genetic manipulations that may lead to further improving blueberry flavor in the future.Superior fruit quality is also associated with sugar levels. During fruit ripening, sugar levels of the endocarp increase by importing hexose symplastically and/or apoplastically. Sugar transporters , sucrose transporter, and tonoplast sugar transporter have been demonstrated to regulate intercellular sugar transport in phloem and fruit . In A. thaliana, all clade III SWEET play a role in sucrose transport, with AtSWEET9 primarily functioning in nectary secretion, while AtSWEET15 is required for seed filling by acting with SWEET11 and SWEET12. In blueberry, the clade III SWEET transporters 9 and 10 were highly expressed during early fruit growth, while clade III SWEET transporter 15 was mainly expressed in ripe fruit . Interestingly, one of the blueberry SWEET15 homologs showed a distinct pattern of expression compared to the other three homologs. To the best of our knowledge, we are the first to report on the potential role of these genes during blueberry fruit development. In addition, homologs of A. thaliana TST1 and watermelon ClTST1 and ClTST3 were expressed during fruit ripening in blueberry. Elevated expression of a ClTST1 homolog was observed throughout fruit development, but the ClTST3 homolog showed very low expression. Another gene that is highly expressed during fruit maturation is vacuolar invertase. As described in other systems,10 liter drainage collection pot its upregulation during fruit ripening coincided with the breakdown of starch to sucrose or a mixture of glucose and fructose, suggesting that it may be involved in the regulation of sugar accumulation in blueberry fruit. It was previously reported that vacuolar invertase modulates the hexose to sucrose ratio in ripening fruit. In addition, there are also two sugar transport protein homologs that exhibited developmental specific expression. However, their function remains largely unknown, thus, their potential role in sugar accumulation in the developing berry requires further investigation.Tandemly duplicated genes arise as a result of unequal crossing over or template slippage during DNA repair , exhibit high birth-death rates, and typically are in co-regulated clusters in the genome. Smaller scale duplications, which include tandem duplicates, are highly biased toward certain gene families including those involved in specialized metabolism. Furthermore, tandem duplications often results in the increased dosage of gene products and may improve the metabolic flux of rate limiting steps in certain bio-synthetic pathways. Most genes associated with the biosynthesis of antioxidants have at least one tandem duplicate present in the high bush blueberry genome, with tandem array sizes ranging from 2 to 10 gene copies . The largest tandem arrays were found for HQT and HCT genes, which are co-regulated and involved in the CGA pathway . Differences in tandem array sizes were also observed between homoeologous chromosomes for various genes. For example, the C3H gene, which is involved in CGA biosynthesis , was present on all four homoeologous chromosomes but with varying tandem array sizes.

One of the homoeologous chromosomes had two copies of C3H, while the other three homoeologous chromosomes had four copies. This suggests that copy number differences of C3H among sub-genomes may be due to either selection for gene duplication or loss or, in the case of allopolyploidy, may be due to preexisting gene content differences among the diploid progenitor species. Genes in the anthocyanin pathway with other unique duplication patterns include CHS, CHI, OMT, and UFGT. The gene CHS, involved in the conversion of 4-coumaryl-CoA to naringenin chalcone, has two copies, and both have tandem duplicates in at least three of the homoeologous chromosomes. Interestingly, the gene CHI has a single preserved tandem gene duplicate on only one of the homoeologous chromosomes. However, additional copies of CHI were also identified more distantly away from the syntenic ortholog on another homoeologous chromosome, likely involving a transposition event following tandem duplication. The OMT and UFGT genes all have tandem duplicates on all of the homoeologous chromosomes, although with varying array sizes, while the ANR gene involved in the conversion of anthocyanidin to proanthocyanidin is single copy on all homoeologous chromosomes. DFR gene, which is involved inthe conversion of dihydroquercetin/dihyromyricetin to leucoanthocyanidin, has a single tandem duplicate on only one of the homoeologous chromosomes. These findings suggest that there may have been greater selective pressure to retain tandem duplicates for genes encoding enzymes involved in anthocyanin production than conversion to proanthocyanidins. The vast majority of tandem duplicates are eventually lost ; however, in rare instances, some may undergo functional diversification. Gene expression analysis revealed that 83.4% of the tandem duplicates were expressed in at least one transcriptome library with 73.5% expressed in at least one of the fruit developmental stages. This suggests that a subset of these duplicate genes have non-functionalized, subfunctionalized, or neofunctionalized. Future studies are needed to more thoroughly investigate the functions of these genes with more diverse libraries and additional transcriptome analyses.Despite the economic importance of blueberry, molecular breeding approaches to produce superior cultivars have been greatly hampered by inadequate genomic resources and a limited understanding of the underlying genetics encoding important traits. This has resulted in breeders having to solely rely on traditional approaches to generate new cultivars, each with widely varying fruit quality characteristics. For example, our analysis of a diversity panel consisting of 84 cultivars and wild species revealed that ”Draper” has antioxidant levels that are up to 19x higher than other cultivars. Thus, the genome of ”Draper” should serve as a powerful resource to the blueberry community for guiding future breeding efforts aimed at improving antioxidant levels among other important fruit quality traits. Furthermore, to our knowledge, this is not only the first genome assembly of the cultivated high bush blueberry but is also the first chromosome-scale and haplotype-phased genome for any species in the order Ericales. Ericales includes several other high-value crops and wild species with unique life history traits . Thus, we anticipate that this reference genome, plus associated datasets, will be useful for a wide variety of evolutionary studies. Here, we also leveraged the genome to identify candidate genes and pathways that encode superior fruit quality in blueberry, including those associated with pigmentation, sugar, and antioxidant levels. Furthermore, we found that genes encoding key bio-synthetic steps in various antioxidant pathways are enriched with tandem gene duplicates. For example, tandem gene duplications have expanded gene families that are involved in the biosynthesis of anthocyanins. This suggests that, in addition to a recent whole genome duplication, tandem duplications may have greatly contributed to the metabolic diversity observed in blueberry .

The interaction between bacteria and epithelial cells elevates inflammation, leading to increased thinning of the mucus and direct host-bacteria interaction. The thali approach, however, combats this cycle in two different ways: by suppressing bacterial growth with anti-microbial phytochemicals , and by reducing the opportunity for inflammation to occur. One molecular pathway involved in such a cycle involves interleukin 6 . This cytokine is normally expressed during acute inflammatory responses, and among other effects, upregulates the transcription factor STAT3. In the nucleus, STAT3 promotes cell proliferation and differentiation as well as upregulating anti-apoptosis genes. When IL6 is chronically elevated, it can lead to an apoptosis-resistant, constantly expanding T-cell population in the intestinal mucosa. These cells can further contribute to chronic inflammation. Just as a certain diet may promote chronic inflammation, a change in diet can help to restore health. Various bio-active compounds, including anthocyanins, have demonstrated antioxidant activity, reducing local amounts of reactive oxygen species. Low levels of reactive oxygen species can lower the expression of some inflammatory genes, including IL6, and relieve the stresses on both the intestinal microbiota and epithelial cells caused by chronic inflammation. In a study of pigs, we found that supplementing a high-calorie diet with purple potatoes that contains anthocyanins led to a six-fold reduction in levels of interleukin-6 compared to high-fat diet control. Colorectal cancer killed nearly 774,000 people worldwide in 2015,hydroponic vertical garden and nearly an estimated 50,630 deaths in 2018 in America making it the third leading cause of cancer-related deaths in the United States in women and second in men.

Virtually all cases of CRC are considered to result from an interplay of exogenous and endogenous factors with respect to the variable contribution from each factor. Some non-modifiable risk factors include old age and family history of CRC. Other risk factors, however, are associated with lifestyle or behaviors and thus can be changed. These modifiable risk factors include smoking, obesity, low physical activity, deficiency of dietary fiber, deficiency of vitamin D, deficiency of folate, high intake of red and processed meat, and alcohol consumption. Some of these risk factors, however, are closely related. For example, inadequate fiber intake and excessive fat intake are dietary risk factors which tend to lead to a lack of exercise which ultimately may contribute to obesity, particularly in combination. In the US, 40 percent of adults are obese, and so the risk factors discussed are common mainly due to the modern Western lifestyle. Therefore, it is no surprise that nearly half of the CRC cases arise in the developed nations. The Western diet in its current form contains more risk factors than the calorie and fat content. Foods that contain heterocyclic amines , polycyclic aromatic hydrocarbons , and emulsifiers can also contribute to carcinogenesis. HCA and PAH are produced in meats when they are fried or grilled over an open flame. These substances have been proved to damage the DNA of colonocytes and potentially promote risk of colon cancer. Emulsifiers are used in foods like ice cream to ensure an even distribution of fat molecules. Recent evidence suggests, however, that emulsifiers promote intestinal inflammation, creating an environment that favors colon carcinogenesis in mice. Some of these risk factors, however, are closely related. For example, inadequate fiber intake and excessive fat intake are dietary risk factors. These tend to lead to a lack of exercise, which ultimately contributes to obesity.

In the US, 40 percent of adults are obese, and so the risk factors discussed are common mainly due to the modern Western lifestyle. Therefore, it is no surprise that nearly half of CRC cases arise in developed nations. However, colon cancer has a long development period . This gives ample time for lifestyle changes to take place, including diet-based intervention. Chronic inflammation, a condition that is promoted by dietary risk factors also contributes to the development of cancer, even in humans. Patients with inflammatory bowel disease have a significantly increased risk of developing CRC, while long-term aspirin treatment is associated with a significantly decreased risk of CRC. The mechanisms by which chronic inflammation promotes tumor development often involve the immune system. For example, the IL6/STAT pathway discussed earlier is also implicated in cancer formation. Over expression of IL6 leads to excess STAT3 transcription, causing unwanted cell proliferation not only in T cells but also in the intestinal epithelium. Another inflammatory cytokine of note is TNF α. While the intestinal bacteria can promote inflammation, they may also affect the likelihood of CRC more directly. Once the intestinal mucus layer is thinned, and direct bacterial-epithelial cell interactions occur, certain bacterial strains promote tumor development. E. coli strains bearing the pks island are of particular interest. This genetic locus codes for the secondary metabolite colibactin, along with the enzymes necessary for its production. Colibactin has been shown to crosslink with DNA, producing double-stranded breaks. Furthermore, pks+ E. coli strains have been shown to be prevalent in CRC patients. In one study, nearly two-thirds of CRC patients had pks+ E. coli strains in their intestinal bacteria. In the same study, pks+ E. coli also existed in about 20 percent of healthy individuals. Colibactin, however, is a reactive and short-lived protein, requiring close contact with epithelial cells to cause DNA damage. A healthy mucosal barrier keeps colibactin at a distance and reduces the chance of affecting the intestinal epithelium. Evidence for the pathogenic relationship between diets, Fusobacterium nucleatum, and CRC has been emerging.

The F. nucleatum levels have been shown to be higher in CRC than in adjacent normal mucosa. Utilizing the molecular pathological epidemiology paradigm and methods, a recent study has shown the association of fiber-rich diets with decreased risk of F. nucleatum-detectable CRC, but not that of F. nucleatum-undetectable CRC. Experimental evidence supports a carcinogenic role of F. nucleatum, as well as its role in modifying therapeutic outcomes. The amount of F. nucleatum in CRC tissue has been associated with proximal tumor location, CpG island methylator phenotype , microsatellite instability, low-level CD3+ T cell infiltrate, high-level macrophage infiltration, and unfavorable patient survival . The amount of F. nucleatum in average increased in CRC from rectum to cecum, supporting the colorectal continuum model. Future studies should examine the role of diets, microbiota, and CRC in detailed tumor locations. Dietary prevention of CRC, then, has two intertwined aims: to reduce inflammation and to promote a healthy intestinal microbiota. As already discussed, preclinical evidence implies that dietary bio-active compounds, particularly anthocyanins, can reduce symptoms of low grade chronic inflammation as well as oxidative stress. It can also aid in balancing the intestinal microbiota by promoting the growth of beneficial bacteria and by reducing the populations of pro-inflammatory bacteria. Clinical trials have had mixed results, but anthocyanins and some polyphenols have shown to counteract against CRC actively. More research, however, is necessary for conclusive results. How, then, are individuals to consume enough bio-active compounds to have an effect on health? Some answers may be found in the food consumption practices of cultures with historically low CRC incidence. Parts of India, for example, have had some of the lowest CRC incidence rates in the world; however, this status has been changing. In recent decades,vertical vegetable tower increasing urbanization and similar factors have led to progressively Westernized diet patterns and lifestyle. CRC incidence rates are similarly rising, lending weight to the hypothesis that the traditional Indian diet may help prevent CRC. Furthermore, Indian immigrants to Western countries have a much higher incidence of CRC compared to Indians in India. Typical components of traditional Indian meals include a broad variety of flavors, as promoted in Ayurvedic medicine, and a variety of other foods. Both are facilitated by using a thali platter to serve the meal. The traditional American main meal includes an entree , one or more carbohydrates , and one or more vegetables. This basic structure can potentially be adapted with inspiration from thali meals by reducing the size of the main dish and serving more vegetables, legumes, pulses, herbs, and spices to accompany it. A unique component to thali is the combination of many tastes and colors. The inclusion of multiple colors in a meal is desirable, because certain bio-active compounds, particularly anthocyanins are also pigments. Blue, purple, and red-purple colors in plant foods indicate high anthocyanin content. Purple-pigmented potatoes can be prepared in the same way as traditional white potatoes, but the anthocyanin content is significantly higher in the pigmented varieties. Purple sweet potatoes also contain more anthocyanins than the more common orange varieties and can be easily substituted for them. Other vegetables with red or purple cultivars include carrots, cauliflower, and cabbage. Different colors can indicate the presence of other bio-active compounds, such as orange , yellow , and red/pink . Thus, healthy bio-active compound consumption may be increased by selecting colorful vegetables. Another way to increase consumption of bio-active compounds is to increase their presence in available foods.

The agricultural industry could greatly impact health by adopting food plant cultivars that produce bio-active compounds in larger amounts than is currently common. New cultivars may need to be developed that retain desirable characteristics such as large size, pest resistance, reduced spoilage, etc., but also have high bio-active content at the time of consumption. bio-active compounds, with some exceptions, tend to deteriorate during storage. Even when compounds have not deteriorated, storage may reduce the anti-inflammatory/antioxidant activity of bio-active compounds to affect health. A second systemic change that would promote increased bio-active compound consumption involves reworking how fruits and vegetables are currently stored and processed, as well as reducing the average storage time and adapting processing to optimize the amount of bio-active compounds. Presently, “nutritional adequacy” does not consider many of the bio-active compounds discussed in this paper. Further clinical studies are needed to support and elucidate the role of bio-active compounds in the prevention and treatment of disease.Natural competence is a phenomenon that allows bacteria to take up DNA segments from the environment and incorporate them into the genome via homologous recombination . Natural competence was first demonstrated in Streptococcus pneumoniae in 1928 by Frederick Griffith . Griffith showed that virulence genes were transferred from donor to recipient cells, converting the nonvirulent recipients into virulent pathogens . Since then, 80 bacterial species in divergent phyla have been described as naturally competent . Although the exact reasons for occurrence of natural competence in bacteria still remain unknown, studies showed that natural competence is induced under conditions of starvation and DNA damage , and it has been hypothesized that the incoming DNA serves as a food source and DNA repair material. Another proposition is that natural competence allows acquisition of new genes and alleles, providing the recipient cells with adaptive advantages. In fact, a previous study showed an increased rate of adaptation by natural competence in Helicobacter pylori . Interestingly, natural competence has been demonstrated in some of the most highly diverse and successful human pathogens such as H. pylori , Neisseria meningitidis and Neisseria gonorrhoeae , and Porphyromonas gingivalis , which require rapid adaptation to evade the immune response. Furthermore, natural competence also was described in two plant pathogens, Ralstonia solanacearumandXylella fastidiosa , both of which have very broad plant host ranges. Xylella fastidiosa is a bacterial pathogen affecting many economically important crops, such as grape, citrus, coffee, peach, and almond . The disease process is not completely understood, but it is proposed that X. fastidiosa forms biofilm-like aggregates and blocks xylem vessels, the conduits for water and nutrient transport in the plants . This blockage hinders xylem sap flow and starves the upper aerial parts of water and mineral nutrients, producing symptoms that resemble those of water and nutrient deficits. X. fastidiosa is transmitted by a number of xylem sap-feeding insects, including sharpshooter leaf hoppers and spittlebugs in which X. fastidiosa forms biofilms in the foregut . Taxonomically, X. fastidiosa is divided into five subspecies based on multilocus sequence typing . Even within the subspecies, host range and genotype diversity have been described , and recombination events among strains have been detected among field-collected samples . In fact, homologous recombination was shown to have a greater effect in generating genetic diversity in X. fastidiosa than point mutation .

The boundaries of the DWZ are shown in Figure 3.2. Only users within this zone have access to the alternative water supplies. This region was targeted because the negative externality that groundwater pumping imposes is larger for growers directly on the coast than for growers further inland. Moreover, underlying hydrologic characteristics of the aquifer mean that groundwater pumping in the southern part of the region has a greater externality than in the north. The eastern boundary of the DWZ is Highway 1, rather than a particular aquifer feature. The benefits that the recycled water has in the DWZ are threefold: the higher quality water allows growers with saline groundwater to improve their crop yields, the alternative water supply reduces pumping on the coast, and the runoff from the application of this water helps to recharge the aquifer. For most of the groundwater irrigation in the Pajaro Valley, growers bore individual tube wells on their property, rather than using canals or a shared water conveyance system. With the development of the recycled water program, the Delivered Water Zone needed a network of pipes, called the “Coastal Distribution System” to move the recycled water to eligible growers. Construction began on the CDS in 2005, and has slowly increased over time. As of 2020, the CDS is approximately 20 miles long,tower garden and provides water to 5100 of the most severely affected agricultural acres. A map of the Coastal Delivery System can be found in Figure 3.3. Along the CDS, turnouts , are installed in order to provide access to growers.

In order for a grower in the DWZ to receive recycled water, the CDS needs to reach their parcel and have a turnout, the grower needs to submit an application, and there must be enough recycled water to meet both the needs of the current users and of the applicant. Recycled water is sourced from the Watsonville Recycled Water Facility, which is a treated urban wastewater facility. It began operation in 2009. In the first full year of operation, the recycled water facility supplied 2700 acre-feet, but the facility has capacity for up to 6000 AFY, and plans have been approved to expand the facility further. While the recycled water is the main source of delivered water, there is some water available from the Harkins Slough Recharge and Recovery Facility. This facility intercepts some of the surface outflows from the Harkins Slough, which are wetlands just south of the Pajaro Valley. If not redirected for use in the valley, the outflow would have run into Monterey Bay, mixing with seawater. This storage facility has been in existence since 2002, and was the first groundwater recharge project constructed by the water management agency. While PVWMA has a permit to pump 2000 AFY from the Harkins Slough, the reality has been closer to 1000 AFY , due to a lack of flow through the Slough and the limited capacity in the recharge pond. Since recycled water comes into contact with crops, proper treatment of the recycled water is paramount. In order to meet California’s stringent recycled water standards, the water is tertiary treated, which means that all solids larger than 10 microns are removed, and the water is treated with UV light to kill pathogens. Some salts, nitrates, and phosphates may remain, but the quality is high enough to be directly applied to agricultural products, and safe enough to enter the aquifer for household use. The average total dissolved solids levels in recycled water is approximately 600 mg/L, which is high enough to cause some damage to salt-sensitive agricultural products, but much lower than TDS levels under drought conditions or in seawater-intruded wells.

To ensure that salt contents are sufficiently low, the recycled water is also blended with water from inland wells. To generate revenue to support the program, PVWMA collects augmentation fees for delivered water and fees for groundwater pumping in the basin4 . The pricing of both groundwater and recycled water began in 2002, and a tiered pricing system was established in 2010. A snapshot of 2016-2021 water prices, by category, are found in Table 3.1. The price of water varies in the Pajaro Valley depending on where the water is sourced , if the well is metered or unmetered , and if the well is within the delivered water zone. While fees for recycled water are higher than the cost of groundwater pumping in the DWZ, the fees are structured specifically such that when one factors in the electricity costs of pumping groundwater, the recycled water is slightly cheaper. To price groundwater, PVWMA meters all wells capable of extracting 10 AFY, as well smaller wells, if they serves 10 acres of orchard, 4 acres of berries or row crops, or 2.5 acres of greenhouse facilities. Municipal, agricultural, and industrial wells make up 87% of water use, while rural residential wells make up 2%, and the rest is consumed by delivered water users. Few residential wells have meters, so they are estimated to use 0.5 AFY, and are charged based on that estimate. Pajaro Valley’s water prices are high, relative to other groundwater charges. In most of the United States, groundwater pumping is not metered, and water prices are merely the electricity costs required to operate the pump. Even in locations where water prices have been implemented, they tend to be significantly lower than the prices in Pajaro Valley. In California’s productive Central Valley, water prices are commonly between $70-150 per acre-foot, and the 2018 Farm and Ranch Irrigation Survey finds that California growers pay an average of $67 per acre-foot for “off-farm” water. However, there are some regions facing similar or much higher water prices, depending on water supply constraints. Growers in San Diego county, for example, pay $1700 an acre-foot, due to water scarcity. Moreover, in Pajaro Valley, the irrigation water costs are minor when compared to the revenue and profits for the crops grown in the region. On average, revenues are $34,000 an acre, and reach up to $68,000 per acre for strawberries. The combination of high revenues and low water requirements leads me to believe that growers are not deficit irrigating in response to the water prices.

The Pajaro Valley is known for its production of delicate, high value produce, including strawberries, apples, raspberries, blackberries, artichokes, grapes, lettuce, and a variety of vegetables and herbs. As of 2019, total production value in the region was over $1 billion across 28,500 irrigated acres. The major California berry producer Driscoll’s is headquartered in the region, as is the cider producer Martinelli’s. The temperate, coastal climate is ideal for the production of these crops. Moderate temperatures year-round, sunny days, and foggy nights are excellent growing conditions for sensitive crops. However, the delicate nature of this produce means that they are also susceptible to other challenges, such as salinity damage. Salinity damage impacts almost all stages of plant growth and development,stacking flower pot tower including germination, vegetative growth, and reproduction . These effects lower crop yields and economic returns. For salinity in irrigation water, damages rarely occur until salinity reaches a crop-specific, critical “threshold”. Then, crop yields decline linearly as salinity levels rise. The threshold at which salinity damages begin to occur varies significantly, depending on the crop. For example, strawberry yields begin to decline at TDS levels of around 450 mg/L, while zucchini may not decline in yields before TDS levels reach 2000 mg/L. Grattan estimates and compiles these thresholds and yield declines for a variety of crops grown in California. Figure 3.4 depicts the relationship between irrigation water salinity and yield for a sub-sample of crops in the Pajaro Valley. Since crop revenues are so high for these products, even minor yield declines can lead to significant losses. In 2020, strawberry revenues were around $68,000 per acre, raspberries yielded around $59,000/acre, and apple revenues were $9,800 an acre. A yield loss of 10%, which would correspond to a TDS increase of 128 mg/L for strawberries, decreasing their revenue by $6,800 an acre. Therefore, growers are motivated to find possible solutions to deal with salinity issues in their groundwater, although individual basin management is out of their control. An alternative water source, such as recycled water, with moderate salinity levels, can mitigate severe crop losses while also preventing further seawater intrusion. Data provided from Pajaro Valley Water Management Agency for this analysis consist of water quality measurements from the network of monitoring wells, quarterly pumping and recycled water deliveries, depth to groundwater contour maps, and annual land use data. The details on how these data are built into a parcel-level panel are below. Additionally, I bring in variables on temperature and precipitation, property boundaries and ownership, and crop prices and revenue. Summary statistics are presented in Table 3.2. Pajaro Valley Water Management Agency has been collecting water quality data in the basin since 1957, and has built a network of 286 monitoring wells.

The locations of these monitoring wells are depicted in Figure 3.5 as black dots, overlaid on top of all the metered wells in Pajaro Valley . These monitoring wells are typically sampled twice annually, once in spring and once in the fall . This sampling method captures water quality at two critical time periods: spring is before the primary irrigation season, after winter rains and when water tables are the highest, and fall is after the main irrigation season, when water tables are the lowest. While PVWMA takes multiple salinity measurements, I use the total dissolved solids measurement, as it is generally the most salient to growers5 . For both fall and spring of each year, I take all water quality measurements of TDS and use an inverse distance weighting technique to interpolate a map of water quality for the entire Pajaro Valley. In the analysis, I focus on spring TDS, given that salinity before the growing season is considered to be the most important for agricultural water users, and is the most likely to predict summer basin conditions for growers. Figure 3.6 shows the history of average spring TDS values spanning 2003-2020, highlighting seasonal salinity patterns in the basin. Averages for the delivered water zone and the rest of the Pajaro Valley are compared. For the full region, spring TDS levels averaged 645.9 mg/L and ranged from 272.4 mg/L to 17,103.7 mg/L. The dashed line at 600 mg/L represents the approximate average TDS level of the recycled water. As can be seen, average salinity levels in the basin are frequently lower than the TDS levels of the recycled water, except in years of very high salinity. The spikes in salinity, which are especially high within the delivered water zone, are largely caused by drought conditions: groundwater pumping stays relatively stable, but the lack of precipitation leads to less groundwater recharge. With less freshwater percolating through to the aquifer, TDS levels in the remaining water are higher, and seawater intrusion is more likely to occur. As outlined above, there is significant variation in salinity across time. Importantly for our analysis, there is also spatial variation in salinity. This spatial variation is largely driven by inherent underlying characteristics of the aquifer, as well as distance to the coast and surface water sources. Parcel characteristics, such as soil properties, slope, and land elevation also play a role. Figure 3.7 shows average salinity levels across the Pajaro Valley basin from 2009-2020, plotted by decile. This figure indicates that inland regions, aside from those located near the Pajaro River, experience significantly lower levels of salinity, especially towards the south. Notably, the coastal region just north of the delivered water zone experiences some of the highest TDS levels, providing some initial evidence that recycled water may be having an impact within the delivered water zone. An impressive feature of the data from Pajaro Valley are the data on annual land use, which covers the 2009 and 2011-2020 growing seasons. PVWMA also engages in quality control practices, including randomly sampling parcels for additional checks. These ground-truthed land use data have key advantages over satellite data, which is known to have substantial error in measuring land use among California’s unique crop set . Agricultural land use types include vegetable row crops, strawberries, blackberries and raspberries , vine crops, artichokes, orchards, nursery crops, greenhouses, fallow ground, cover crops, and unknown agricultural use.

Our main contributions in this work are two-folds: we propose to merge the CMSFF in the backbone network to enhance the feature representation, and combine the CA to focus on the informative channels; we propose a group of training strategies to match the different generalization scenarios. Although FSL is very suitable for plant disease recognition, the applications of smart agriculture have just begun . In this research direction,there are still huge potential space needed to explore. In here, we discuss the limitations of this work and some future works. 1. Multi-disease. The PV and AFD used in this work as target data which have a common characteristic that only single disease is included in per image. In fact, once a plant is infected by the first disease, it is easily infected by other diseases because the immune system is attacked and becomes weak . Multiple diseases occur in a plant is more common in the real field condition. But the combinations of different diseases are too many to collect sufficient samples for each category from classification perspective . The current researches prefer to solve this problem by semantic segmentation. We do not cover this challenging problem due to limitations of data resources in this work. 2. Formulation of meta-learning data. The samples of PV were taken under controlled condition , which have a clean board as the unified background,dutch buckets for sale the illumination is under controlled, only single leaf in per image, only single disease occurs in per leaf. The settings are simple and very different from the in-wild conditions.

That is the reason many researches already achieved high accuracy by using deep learning CNNs on PV . But the samples of AFD were taken under in-wild condition, which have complex surroundings. When testing with AFD, we use PV in meta learning, mainly considering that both datasets are about plant diseases. Since we did not find any other appropriate dataset, the degree of similarity of the data used in training and test was not taken in account. According to our hypothesis, the degree of similarity of data used in meta-learning and test is higher, the adapting is easier, and the result would be better. It is demonstrated that the selection of meta-learning data is critical in this pipeline. The data used in meta-learning stage should be determined by the target. When the application scenarios cannot be predicted, how to formulate an appropriate meta-learning dataset is worthy to study. Inspired by Nuthalapati and Tunga and Li and Yang , the effectiveness of a mixed dataset for meta learning will be considered. 3. Sub-class classification. For the application of plant disease recognition, it is more meaningful to distinguish the diseases belonging to the same species. What farmers need more than anything else is a diagnostic assistant that can identify similar diseases belonging to the same plant. Although sub-class classification is difficult , it is an inescapable work in plant disease recognition and the performance is needed to be improved urgently. Fine-grained features of the lesions being the distinguishable features to solve this issue. In this direction, lesion detection and segmentation, fine-grained visual classification are involved. 4. The quality and quantity of training data. Most of the current researches of FSL deal with the configuration of data used in test, but very little work has concerned the data used in training. The common sense is that deep learning networks rely on large-scale data. However, a new direction is discussing the quality and quantity of training data recently . These works indicate that part of data can achieve at the same performance as full data.

Date quality can be assessed, which can guide to establish a dataset with enough diversity data while without redundant samples. The networks of appropriate depth using good data can achieve optimal results in many traditional CNN classification tasks. In this work, we use large-scale data in base-training and meta-learning. The quantity of data follows the conventional settings for comparison purposes. The data quality assessment work is not involved in this work. For the specific topic of plant disease, the data quality is very important. We know that at different stages of development of plants and diseases, the symptom appearances are very different. How to construct a comprehensive set without redundant data to represent a disease is a valuable work in the future . 5. Cross-domain. The significance of cross-domain has been introduced in prior sections. We emphasize cross-domain again because it is common when we cannot predict the species, surroundings, and photo conditions in test. In this work, we consider it from training strategies. There are many aspects to explore in future work, such as network architecture, feature distribution calibration etc.The Pajaro Valley is a productive agricultural region located on the Central California coastline, spanning across portions of Monterey and Santa Cruz counties. It provides an excellent study region for examining the implications of seawater intrusion on agriculture. Seawater intrusion in the region is well-documented, severe, and increasing over time. The local water management agency has done a rigorous job in tracking changes in salinity and agricultural production, as well as monitoring groundwater use. In addition, the region has engaged in large-scale mitigation strategy efforts, with the use of municipal treated wastewater. While the Pajaro Valley has experienced more severe seawater intrusion issues than most coastal agricultural regions, it is also an early adopter of recycled water as an alternative water source. Understanding the dynamics of seawater intrusion and management in this region can provide important implications for other regions wrestling with salinity problems under climate change.

In the Pajaro Valley, approximately 30% of the land and 85% of total water consumption is used for agricultural production. Due to the temperate Mediterranean micro-climate, Pajaro Valley has some of highest valued land in the country. In 2019, the crop revenue generated by the Pajaro Valley was approximately $1 billion across 28,500 irrigated acres . The region is well known for a variety of produce, including strawberries, raspberries and blackberries , apples, artichokes, and vegetable and nursery products. The major companies Driscoll’s and Martinelli’s are headquartered in the valley. Many of the crops in the Pajaro Valley require a significant amount of water for production, with most requiring between 2-3 acre ft. With virtually no access to surface water , irrigation water is sourced.Groundwater is the primary source of water for the entire basin, making up 93% of the water used in 2020. In fact, the Central Coast relies mostly on groundwater for agriculture,hydroponic net pots although a few farmers receive water through surface sources, the State Water Project and the Central Valley Project . Less than one percent of the Pajaro Valley’s water supply came from surface sources in 2020 . . On average, total annual groundwater use from 2010-2020 typically ranged from about 50,000-55,000 acre-feet per year , although this increased up to 60,000 AFY during the height of the 2013-2015 drought . Groundwater pumping in the Pajaro Valley is nearly twice the sustainable yield of the basin annually, which is defined as the quantity of water that enters the basin, through agricultural runoff and precipitation. By the 1940s, groundwater depletion was significant enough for growers to adopt deep well turbine pumps from the oil industry in order to reach the groundwater . Artesian wells, which were prevalent until this era, started to be artesian only during winter . The installation of the tube wells has led to an additional, significant groundwater concern: that of seawater intrusion. Seawater intrusion is the process of ocean water entering groundwater tables, contaminating freshwater resources. Many factors contribute to saltwater intrusion, including irrigation wells, excess pumping of groundwater, climate change, and sea-level rise. Mechanically, seawater intrusion works across four major dimensions. In the Pajaro Valley, the primary movement of seawater into freshwater is lateral . When a groundwater aquifer falls below sea-level, it creates a landward gradient where the dense seawater moves horizontally into the freshwater. Secondly, major storms and coastal flooding lead to seawater inundating nearby land, resulting in seawater percolating through the soil and leaching into the underlying groundwater. Additionally, seawater can enter coastal groundwater aquifers from below, since groundwater commonly sits directly on top of seawater, with only the relative density difference separating the two water bodies.

The use of tube wells in the freshwater aquifer leads to pressure changes, where the resulting “cones of depression” allow seawater to mix upwards into the freshwater aquifer. Finally, sea-level rise intermingles with seawater intrusion in multiple ways: by increasing the frequency and severity of coastal flooding, and by increasing the extent of the seawater “toe”, or how far inland the seawater sits below the groundwater aquifer. Altogether, seawater intrusion is a complex, dynamic system that is difficult to combat once in motion. Seawater intrusion was first noticed in the Pajaro Valley in 1951, with the extent of seawater intrusion increasing seven-fold since its discovery. However, in years of high rainfall, groundwater levels were historically high enough to prevent significant seawater intrusion. Simulations from the Pajaro Valley Hydrologic Model suggest that before the 1984- 1992 drought, groundwater levels only dropped below sea level during drought years. Since 1984 however, the groundwater level has been on a largely continuous decline . In 2010, the Pajaro Valley Water Management Agency reported that long term rates of saline intrusion are about 200 ft/year, and intrusion renders 11,000 acre-feet of water unusable annually. One-half of the groundwater table is below sea-level year round, and two-thirds is below sea level after irrigation season in the fall. Even with fluctuations in rainfall, in much of the Pajaro Valley, today the groundwater table remains consistently below sea level . Seawater intrusion is typically measured by the concentration of chloride present in a water body. However, for agricultural purposes, chlorides affect crops and yields in the same ways as other salts that may be present in irrigation water. Total salt content is generally measured using electrical conductivity and Total Dissolved Solids . Irrigation water with a salinity value of less than 500 mg/L TDS is the objective for irrigated agriculture. Strawberries, however, are a particularly salt-sensitive crop, with yields beginning to decline at TDS values of 450 mg/L . Irrigation water that has high TDS levels can lead to root and foliar absorption, negatively impacting crop yields1 . The relationship between irrigation water salinity and crop yields is depicted in Figure 3.4. Plants can typically tolerate salinity in irrigation water up until a crop-specific threshold, at which point yields decline linearly. Additionally, irrigation water that is high in sodium can lead to a loss of soil permeability, especially for soils with a lot of clay . While salinity issues especially impact the coast of the Pajaro Valley, TDS levels vary significantly across the region. As discussed above, there are many channels for seawater intrusion, and transport of water between aquifer layers is possible. Groundwater will move from areas of high to low pressure, through naturally occurring gaps, vertically, or through well bores. The Murphy Crossing area, on the eastern side of the Pajaro Valley, contains especially high levels of total dissolved solids . The highest chloride levels tend to occur in aquifers consisting of Aromas Red Sands and the Purisima geologic formation,with values from fewer than 5 mg/L to 14,600 mg/L. The average total dissolved solids levels across the Pajaro Valley, from 2003-2020, are shown in Figure? Salinity also varies significantly over time, due to changes in precipitation and groundwater use. There are other pollutants that lead to water quality concerns in the Pajaro Valley, including nitrates and phosphates. However, while nitrates and phosphates are of concern to human and environmental health, they do not have a negative impact on crop yields. The Central Coast Regional Water Quality Control Board has water quality objectives for its irrigation supplies . Nitrate contamination is largely due to fertilizer, while the source of salts is primarily saltwater intrusion, although seawater also contains nitrates. Therefore, while these contaminants are essential to keep track of, for agricultural producers, the concerns are negligible.While seawater intrusion had been discovered in the Pajaro Valley in the 1950s, broader management did not take place until a California-wide drought in the late 1970s spurred statewide action. In 1977, the Governor’s Commission to Review Water Rights in California was created, and their report contained recommendations to improve groundwater management and overdraft.

Many human intervention studies have therefore focused on middle-aged and elderly adults at increased vascular risk who are also known to be at increased risk of cognitive impairment and dementia, allowing for improvement by lifestyle-based intervention strategies.CBF is defined as the volume of arterial blood delivered to a unit mass of brain tissue per unit of time. The different imaging techniques to assess brain perfusion will be mentioned briefly, as they have already been critically reviewed. The direct methods discussed below have been developed to measure the delivery of arterial blood to the capillary bed. A frequently observed value in human gray matter is about 60 mL/100 g/min, corresponding to the delivery of approximately 1 mL of blood to 100 g of brain tissue per second. Assuming an average brain tissue density of 1 g/mL, this means that approximately 1% of the total tissue volume is provided with freshly delivered blood each second. In earlier studies, radioactive tracers were used to measure the absolute blood flow in the brain. However, CBF measurements using radio tracers require a specialized imaging unit, and time intervals between repeated measurements are also required to minimize overexposure to radiation. These delays significantly reduce the usefulness of radioactive CBF measurements in human intervention studies. Therefore,dutch bucket hydroponic increasing attention has now been directed to recent developments in magnetic resonance imaging that enable the non-invasive measurement of cerebral perfusion in human volunteers.

Direct methods for measuring CBF in human subjects include, but are not limited to, single-photon emission computed tomography , positron emission tomography , MRI with contrast agents, and arterial spin labeling MRI. All these methods are based on the measurement of the amount of a tracer delivered to the human brain tissue by blood flow. PET using injection of 15O-labeled water radio tracers is still considered the gold standard approach. Important limitations, however, include the need for an on-site cyclotron and the invasive nature and complexity of the measurement. As a promising alternative, ASL is a relatively new, non-invasive MRI method that uses magnetically labeled water molecules in arterial blood as a tracer. This method is currently available on MRI systems produced by the major manufacturers. The general principles have been described in detail before. Briefly, this non-invasive measurement of CBF works by manipulating the magnetic resonance signal of in flowing blood in feeding arteries before it is delivered to the capillary bed of the different areas in the brain. Separate “label” and “control” images are acquired, and the resulting signal difference can be scaled to yield highly repeatable quantitative measures of CBF. Figure 2 shows an example of an ASL CBF map. Recently, human studies that performed both PET and ASL MRI to measure brain perfusion were systematically reviewed. It was concluded that ASL is a promising method for accurate and reproducible CBF measurements, and comparative studies show that ASL is a validated method for non-invasive perfusion imaging in humans. Dietary nitrate, which is found in high concentrations in red beetroot, lettuce, and spinach, may improve CBF through beneficial effects on vascular endothelial function, which is an important mechanistic determinant of cerebral perfusion. In the mouth, dietary nitrate can be reduced to nitrite by facultative bacteria from the dorsal surface of the tongue.

Once in the blood, nitrite can be further converted into nitric oxide in the human vasculature, thereby improving endothelial function via an increased NO bio-availability. Several human intervention studies have examined the acute effect of dietary nitrate intake on measures of CBF . Presley and colleagues measured cerebral perfusion using ASL MRI after administering a high versus low-nitrate diet for 24 h to a group of elderly humans . The test diet included beetroot juice and provided 773 mg of nitrate compared to 5.5 mg for the low-nitrate diet. The authors demonstrated that the diet high in dietary nitrate did not significantly increase global CBF, while regional cerebral perfusion improved in frontal lobe white matter, especially between the dorsolateral prefrontal cortex and the anterior cingulate cortex, which are known to be involved in executive functioning. However, whether the observed increase in regional CBF in coincides with concurrent improvements in cognitive functioning remains to be elucidated. A single dose of 500 mL nitrate-rich beetroot juice acutely increased MCA mean blood flow velocity, measured non-invasively with transcranial Doppler ultrasonography during submaximal exercise in twelve healthy, normotensive young adult females. More recently, Wightman et al. investigated the acute effects of 450 mL of beetroot juice on prefrontal cortex CBF parameters in 40 apparently healthy adults. It was found that a single dose of beetroot juice modulated the NIRS-monitored CBF hemodynamic response during the performance of tasks, which activated the prefrontal cortex. In fact, an initial rise in prefrontal cortex perfusion at the start of the task period was followed by consistent reductions in cerebral perfusion during the least demanding task, while performance on one of the three cognitive tasks—requiring resources in terms of working memory, psychomotor speed and executive functioning—was improved.

Polyphenols are predominantly found in fruits and vegetables, as well as red wine, tea and chocolate. These phytochemicals may exert beneficial effects on brain health due to their positive impact on endothelial function and other aspects of the vasculature through an increased NO bio-availability, which may translate into increased CBF. Acute intake of trans-resveratrol, which is present in the skin of a range of foods including red grapes, raised CBF in healthy adults . In a randomized, placebo-controlled, crossover study, trans-resveratrol administration resulted in dose-dependent increases in prefrontal cortex CBF during task performances which activated this brain region, as assessed with NIRS. The performance of cognitive tasks was not changed. These results were in line with those of another clinical trial on the acute effects of 250 mg trans-resveratrol co-supplemented with 20 mg of piperine, which increases the bio-availability of polyphenols. More recently, the effects of long-term trans-resveratrol supplementation on CBF were investigated in 60 adult subjects between the ages of 18 and 30 years. In that study, a single 500 mg dose of trans-resveratrol on the first day of the study increased the CBF response in the frontal cortex during tasks which activate this brain region. However, this effect was not observed with transcranial Doppler ultrasound parameters after 28 days of daily supplementation of 500 mg of trans-resveratrol. In addition, no unambiguous evidence was provided to support that the intake of trans-resveratrol improved cognitive function. The effects of trans-resveratrol intake have also been investigated in populations at an increased risk of accelerated cognitive decline. In 36 older type 2 diabetic patients, acute consumption of 75 mg of trans-resveratrol significantly improved hypercapnia-induced mean blood flow velocity responses in major cerebral arteries by about 13%. Also, Evans and colleagues reported the beneficial effects of long-term trans-resveratrol supplementation in postmenopausal women aged 45–80 years. In that study, increases of 17% were found in the MCA mean blood flow velocity response to cognitive stimuli and hypercapnia. In addition, performance of a cognitive task in the domain of verbal memory and in overall cognitive performance improved, which correlated with improvements in transcranial Doppler ultrasound parameters. A smaller number of intervention trials has assessed the cerebral hemodynamic effects of other dietary polyphenols . In a double-blind, placebo-controlled,dutch buckets system crossover study with 27 healthy adults, the acute effects of a single oral dose of epigallocatechin gallate—the most abundant polyphenol found in green tea—were investigated on CBF. The administration of 135 mg of epigallocatechin gallate reduced cerebral perfusion in the frontal cortex during performance of cognitive tasks activating the frontal cortex, but no changes in cognitive performance were observed. More recently, a human crossover trial was conducted on the cerebrovascular effects of flavanol-rich cocoa. Regional CBF was measured using ASL prior to and two hours following consumption of a high flavanol drink or placebo. In agreement with an RCT involving healthy young men and a pilot trial of four healthy females consuming 516 mg of cocoa flavonoids, acute improvements in resting CBF were observed following the consumption of the high cocoa flavanol drink in eight men and ten women aged 50–65 years. More specifically, higher resting CBF was observed in both the anterior cingulate cortex and the central opercular cortex of the left parietal lobe. Unfortunately, the effects on cognitive performance were not evaluated. In another study with elderly subjects, a single dose of cocoa increased hypercapnia-induced MCA blood flow velocity.

The effects, however, were not evident after a daily supplementation of 900 mg of cocoa flavanols for one week. Finally, Bowtell and colleagues investigated the effects of twelve weeks of blueberry concentrate supplementation on cerebral perfusion using ASL MRI in healthy elderly adults. The concentrate provided 387 mg of anthocyanins . They found improvements in gray matter CBF in the parietal and occipital lobes, as well as some evidence suggesting an improved working memory after blueberry versus placebo supplementation.Haast and Kiliaan recently summarized the effects of the n-3 long-chain polyunsaturated fatty acids , eicosapentaenoic acid , and docosahexaenoic acid , which are predominantly found in fatty fish and fish oils, on indicators of brain health. These dietary fatty acids can be incorporated in all lipid fractions. In fact, LC-PUFAs may have anti-inflammatory effects and increase the fluidity of cell membranes. They may also improve vascular endothelial function and arterial stiffness, which are both important mechanistic determinants of CBF. Two human intervention trials investigating the longer-term effects of these fatty acids on CBF were discussed by Haast and Kiliaan. One study indeed showed that regional cerebral perfusion in the prefrontal cortex improved during the performance of nine computerized cognitive tasks. In the study, 65 healthy adults received for 12 weeks a daily DHA-rich fish oil supplement of either 1000 or 2000 mg. The total daily dose of LC-PUFAs for the 1000 mg fish oil group was 450 mg DHA + 90 mg EPA, and for the 2000 mg fish oil group, these amounts were 900 mg DHA + 180 mg EPA. Relative changes in the concentration of hemoglobin were assessed in the prefrontal cortex using NIRS. However, no beneficial effects on cognitive performance were found. Furthermore, PET experiments in humans that were injected intravenously with labeled DHA showed that the rate of DHA incorporation into brain lipids correlated with the regional CBF in that particular region. Konagai and colleagues provided further evidence of the beneficial modulation of cerebral hemodynamics in the prefrontal cortex during working memory task completion, when 45 elderly men were supplemented for 12 weeks with n-3 LC-PUFAs from krill oil. However, these findings could not be replicated in a recent large RCT. In 86 healthy older adults who reported memory deficits, no effects of long-term supplementation of 2000 mg DHA-rich fish oil alone or in combination with other nutrients were observed on NIRS measures during task performance or on cognitive demand battery task outcomes. These results, however, should be interpreted with caution. As discussed by the authors, the study was limited by the fact that the utilized methodology only provides a measure of acute changes that have taken place during each discrete recording session. This limitation should be taken into account in long-term supplementation studies, because long-lasting changes in hemodynamic parameters between consecutive recording sessions—undetectable by NIRS—might be induced. The most widely consumed psychoactive compound is caffeine, which is found in various drinks and foods, such as coffee, tea, soft drinks and chocolate. Caffeine is a well-known cerebral vasoconstrictor, which significantly reduces resting cerebral perfusion by antagonizing adenosine receptors in the human brain, especially A1 and A2A subtypes that mediate vasodilation. By using PET methodology, Cameron et al. quantified the magnitude of the decrease in CBF in 1990. A single dose of 250 mg caffeine reduced resting CBF, with decreases ranging from 22% to 30%; this is in line with later studies using ASL and PET. Recently, Turnbull and colleagues evaluated the literature with respect to the effects of acute caffeine intake on CBF in adult subjects. Trials investigating intakes of ≥175 mg observed significant decreases in CBF in all study populations. Studies that administered lower doses only reported significant decreases in caffeine-naïve or low-caffeine consumers, but not in habitual consumers. Altogether, the authors of the recent review concluded that there is some evidence for a dose-response relationship between caffeine intake and CBF, with greater sensitivity in caffeine-naïve study subjects as compared to habitual caffeine consumers.