Month: August 2024

The same miRNA candidate was described in the grape miRNA atlas also predicted to target several genes of DFR-like and one CCR. As for known miRNAs, several members of the miR395 family are differentially expressed at 19 ◦Brix and at harvest in Bolgheri and in both Bolgheri and Riccione, respectively, when comparing the two cultivars. Moreover, miR395f is differentially expressed also in CS at harvest between Montalcino and Bolgheri. This miRNA has been shown to target genes involved in Sulphate assimilation and metabolism , and hence it could be connected to flavonoid and stilbene pathways as suggested by Tavares et al. . miR399 family members are also differentially expressed in several comparisons: at 19 ◦Brix between Riccione and Bolgheri in CS and between Riccione and Montalcino in SG, plus in Montalcino between CS and SG. At harvest, miR399 are differentially expressed in SG in all the three comparisons among vineyards and in Riccione between CS and SG. miR399 is implicated in Phosphate homeostasis being rapidly up-regulated upon Pi starvation . miR399 regulatory network has been shown to be important in flowering time and was identified as a temperature-sensitive miRNA , however its characterization in fruit ripening is lacking, although intriguing. miR396 family members are known to be regulated during organ development, targeting Growth Regulating Factors and also in berry development , and we observed their modulation during berry ripening in our data as well, but more interestingly, drainage planter pot they are also differentially expressed between CS and SG in berries sampled in Bolgheri at 19 ◦Brix.

Finally, the investigation of the global relationships of different small RNA classes and miRNAs expressed in different grapevine cultivars, collected in different vineyards and developmental stages, suggests that although the vineyard may influence their profile of abundance it probably does in less proportion than developmental stage and cultivar. Somehow, this behavior would be expected because although the epigenetic state is dynamic and responsive to both developmental and environmental signals, small RNAs in general and even more miRNAs are well known to play numerous crucial roles at each major stage of plants development . The results here described are in agreement with those reported in the grapevine miRNA atlas , especially with respect to the clustering of berries according to their developmental stage, sustaining the idea that miRNAs influence organ identity and clearly separate green and ripened berries. Also, in the study of the grapevine transcriptome performed by Dal Santo et al. , they observed that other factors such as year and developmental stage had more influence on the gene expression, rather than the environment. Garden or English peas are hardy, cool season, vining annuals grown for their fresh immature green seeds and pods. Peas are classified in the Fabaceae family, which consists of approximately seven hundred genera and seventeen thousand species, with cosmopolitan distribution throughout the temperate, subtropical, and tropical zones of the world. Many species in this family are used as food, forage, timber, and dye plants. Peas are thought to have originated on the eastern rim of the Mediterranean into the mideast. Remains of 7,000- year-old carbonized seeds have been found in Switzerland. By the height of the Greek and Roman civilizations, peas were well established garden, field, and green manure crops. Although peas are not heavy yielders , they are well worth the effort in small gardens. A fresh garden pea’s taste is so far superior to its store-bought equivalent that it is in fact a different vegetable—sugar vs. starch, fresh and lively vs. dull and soggy. Along with spinach, peas usually herald the first working of the soil and planting in spring. If all goes well, sweetness and succulence await you 50 to 70 days after planting seeds. Because they need to be trellised, peas afford excellent opportunities for intercropping .

Once established, peas don’t require much work. They are able to grab onto the trellis and spread themselves out for greater exposed photosynthetic area and better air circulation to reduce the incidence of mildew. They are not very sensitive to weed pressure. In fact, weeding established pea patches can do more harm than good, as peas have numerous surface roots that are sensitive to disturbance.Cultivation. All peas are emphatically cool season crops. Optimally, they are direct sown when the soil temperature averages over 50° F. Sixty to eighty days of temperatures below 80° F are requisite for good production. Soil temperatures of 55°–75° F will yield germinating seedlings in 7–10 days. Overly wet and cold or wet and warm soil increases the percentage of pre-emergent rot. In fact, because pea seeds are large and can imbibe and hold so much water, allowing the soil to dry down significantly between waterings will reduce rot and ensure good germination. Soils. Good drainage is essential for vigorous growth. Early cropping favors sandy soils as they drain and warm more quickly than clays. Peas, as do most legumes, prefer a slightly acid to slightly alkaline soil pH. This higher pH range also provides for the high calcium needs of peas. Peas are intolerant of acid soils. Planting. Peas should be direct seeded or gently transplanted from speedling/plug trays. Seeds can either be drilled in rows or broadcast sown. Drills can be single or double rows 2–4 inches from the trellis to facilitate the tendrils finding the fence. Seeds should be sown heavily , as pea seeds generally have a moderate germination percentage even under ideal conditions. Thin to 8–12 seeds per foot if necessary. The general adage about covering seed two to three times its narrowest diameter applies here; seeds should be planted 1–1 1/2 inches deep, then gently tamped or watered in.

Pea seeds can also be thickly broadcast at 2–3 seeds per square inch, and raked in or covered with soil. Twiggy brush or one to two layers of horizontal netting creates the trellis for support. This broadcast method nets a higher yield per area but can increase incidence of powdery mildew due to restricted air circulation. Note that pea seed viability is relatively short under ideal circumstances. In most home garden situations seed will only last 1–3 years. When ordering pea seeds, think in 1/2 and 1 pound increments . Varietal selection is important as to plant height and time to maturation, but most importantly, pay attention to disease resistance. Basically, if a varietal description doesn’t tout or mention disease resistance, be a smart shopper and realize it probably has none. The more recent the varietal introduction, the more disease resistant it is. Unfortunately, the converse is true as regards heirloom varieties. Nutrients. Because legumes are capable of fixing nitrogen via association with soil bacteria, garden peas are mistakenly thought to need little or no supplemental nitrogen. The truth is that they fix very little nitrogen unless inoculated with the appropriate species of bacterium . They will also use most of the nitrogen they fix and thus don’t particularly enrich the soil for the following crop. Phosphorous is an important nutrient for early root development and to assist with flowering, fruiting and sugar development. Fortunately legumes are efficient at gathering and concentrating phosphorous. Fertilizing the peas prior to planting is optional on enriched or improved soils. A compost of chicken manure, mixed greens, and straw or leaves will boost nitrogen and phosphorous levels. Composts of brassicas and legumes will concentrate phosphorous and calcium. With a single or double row of peas on a trellis in the center of a 48-50-inch-wide raised bed, plant pot with drainage a crop of quick-maturing plants can be grown along the bed edges for more efficient use of space. These include — Planting Days to Crop method harvest baby spinach direct sown 20-30 days mature spinach direct sown 40-50 days cutting lettuces transplanted 20-30 day mature leaf or transplanted 40-50 days mini romaine lettuce butter lettuce transplanted 50-60 days arugula direct sown 20-30 days direct-seeded radishes direct sown 30-40 days Inoculation. Pea plant vigor and thus production is markedly increased when the seed is inoculated with the appropriate species of Rhizobium bacteria . These bacteria can be purchased in a powdered carrying agent from most seed catalogues and nurseries. To inoculate, simply dampen the seed, add powdered inoculate and mix until the seeds have a blackened, peppered look. Plant as soon as possible as the water activates the bacterial population and desiccation is harmful. Watering. Peas require 1–2 inches of water per week. They are intolerant of water stress ; stress will reduce plant size, decrease yield quality—resulting in tough, starchy peas—and severely shorten the length of cropping. Flowering and early fruit set are key times to ensure an even flow of water. While peas have a tap root that can penetrate up to 3 feet, most of the effective feeding roots range from just under the surface to 12–15 inches deep.

Once peas are established, and especially as they begin fruiting, they are subject to a fungal disease called powdery mildew. Overhead watering in conjunction with high humidity will bring on the disease. To help avoid the problem, either water overhead in the morning prior to a sunny stretch of weather so that the plants will dry out, or use drip tape or soaker hose around the base of the plants. Trellis or Fencing. All but the shortest varieties of peas need some sort of support. Although many varieties are advertised as self-supporting , this is not true. Fencing allows closer plant spacing , because the plants can spread out on the trellis or fence. Fencing also increases sunlight interception, minimizes disease, and facilitates easier picking. One age-old tradition for trellising peas is what the British refer to as “twiggy brush.” The branched prunings of last year’s growth from fruit trees inserted into the soil make an excellent, cheap, and somewhat artistic fence. The brush is usually good for two to three years. One- and two-inch chicken wire will also suffice. Unlike beans, peas aren’t a heavy plant or fruit, thus they don’t need as strong a fence. In fact, garden twine run vertically or woven between horizontal 2x4s makes a biodegradable/compostable trellis. String on a wooden A-frame also works. The important thing is to install the trellis prior to planting and to rotate it around the garden so as not to be tempted to repeat the crop in the same bed before two to three years have passed. Crop Establishment. Unless peas are ridiculously oversown, thinning is unnecessary. Spacing plants farther than 3–4 inches apart makes no sense, nor increases yield per foot. One weeding at the 3-inch stage usually keeps the peas ahead of the weeds. Because peas are so succulent, the less the crop is handled the less the physical damage. Even micro-breaks in the foliage can lead to an “invasion” of powdery mildew. Mulch. Mulching helps protect the surface roots from heat and desiccation, thus prolonging cropping as summer approaches. Harvesting. This is usually not a problem on a garden scale. To avoid harming the plants as you pick, hold the stem in one hand and pinch the pod off the vine just behind the calyx with the other hand.As the worldwide obesity epidemic continues to grow, the prevalence of type II diabetes is also rising to a projected 439 million of individuals globally by 2030. Of all obesity-related chronic conditions, diabetes is most strongly associated because of their similar symptomatic manifestations. Type II diabetes and obesity are both characterized by insulin resistance, glucose intolerance, hypoadiponectinemia, endoplasmic reticulum stress, and low-grade inflammation. Over 11% of the 34% of U.S. obese adults are reported to be diabetic in 2011.2 Obesity is generally thought to stem from a combination of genetic and environmental factors. Increased dietary consumption of fat and refined carbohydrates along with decreased physical activity contributes to excessive weight gain while underlying genetic dispositions may lead to differential clinical progression. It has become clear that modest weight reduction can improve glycemic control and alleviate insulin resistance as obesity is considered a modifiable risk factor for diabetes. Furthermore, the comorbidity of diabetes and obesity has been linked to liver and colon cancer risk, although the precise mechanisms remain unresolved.

An anticipated management solution to phenological shifts is planting later ripening and stress tolerant alternative varieties. Government response to climate change will determine the actions European growers are allowed to take to adapt to climate change, considering the current trials of alternative varieties planted in small diversity blocks in France as a positive example . Ancient varieties being tested in temperature gradient greenhouses in Spain for response to combination stresses of drought, heat, and elevated CO2 showed greater resiliency to stress and did not shift phenological timing, although this was a short-term experiment . In some cases, alternative varieties may be hybrid crosses between existing cultivars and later ripening varieties. However, hypothetical crosses between very late ripening varieties were modelled and still struggle to be late-ripening enough to endure the predicted 23-day shift and potential increase of 7°C expected by the end of this century for major wine grape growing areas . Alternative varieties can be identified by oenological and ecological principals that make them suitable candidates for replacing existing cultivars, such as flavor profile and ability to survive long term through stressful climate change conditions . The challenge of adapting new varieties is highlighted by current popular varieties struggling with increases in growing season temperatures , drainage collection pot however a combination of diversity block trials and greenhouse experiments will guide predictions of the best alternatives .

Our present knowledge of grapevine climate niches is limited relative to the vast diversity of cultivars . With California as an example, there are many potential late ripening varieties suitable as alternatives to early ripening Chardonnay that have yet to be tested in diversity blocks . Even clones can have a varied response to climate change variables . Varieties with heat and drought tolerance traits are a starting point for elevated CO2 studies, as we expand from understanding the mechanisms of change into exploring mitigation strategies. Exploring the vast diversity of grapevine using diversity plots is a straightforward ecological approach, which could be enhanced by evaluating the success of plants under several biotic and abiotic stresses predicted for the future. Many studies on the impacts of leaf removal suggest that manipulating canopy cover is an effective way to mitigate phenological shifts caused by climate change . Leaf removal at pre-bloom positively influences cell division in inflorescence, by reducing sugar transport and decreasing flower fertility, which mitigates cluster compactness . Not only can leaf removal aid in delaying phenology, but other positive impacts also include increasing acid to sugar ratio at harvest, increasing production of anthocyanins and flavonoids, and decreasing incidence of bunch rot disease . Ecologists generally study a system’s responses and interactions, and viticulturists need this system perspective for the challenges presented by climate change. Our understanding of the effects of elevated CO2 on the vineyard system is profoundly complicated by the interactive effects of other biotic and abiotic stressors. From an ecological perspective, long-term FACE studies are the most realistic predictors of response to elevated CO2.

Advocating for long-term agroecological studies is necessary to evaluate the top-down and bottom-up impacts of higher carbon availability on pest/disease interactions, grapevine growth and phenology dynamics, and the resulting quality of wine produced. Grapevine physiology will be impacted by elevated carbon dioxide, increasing temperatures, and extreme heat events during the growing season . FACE experiments highlight the necessity of water availability for grapevines to take advantage of increased carbon dioxide for productivity. Soil water availability impacts the opening of stomata, and in the case of Vineyard FACE, the vines had increased gs with more CO2 available . Grapevines may need more water under future climate conditions of elevated CO2 and temperature, while precipitation is expected to decrease in most of the wine growing regions of the world. Desiccation threatens vines through water loss from latent cooling under elevated temperature, resulting in higher cumulative water loss even when operating at higher water use efficiency. The modulating response of stomata documented across literature is dependent on the soil water availability and temperature regimes . In this synthesis, the varying levels of CO2, ambient temperatures, and duration of these experiments could have contributed to these contrasting results of stomatal behavior, as well as the conditions of the chambers and greenhouses, versus FACE infrastructure. Physiological response to abiotic stresses in future climate change conditions is likely to weaken grapevine, creating a vulnerability for biotic stresses such as pests. Overall, chewing pest pressure is anticipated to increase as carbon dioxide and temperature increase . It is unknown whether pest pressure can be compensated by the predicted increase in foliar growth and the effect of lower nutrient density on the populations of pests.

The growing season for grapes may require drastic changes in viticultural practices to manage pests, alleviate heat and drought stress, and predict harvest dates. Fungal infections are responsible for a majority of crop damage; therefore, it is critical to clarify if fungal infection will decrease in the future for predictions of grapevine yield. One of the biggest challenges for grape growers will be the shifts in phenological timing, with the potential for frost at early bud break, alterations in cluster formation and density, and compromising harvest with early maturation. Many of the short-term experiments described here did not find significant effects on phenology and yield, while long term studies account for acclimation and compounding effects of seasonal exposure to elevated carbon dioxide. Predictions of overall vineyard response to climate change are more accurate when experiments are field based, multi-seasonal, and combine the variables of water availability and temperature. Climate change is increasing the growing season temperatures in many of the world’s most important winegrape growing regions. According to the most recent IPCC Assessment Report, Climate Change 2021, global warming is expected to exceed 1.5°C – 2°C during this century . Warming caused by anthropogenic greenhouse gas emissions advances phenology in hundreds of plant species, with increased consequences for perennial crops . Climate warming has already altered the phenology of many plant species globally, including the phenology of valuable crop plants such as grapevine . Winegrapes, a globally important crop both economically and culturally, have become an important indicator of climate change, with well documented advancing phenology, shorter periods between phenological stages , and large inter-annual variability . Adapting to climate change has become a global priority, and the wine industry is likewise looking for more accurate predictive measures of phenology and strategies for future planting. Culturally and economically, grapevine is one of the most valuable crops in the world, evidenced by an annual production of 60 million tons of fruit , with varieties that have been cultivated for thousands of years, selected for color, flavor, and phenological timing . Grape growth and qualities are sensitive to growing season climate fluctuations, and there is a direct link between warming temperatures and early harvest dates . Earlier ripening forces farmers to harvest grapes at optimal sugar levels during warmer periods of the summer. Harvest should ideally occur later during a cooler period of the growing season after the berry has accumulated an appropriate balance of acids of sugars. Early harvesting decreases the quality of wine, round plastic pot evidenced by early ripening significantly altering berry chemical composition . Higher year-round temperatures impact varieties with chilling requirements, such as California’s premiere wine grape, Chardonnay . Globally, there have been shifts of 1-2 weeks for winegrape growing regions . In Europe, the growing season has lengthened by about 11 days over the last 30 years, which will impact grape berry and wine quality . Early bud burst threatens frost damage during volatile Spring temperatures . At present, the winegrape crop in Bordeaux has a month earlier harvest than it did 50 years ago . Models of warming indicate that increases in temperature are not uniform globally and that warming has increased in the major wine growing areas of California and Western Europe more than South America and Australia during the past 50 years . The phenological shifts resulting from growing season temperature increases are documented internationally, and models predicting phenology using temperature are becoming more precise . A multitude of studies both observational and experimental have identified an acceleration of phenology and decrease in periods between stages in response to warming growing seasons , but some show trends of the intervals between each stage widening . Previous grapevine modeling which quantified relative sensitivity of many varieties combined records of phenology across variable microclimates and conditions . Comparing phenological timing from different vineyards done does not capture the influence of the microclimate and microhabitat; elevation, management, soil type, and a multitude of other environmental factors can impact flowering time . The ampelography vineyard at University of California Davis allows for attributing the variation in phenology to the specific sensitivity of cultivars to changes in climate, rather than soil type, irrigation method, pruning, or other major sources of variability found when comparing multiple vineyards.

Temperature is the main driver of phenological development for grapes; heat accumulation impacts the biochemistry important for cell growth . A study of 15 cultivars in Australia documented a plateau in growth between 22-29°C . For many plant species, higher temperatures can stagnate growth, and we expect that some varieties of grapevine would be sensitive to temperatures greater than 40°C . In extreme cases, beyond inducing premature veraison, heat stress will cause loss of berries, inactivate enzymes, and reduce development of flavors critical for wine quality . We integrate into our models a measure of extreme heat to determine its effect on veraison, the stage most likely impacted by these events. In this study, we examined variability in the phenological responses of 137 varieties of Vitis vinifera over a 5-year period. We examined variability in the timing, in terms of growing degree days, of the three major phenological stages: budburst, flowering, and veraison. Our data provide an updated reference to the last major study of variety-level phenological responses in California, which examined 114 varieties nearly 40 years ago . We also compare traditional Vitis vinifera species with hybrids grown at the University of California Davis, originally cultivated by Harold Olmo. Overall, this study offers a comprehensive look at international varieties planted in California their relative phenological response to climate. This study aims to evaluate a wide range of cultivars to identify regions with lower sensitivity to climate change that may be used in adaptation, either through breeding or planting as alternatives. The UC Davis ampelography learning vineyard has been developed over the past decade to include approximately 300 international varieties planted adjacent to the Viticulture and Enology academic building. The vines are planted in groupings by geographic origin, for the purpose of teaching. The vines are trellised using vertical shoot position , with regular irrigation, and are treated throughout the growing season with sulfur sprays for pests and disease. The current study of phenology has been tracking over 130 varieties for over four years and measures the response of the varieties through three main phenological stages: budburst, flowering, and veraison. The phenological data has been collected from UC Davis starting in 2014, continued through 2019. For each of 137 varieties, we recorded the timing of three major phenological stages: Budburst, Flowering, and Veraison. The same individuals were monitored for 5 years. For each vine, three positions on the cordon were chosen at the start of each season before budburst, following the previous year’s recorded positions unless damage had occurred, in which case a nearby cordon was chosen . The primary buds from each two-bud spur were chosen at the most basal position. The three buds were tracked through each phase, treated as technical replicates averaged for an overall estimate for each individual vine. Each vine is a biological replicate, and two vines per cultivar were measured. The timing of budburst was recorded as stages 1-13 , based on the modified Eichhorn–Lorenz stage of the three positions monitored for each vine . The EL scale describes the phenological stages of grapevine and categorizes the stages as follows: budbreak, shoot development, flowering, fruit set, berries pea-sized, veraison, and harvest . Flowering was monitored from these same shoot positions, and once clusters started to develop, they were marked with flagging tape.

The BIA also established a GIS branch that encourages tribes and offers advice on tribal GIS development-although recent funding cutbacks have hampered this effort-and has stockpiled a considerable amount of tribal GIS data in their own library.68 Partly in response to these developments and partly because many Indian communities are deeply suspicious of the BIA-backed tribal governments where GIS managers are housed, a consortium of tribes in the northern Plains and another in the Rio Grande corridor have limited BIA and other federal agencies’ access to some of their databases, declaring some of their GIS proprietary in an attempt to protect sensitive and sacred geographical information. These and other longstanding problems associated with the allocation of political authority in Indian Country caused one geographer to raise questions about the path of GIs development, especially its transformative powers, surveillant capabilities, and political uses.69 Through experience working with GIS, many have come to see it as a contradictory technology that can both empower and marginalize people and communities. Arguments about the social impacts of GIS have grown in recent years, and a debate has surfaced in geography under the heading “GIS and Society.” One of the more interesting proposals emerging from that debate, and worth considering in Indian Country, is for development of “community-integrated GIS that focus on local empowerment through community, not government, 10 liter pot control of and access to digital geographic information. We think this review signals the arrival of geography as a small but important participant in American Indian studies.

Geographers are helping to illuminate the complexity and refinement of environmental modifications made by early Indians and perpetually revise our knowledge of these matters in virtually every region of the continent. They also are busy telling mainstream society that water is a vital cultural source-not just a scarce but necessary physical commodity-with the intent of altering the allocation and cost-benefit models used in managing it. Geographers continue to document land fraud through dispossession research in both historical and contemporary periods, sitting in courtrooms as expert witnesses to do so, and by trying to educate other geographers still steeped in traditions of seeing Indian land claims as an insignificant “interest” competing against “higher” uses. Geographers also continue to assert the centrality of land and place in Indian identity and to explore how attachments to place are manipulated by both individuals and the institutions that would control them. They continue to deconstruct the imprint of European and Euro-North American colonization and to unpack the sounds and silences in historical and contemporary maps and GIS, in part to promote more culturally sensitive applications of technology. Geographers are working with planners and tribal leaders to develop models for cooperative planning for future economic development. Increasingly, they are reflecting on their own positions as privileged researchers, teachers, and consultants. Finally, they are teaching all this to their students. By no means are we implying that everything is just fine in geography. For example, there is a sense among many AISG members that we can and should become more active and involved in issues of importance to Native people throughout North America, to the point of adopting advocacy stances more frequently.

Some of the work cited here leads in that direction, especially the accomplishments of those working on sources and development. However, much of the other work often seems to hold Indians at arm’s length. This may be because many geographers still look askance at colleagues who take on advocacy roles, believing that the mask of apolitical objectivity so often donned in the past is still worth wearing. Perhaps some are justified in their aloofness, preferring the detachment afforded by theoretical questions, or the solitude available in archives and libraries. On the other hand, theoretical and empirical work on material and ideal landscapes, identities, and represen- tations, and the research on historical and contemporary cartographies are among the fastest growing and most intellectually active areas of the field. It is also certain that there is much more that is needed in the field: historical studies exploring continuities in land use and governance for land claims; land use and place-name mapping and GIS for preservation of cultural sources; examinations of the spatial basis for self-governance and self determination to support sovereignty; critical approaches to the role of space and place in the social construction of “Indians” via public perceptions, legislative agendas, corporate intentions, and classroom teaching; continued work in deconstructing colonial legacies and postcolonial discourse in the effort to achieve genuine polyvocality; and analyses of the health care distribution system of the majority and its relationship to alternative medical systems available through local cultural practices. It is encouraging to see a diversity of topics and approaches being engaged with enthusiasm. And in all of it geographers increasingly realize that it is no longer possible to remain completely indifferent about the politics of their own research when studying North America’s Native communities, places where research, self-determination, and sovereignty now typically go hand in hand. Grapevine berry ripening can be divided into three major stages. In stage 1, berry size increases sigmoidally.

Stage 2 is known as a lag phase where there is no increase in berry size. Stage 3 is considered the ripening stage. Veraison is at the beginning of the ripening stage and is characterized by the initiation of color development, softening of the berry and rapid accumulation of the hexoses, glucose and fructose. Berry growth is sigmoidal in Stage 3 and the berries double in size. Many of the flavor compounds and volatile aromas are derived from the skin and synthesized at the end of this stage. Many grape flavor compounds are produced as glycosylated, cysteinylated and glutathionylated precursors and phenolics and many of the precursors of the flavor compounds are converted to various flavors by yeast during the fermentation process of wine. Nevertheless, there are distinct fruit flavors and aromas that are produced and can be tasted in the fruit, many of which are derived from terpenoids, fatty acids and amino acids. Terpenes are important compounds for distinguishing important cultivar fruit characteristics. There are 69 putatively functional, 20 partial and 63 partial pseudogenes in the terpene synthase family that have been identified in the Pinot Noir reference genome. Terpene synthases are multi-functional enzymes using multiple substrates and producing multiple products. More than half of the putatively functional terpene synthases in the Pinot Noir reference genome have been functionally annotated experimentally and distinct differences have been found in some of these enzymes amongst three grape varieties: Pinot Noir, Cabernet Sauvignon and Gewürztraminer. Other aromatic compounds also contribute significant cultivar characteristics. C13-norisoprenoids are flavor compounds derived from carotenoids by the action of the carotenoid cleavage dioxygenase enzymes. Cabernet Sauvignon, Sauvignon Blanc and Cabernet Franc are characterized by specific volatile thiols and methoxypyrazines. Enzymes involved in the production of these aromas have been recently characterized. Phenolic compounds play a central role in the physical mouthfeel properties of red wine; recent work relates quality with tannin levels. While the grape genotype has a tremendous impact on tannin content, the environment also plays a very large role in grape composition. The pathway for phenolic biosynthesis is well known, but the mechanisms of environmental influence are poorly understood. Ultimately, there is an interaction between molecular genetics and the environment. Flavor is influenced by climate, topography and viticultural practices. For example, water deficit alters gene expression of enzymes involved in aroma biosynthesis in grapes, which is genotype dependent, and may lead to increased levels of compounds, such as terpenes and hexyl acetate, 10 liter drainage collection pot that contribute to fruity volatile aromas. The grapevine berry can be subdivided into the skin, pulp and seeds. The skin includes the outer epidermis and inner hypodermis . A thick waxy cuticle covers the epidermis. The hypodermal cells contain chloroplasts, which lose their chlorophyll at veraison and become modified plastids; they are the sites of terpenoid biosynthesis and carotenoid catabolism. Anthocyanins and tannins accumulate in the vacuoles of hypodermal cells. Pulp cells are the main contributors to the sugar and organic acid content of the berries. Pulp cells also have a much higher set of transcripts involved in carbohydrate metabolism, but a lower set of transcripts involved in lipid, amino acid, vitamin, nitrogen and sulfur metabolism than in the skins. Concentrations of auxin, cytokinins and gibberellins tend to increase in early fruit development of the first stage. At veraison, these hormone concentrations have declined concomitant with a peak in abscisic acid concentration just before veraison.

Auxin prolongs the Stage 2 lag phase and inhibits anthocyanin biosynthesis and color development in Stage 3. Grapevine, a non-climacteric fruit, is not very sensitive to ethylene; however, ethylene appears to be necessary for normal fruit ripening. Ethylene concentration is highest at anthesis, but declines to low levels upon fruit set; ethylene concentrations rise slightly thereafter and peak just before veraison then decline to low levels by maturity. Ethylene also plays a role in the ripening of another non-climacteric fruit, strawberry. ABA also appears to be important in grape berry ripening during veraison when ABA concentrations increase resulting in increased expression of anthocyanin biosynthetic genes and anthocyanin accumulation in the skin. ABA induces ABF2, a transcription factor that affects berry ripening by stimulating berry softening and phenylpropanoid accumulation. In addition, ABA affects sugar accumulation in ripening berries by stimulating acid invertase activity and the induction of sugar transporters. It is not clear whether ABA directly affects flavor volatiles , but there could be indirect effects due to competition for common precursors in the carotenoid pathway. Many grape berry ripening studies have focused on targeted sampling over a broad range of berry development stages, but generally with an emphasis around veraison, when berry ripening is considered to begin. In this study, a narrower focus is taken on the late ripening stages where many berry flavors are known to develop in the skin. We show that that the abundance of transcripts involved in ethylene signaling is increased along with those associated with terpenoid and fatty acid metabolism, particularly in the skin.Cabernet Sauvignon clusters were harvested in 2008 from a commercial vineyard in Paso Robles, California at various times after veraison with a focus on targeting °Brix levels near maturity. Dates and metabolic details that establish the developmental state of the berries at each harvest are presented in Additional file 1. Berries advanced by harvest date with the typical developmental changes for Cabernet Sauvignon: decreases in titratable acidity and 2- isobutyl-3-methoxypyrazine concentrations and increases in sugar and color . Transcriptomic analysis focused on four harvest dates having average cluster °Brix levels of 22.6, 23.2, 25.0 and 36.7. Wines made in an earlier study from grapes harvested at comparable levels of sugars or total soluble solids to those in the present study showed clear sensory differences. Six biological replicates, comprising two clusters each, were separated into skins and pulp in preparation for RNA extraction and transcriptomic analysis using the NimbleGen Grape Whole-Genome Microarray.A note of caution must be added here. There are high similarities amongst members in certain Vitis gene families , making it very likely that cross-hybridization can occur with probes on the microarray with high similarity to other genes. We estimate approximately 13,000 genes have the potential for cross-hybridization, with at least one probe of a set of four unique probes for that gene on the microarray potentially cross-hybridizing with probes for another gene on the microarray. Genes with the potential for crosshybridization have been identified and are highlighted in light red in Additional file 2. The rationale to include them is that although individual genes can not be uniquely separated, the probe sets can identify a gene and its highly similar gene family members, thus, providing some useful information about the biological responses of the plant. An additional approach was taken, removing cross-hybridizing probes before quantitative data analysis . Many of the significant genes were unaffected by this processing, but 3600 genes were completely removed from the analysis. Thus, it was felt that valuable information was lost using such a stringent approach. The less stringent approach allowing for analysis of genes with potential crosshybridization was used here in the rest of the analyses. To assess the main processes affected by these treatments, the gene ontologies of significantly affected transcripts were analyzed for statistical significance using BinGO. Based on transcripts that had significant changes in abundance with °Brix level, 230 biological processes were significantly over represented in this group . The three top over represented processes were response to abiotic stress, biosynthetic process, and response to chemical stimulus, a rather generic set of categories.

The closest imaginable analog of the tBLG/hBN Chern magnet in this system is one in which interactions favor the formation of a valley-polarized ferromagnet, at which point the finite Chern number of the valley subbands would produce a Chern magnet. This was widely assumed to be the case at the time of the system’s discovery. There is now substantial evidence that this system instead forms a valley coherent state stabilized by its spin order, which would require a new mechanism for generating the Berry curvature necessary to produce a Chern magnet. In general I think it is fair to say that the details of the microscopic mechanism responsible for producing the Chern magnet in this system are not yet well understood. In light of the differences between these two systems, there was no particular reason to expect the same phenomena in MoTe2/WSe2 as in tBLG/hBN. As will shortly be explained, current-switching of the magnetic order was indeed found in MoTe2/WSe2. The fact that we find current-switching of magnetic order in both the tBLG/hBN Chern magnet and the AB-MoTe2/WSe2 Chern magnet is interesting. It may suggest that the phenomenon is a simple consequence of the presence of a finite Chern number; i.e., that it is a consequence of a local torque exerted by the spin/valley Hall effect, which is itself a simple consequence of the spin Hall effect and finite Berry curvature. These ideas will be discussed in the following sections. In spin torque magnetic memories, electrically actuated spin currents are used to switch a magnetic bit. Typically, hydroponic vertical garden these require a multi-layer geometry including both a free ferromagnetic layer and a second layer providing spin injection.

For example, spin may be injected by a nonmagnetic layer exhibiting a large spin Hall effect, a phenomenon known as spin-orbit torque. Here, we demonstrate a spin-orbit torque magnetic bit in a single two-dimensional system with intrinsic magnetism and strong Berry curvature. We study AB-stacked MoTe2/WSe2, which hosts a magnetic Chern insulator at a carrier density of one hole per moir´e superlattice site. Magnetic imaging reveals that current switches correspond to reversals of individual magnetic domains. The real space pattern of domain reversals aligns with spin accumulation measured near the high Berry curvature Hubbard band edges. This suggests that intrinsic spin or valley Hall torques drive the observed current-driven magnetic switching in both MoTe2/WSe2 and other moir´e materials. The switching current density is significantly less than those reported in other platforms, suggesting moir´e heterostructures are a suitable platform for efficient control of magnetic order. To support a magnetic Chern insulator and thus exhibit a quantized anomalous Hall effect, a two dimensional electron system must host both spontaneously broken time-reversal symmetry and bands with finite Chern numbers. This makes Chern magnets ideal substrates upon which to engineer low-current magnetic switches, because the same Berry curvature responsible for the finite Chern number also produces spin or valley Hall effects that may be used to effect magnetic switching. Recently, moir´e heterostructures emerged as a versatile platform for realizing intrinsic Chern magnets. In these systems, two layers with mismatched lattices are combined, producing a long-wavelength moir´e pattern that reconstructs the single particle band structure within a reduced superlattice Brillouin zone. In certain cases, moir´e heterostructures host superlattice minibands with narrow bandwidth, placing them in a strongly interacting regime where Coulomb repulsion may lead to one or more broken symmetries.

In several such systems, the underlying bands have finite Chern numbers, setting the stage for the appearance of anomalous Hall effects when combined with time-reversal symmetry breaking. Notably, in twisted bilayer graphene low current magnetic switching has been observed, though consensus does not exist on the underlying mechanism. Although these magnets occur in an atomic crystal, they are composed entirely of electrons we have forced into the system with an electrostatic gate, and as a result we can expect their magnetizations to be considerably smaller than fully spin-polarized atomic crystals. We will use the nanoSQUID microscope to image these magnetic phases. An optical image of the ABC trilayer graphene device used to produce data for the publications is presented in Fig. 7.5A. A black dashed lineoutlines the region we will be imaging using the nanoSQUID microscope. A nanoSQUID image of this region using AC bottom gate contrast is presented in Fig. 7.5B. This magnetic image was taken in the same phase in which we observe magnetic hysteresis, as presented in Fig. 7.4E. Clearly the system is quite magnetized; we also see evidence of internal disorder, likely corresponding to bubbles between layers of the heterostructure. We can park the SQUID over a corner of the device and extract a density- and displacement field-tuned phase diagram of the magnetic field generated by the magnetization of the device; this is presented in Fig. 7.5C. Electronic transport data of the same region is presented in Fig. 7.5D. The spin magnet has only a weak impact on electronic transport, but the valley ferromagnet couples extremely strongly to electrical resistance. The system also supports a pair of superconductors, including a spin-polarized one; these phases are subjects ofcontinued study. Capacitance data over the same region of phase space is presented in Fig. 7.5E. The first systems with nonzero Chern numbers to be discovered were systems with quantum Hall effects. Quantum Hall insulators behave a lot like Chern magnets but are generally realized at much higher magnetic fields, and Berry curvature in these systems comes from the applied magnetic field, not from band structure. The fact that resistance in these materials is an intrinsic property and not an extrinsic one had implications for metrology that were immediately obvious to the earliest researchers that encountered the phenomenon. All of these devices have resistances that depend only on fundamental physical constants, so a resistance standard composed of these materials need not obey any particular geometric constraints, and can thus be easily replicated. The case for quantum Hall resistance standards was strong enough for the the National Institute for Standards and Technology to rapidly adopt them, and today the Ohm is defined by a graphene quantum Hall resistance standard at NIST. There are some downsides to the quantum Hall resistance standard.

The modern voltage standard is a superconducting integrated circuit known as the Josephson voltage standard; it uses Shapiro steps to relate the absolute size of a set of voltage steps to a frequency standard. Because the voltage standard and resistance standard are independently fixed to physical phenomena, current standards are necessarily defined by the relationship between these two different standards. Unfortunately, the superconducting integrated circuits used as Josephson voltage standards must be operated in very low ambient magnetic field, because large magnetic fields destroy superconductivity. This makes them incompatible with the graphene quantum Hall resistance standard, which must operate in large magnetic fields, generally B > 5T. This is a surmountable problem- in practice it is handled by storing the two standards in different cryostats, or with significant magnetic shielding between them- but the significant distance separating the standards reduces the precision with which the current standard can be defined with respect to our current resistance and voltage standards. One possible way to resolve this conflict is to replace the quantum Hall resistance standard with a Chern magnet resistance standard. Chern magnets show quantized anomalous Hall effects at low or zero magnetic field, meaning they can be installed in very close proximity to Josephson voltage standards in calibration cryostats. Unfortunately, doped topological insulators have such small band gaps that even at the base temperatures of dilution fridges, vertical vegetable tower there is enough thermal activation of electrons into the bulk to limit the precision of quantization of the quantized anomalous Hall effect in these systems. This made the class of Chern magnets discovered in 2013 unsuitable as replacements for the graphene quantum Hall resistance standard. Since intrinsic Chern magnets have now been discovered, and are observed to have band gaps considerably exceeding those of doped topological insulators, it might make sense to replace the graphene quantum Hall resistance standard with an intrinsic Chern magnet resistance standard. The ease of replication of the fabrication process of MoTe2/WSe2 makes that material particularly intriguing as a candidate material for a new resistance standard, but over the past few years new intrinsic Chern magnets have been discovered almost every year, so we may soon be discussing much better materials for this application. In any case, it seems possible and perhaps even likely that Chern magnets will supplant quantum Hall systems as resistance standards in the near future.Of course, that fact didn’t take away the many advantages of magnetic memories, and magnetic memories still persist in a variety of niche applications that depend particularly strongly on one of these advantages. Many computers destined to spend their lives in space still use hard drives, and sensors designed to operate over a wide range of temperatures and with intermittent access to power often use non-volatile magnetic memories as well. This has led researchers to search for phenomena and device architectures that allow magnetic order to be switched either with electrical currents or electrostatic gates.

Until recently, the best technology available capable of electronic switching of magnetism used spin-orbit torques. In a spin-orbit torque device, current through a system with a strong spin Hall effect pumps spin into a separate magnet, which is eventually inverted by the torque exerted by those spins. This technology has matured considerably over the past few years, producing a cascade of new records for low current density magnetic switching and even a few consumer products in the memory market. The discovery of the first intrinsic Chern magnets produced a fascinating surprise for this field. The exotic orbital magnet in twisted bilayer graphene was found to be switchable with extremely small pulses of current, and the resulting current-switchable magnetic bits displaced previously realized spin-orbit torque devices as the ultimate limit in low-current control of magnetism. A flurry of theoretical investigation of these systems followed, dedicated primarily to identifying and generalizing the mechanism underlying current control of magnetism in these systems. A few years later, AB-MoTe2/WSe2 joined twisted bilayer graphene, with a similarly small magnetic switching current. In the intervening time, a new phenomenon had been observed- switching of a Chern magnet with an electrostatic gate, in twisted monolayer/bilayer graphene. All of these phenomena represent newly discovered and now more or less well understood mechanisms for controlling magnetic bits electronically, and by the performance metrics used in the literature they reign supreme. Several electronic switching phenomena known in intrinsic Chern magnets are summarized in Fig. 8.3. Chern magnets differ from the magnetic materials used in more traditional magnetic memories in a wide variety of intriguing ways other than their electronic switch ability. Chern magnets are not metals and thus don’t have the same limitations as metallic magnetic memories. For example, the resistance of a Chern magnet is independent of its size, depending only on fundamental physical constants. This makes the resistance of a Chern magnet completely insensitive to miniaturization. Dissipation does occur in Chern magnets, but it occurs only at the contacts to the Chern magnet, so once electrons enter the crystal they can undergo very long range transport completely free of dissipation. Chern magnets are atomically thin in the out-of-plane direction, and of course if they are separated by insulators they can easily be stacked to increase magnetic bit density. Chern magnets are two dimensional materials, and two dimensional materials already have small radiation cross-sections relative to three dimensional crystals like silicon, but the conduction path through a Chern magnet is both one dimensional and topologically protected, so it is overwhelmingly likely that Chern magnet memories would be even more radiation hard than the thin semiconducting films that form the current state of the art. All of these ideas make Chern magnets interesting candidates as substrates for magnetic memories of the distant future. Of course none of these ideas have been implemented in technologies yet, and that is because intrinsic Chern magnets have only been realized at fairly low temperatures . All of the magnetic memory applications we’ve discussed depend critically on the discovery of intrinsic Chern magnets at considerably higher temperatures, and ideally room temperature.

It also depends on very strong in-plane bonds within the material, which must support the large stresses associated with reaching such high aspect ratios; materials with weaker in-plane bonds will rip or crumble. In practice these materials are almost always processed further after they have been mechanically exfoliated, and the preparation process typically begins when they are pressed onto a silicon wafer to facilitate easy handling. Samples prepared in this way are called ‘exfoliated heterostructures.’ It is of course interesting that this process allows us to prepare atomically thin crystals, but another important advantage it provides is a way to produce monocrystalline samples without investing much effort in cleanly crystallizing the material; mechanical separation functions in these materials as a way to separate the domains of polycrystalline materials. Graphene was the first material to be more or less mastered in the context of mechanical exfoliation, but a variety of other van der Waals materials followed, adding substantial diversity to the kinds of material properties that can be integrated into devices composed of exfoliated heterostructures. Monolayer graphene is metallic at all available electron densities and displacement fields, but hexagonal boron nitride, or hBN, is a large bandgap insulator, making it useful as a dielectric in electronic devices. Exfoliatable semiconductors exist as well, hydroponic bucket in the form of a large class of materials known as transition metal dichalcogenides, or TMDs, including WSe2, WS2, WTe2, MoSe2, MoS2, and MoTe2.

Exfoliatable superconductors, magnets, and other exotic phases are all now known, and the preparation and mechanical exfoliation of new classes of van der Waals materials remains an area of active research. Once two dimensional crystals have been placed onto a silicon substrate, they can be picked up and manipulated by soft, sticky plastic stamps under an optical microscope. This allows researchers to prepare entire electronic devices composed only of two dimensional crystals; these are known as ‘stacks.’ These structures have projections onto the silicon surface that are reasonably large, but remain atomically thin- capacitors have been demonstrated with gates a single atom thick, and dielectrics a few atoms thick. Researchers have developed fabrication recipes for executing many of the operations with which an electrical engineer working with silicon integrated circuits would be familiar, including photolithography, etching, and metallization. I think it is important to be clear about what the process of exfoliation is and what it isn’t. It is true that mechanical exfoliation makes it possible to fabricate devices that are smaller than the current state of the art of silicon lithography in the out-of-plane direction. However, these techniques hold few advantages for reducing the planar footprint of electronic devices, so there is no meaningful sense in which they themselves represent an important technological breakthrough in the process of miniaturization of commercial electronic devices. Furthermore, and perhaps more importantly, it has not yet been demonstrated that these techniques can be scaled to produce large numbers of devices, and there are plenty of reasons to believe that this will be uniquely challenging. What they do provide is a convenient way for us to produce two dimensional monocrystalline devices with exceptionally low disorder for which electron density and band structure can be conveniently accessed as independent variables.

That is valuable for furthering our understanding of condensed matter phenomena, independent of whether the fabrication procedures for making these material systems can ever be scaled up enough to be viable for use in technologies. Consider the following procedure: we obtain a pair of identical two dimensional atomic crystals. We slightly rotate one relative to the other, and then place the rotated crystal on top of the other . The resulting pattern brings the top layer atoms in alignment with the bottom layer atoms periodically, but with a lattice constant that is different from and in practice often much larger than the lattice constant of the original two atomic lattices. We call the resulting lattice a ‘moir´e superlattice.’ The idea to do this with two dimensional materials is relatively new, but the notion of a moir´e pattern is much older, and it applies to many situations outside of condensed matter physics. Pairs of incommensurate lattices will always produce moir´e patterns, and there are many situations in daily life in which we are exposed to pairs of incommensurate lattices, like when we look out a window through two slightly misaligned screens, or try to take pictures of televisions or computer screens with our camera phones. Of course these ‘crystals’ differ pretty significantly from the vast majority of crystals with which we have practical experience, so we’ll have to tread carefully while working to understand their properties. To start with, if we attempt to proceed as we normally would- by assigning atomicorbitals to all of the atoms in the unit cell, computing overlap integrals, and then diagonalizing the resulting matrix to extract the hybridized eigenstates of the system- we would immediately run into problems, because the unit cell has far too many atoms for this calculation to be feasible. Some moir´e superlattices that have been studied in experiment have thousands of atoms per unit cell. There exist clever approximations that allow us to sidestep this issue, and these have been developed into very powerful tools over the past few years, but they are mostly beyond the scope of this document. I’d like to instead focus on conclusions we can draw about these systems using much simpler arguments.

The physical arguments justifying the existence of electronic bands apply wherever and whenever an electron is exposed to an electric potential that is periodic, and thus has a set of discrete translation symmetries. For this reason, even though the moir´e superlattice is not an atomic crystal, we can always expect it to support electronic band structure for the same reason that we can always expect atomic crystals to support band structure. Two crystals with identical crystal symmetries will always produce moir´e superlattices with the same crystal symmetry, so we don’t need to worry about putting two triangular lattices together and ending up with something else.Another property we can immediately notice is that the electron density required to fill a moir´e superlattice band is not very large. This can be made clear by simply comparing the original atomic lattice to a moir´e superlattice in real space . Full depletion of a band in an atomic crystal requires removing an electron for every unit cell , and full filling of the band occurs when we have added an electron for every unit cell. We have already discussed how this is not possible for the vast majority of materials using only electrostatic gating, because the resulting charge densities are immense. Full depletion of the moir´e band, on the other hand, requires removing one electron per moir´e unit cell, and the moir´e unit cell contains many atoms . So the difference in charge density between full filling and full depletion of an electronic band in a moir´e superlattice is actually not so great , and indeed this is easily achievable with available technology. Before we go on, I want to make a few of the limitations of this argument clear. There are two things this argument does not necessarily imply: the moir´e bands we produce might not be near the Fermi level of the system at charge neutrality, and the bandwidth of the moir´e superlattice need not be small. In the first case, we won’t be apply to modify the electron density enough to reach the moir´e band, and in the latter, stackable planters we won’t be able to fill the moir´e band’s highest energy levels using our electrostatic gate. We know of examples of real systems with moir´e superlattice bands that fail each of those criteria. But if these moir´e superlattice bands are near charge neutrality, and if their bandwidths are small, then we should be able to easily fill and deplete them with an electrostic gate. A variety of scanning probe microscopy techniques have been developed for examining condensed matter systems. It’s easy to justify why magnetic imaging might be interesting in gate-tuned two dimensional crystals, but magnetic properties of materials form only a small subset of the properties in which we are interested. Scanning tunneling microscopy is capable of probing the atomic-scale topography of a crystal as well as its local density of states, and a variety of scanning probe electrometry techniques exist as well, mostly based on single electron transistors. It’s worth pointing out that if you’re interested specifically in performing a scanning probe microscopy experiment on a dual-gated device, then these techniques both struggle, because the top gate both blocks tunnel current and screens out the electric fields to which a single electron transistor would be sensitive. Magnetic fields have an important advantage over electric fields: most materials have very low magnetic susceptibility, and thus magnetic fields pass unmodified through the vast majority of materials . This means that magnetic imaging is more than just one of many interesting things one can do with a dual-gated device; in these systems, magnetic imaging is a member of a very short list of usable scanning probe microscopy techniques.

The simplest way in which we can use our nanoSQUID magnetometry microscope is as a DC magnetometer, probing the static magnetic field at a particular position in space . There are situations in which this is a valuable tool, and we will look at some DC magnetometry data shortly, but in practice our nanoSQUID sensors often suffer from 1/f noise, spoiling our sensitivity for signals at low or zero frequency. One of the primary advantages of the technique is its sensitivity, and to make the best of the sensor’s sensitivity we must measure magnetic fields at finite frequencies. We have already discussed how we can use electrostatic gates to change the electron density and band structure of two dimensional crystals. We will discuss shortly a variety of gate-tunable phenomena with magnetic signatures that appear in these systems. It follows, of course, that we can modulate the magnetic fields emitted by these electronic phases and phenomena by modulating the voltages applied to the electrostatic gates we use to stabilize these phases. This is illustrated in Fig. 1.15C: an AC voltage is applied to the bottom gate relative to the two dimensional crystal, and the local magnetic field is sampled at the same frequency by the SQUID. We can use this techniqueto extract δV δB at an array of positions above the two dimensional crystal. This technique is very simple and powerful, but it has a few important drawbacks. It can only produce a quantitative measurement of B if the same scan is performed for a large set of gate voltages, so that δV δB can be integrated. Many ferromagnets, for example, can be locked into quantum states that aren’t their ground states using a ferromagnetic hysteresis loop, and rapidly tuning the electron density tends to relax these phases to their ground states. So whenever we are interested in probing metastable magnetic states, we need to be careful about using this measurement method. Of course, we can also modulate the magnetic field through the nanoSQUID by modulating the position of the nanoSQUID. Since the magnetic field varies rapidly in space, we can often expect to get strong signals when we probe δB δx this way . The position of the nanoSQUID is rapidly modulated using a piezoelectric tuning fork pressed against the side of the nanoSQUID sensor; the details of the tuning fork hardware and measurement are discussed further in the appendix. This measurement method allows us to use the nanoSQUID to probe metastable or even non-gate-tunable magnetic phenomena at finite frequency. It has a few drawbacks of its own, though. The nanoSQUID sensors have parasitic sensitivities to local temperature and electric potential , and if these vary in space the resulting signals will contaminate our magnetic field data. As a result, whenever we use this contrast mechanism we must try to extract differences between two different magnetic states if we want quantitatively precise information about the magnetic field. We can also apply an AC current in the plane of the two dimensional crystal. Large currents will emit detectable magnetic fields through the Biot-Savart law, and under those conditions we can use this contrast mechanism to reconstruct the current density through our two dimensional crystal.

Our studies suggest a combination of its transmission dynamics and how they are affected by management issues, such as the quantity of shade and the density of planting, plus a variety of control from above elements represent a source of control, which sometimes fails .Understanding the general structure of ecological communities has long been a central goal of ecology, from Haeckel to us. Empiricists commonly, and probably necessarily, focus on the community of X, which is to say an assemblage of species defined by some set of criteria: the fungal community of Lake Wobegon, the community of gall-forming insects of oak trees, the microbial community of the human gut, the community of four ciliate species, and so on. Theoreticians perhaps feel less constraint. In the present article, we have defined the community as the herbivores of the coffee plant and their associates, in which top-down control is the goal of management . The framing of regulation from above from theoretical ecology translates directly into biological control from agroecology. Indeed, in agroecology regulation from above is elementary, in that the top-down agents are frequently obvious . However, stopping at that level of understanding may obscure more than clarify, stacking pots much as the simple phrase controlled from above may indeed obscure . Precisely how that control is affected may involve many complicated interactions and contingencies, making, we argue, the framing of complex systems a necessary one.

The fungus that attacks the scale is most efficient when the scale is hyper dense at a local level, something that cannot happen unless it is under the protection of a mutualistic ant, which deters the other predator , which, however, is able to take advantage of a spatial pattern that is self-organized through a Turing-like process, and so forth. Indeed, we argue that the understanding we claim to have of this system so far comes from detailed study, both empirical and theoretical, and, most importantly is dramatically enriched through the application of some of the concepts newly developed in the distinct field of complex systems. Almost 10 years ago, some of us published a summary of this overall system , suggesting that understanding it required more than just an identification of who eats whom. This update emphasizes that point. Our narrative in the present article is perhaps a bit heterodox. We study a very complicated system , and we seek to understand it through theoretical ecology. To some, at least in the recent past, this might imply a large-scale computer model or sophisticated data manipulation. Our approach is distinct, recalling the wisdom of Levins’ paper on the strategy of model building. We seek to understand, at a deep level, how this system works, not necessarily for the purpose of predicting its future state. We offer theoretical propositions, many of which are stimulated by mathematical arguments, but we do not seek what postmodern thinkers would have called a “totalizing discourse” with a large-scale model. Rather, we seek to use recent advances in complex systems as a way of stimulating thought, with the mathematical models that go along with them as “educating our intuition,” as Levins urged frequently. The models themselves represent approximate metaphors for this complex reality, all fitting into a hierarchy of understanding , which is mainly qualitative even though originally formulated through mathematical reasoning.Furthermore, our claim that this is a complex reality is meant to imply something deeper than the obvious claim that it is complicated. It is a complex system.

For example, if the only players in the system were Azteca, C. viridis, and A. orbigera, the system wouldn’t be exceptionally complicated , but it would be a complex system, because it would have a clear emergent property . Even adding the phorid would mean two predators and two prey, but the spatial pattern that emerges and the dependence of one system on a second system operative at a completely distinct time scale is an essential structural component of the system as a whole. The emergence would defy understanding if only the separate component parts were studied, which is to say if it were approached from a purely reductionist perspective. If the only players were the ants and the coffee berry borer, but the ants did not exhibit trait-mediated indirect interactions, the system would be complicated but not necessarily complex. This distinction between complicated and complex is important for our narrative. Because it is a complex system, it requires a more holistic approach to understand and manage, and there’s more potential for surprise . A merely complicated system would not have these characteristics. That our model system is coffee is significant in several ways. First, traditional coffee management, with its characteristic shade trees, helps to create landscapes that are friendly to biodiversity conservation . It is a classic high-quality matrix for all sorts of animals and plants. Second, it involves a commodity that is of extremely high value, sometimes the main source of wealth for entire countries. Third, it is the basis of livelihood for millions of small farmers the world over. Fourth, when properly cultivated with shade, it joins other agroforestry systems in the worldwide struggle against climate change. Given all that, understanding the details of its operation would seem worthwhile, and marshaling recent insights from complex systems to anchor that narrative brings one of the classical questions of community ecology into focus as a practical issue. Consequently, besides being of potential importance for ecology, it makes ecology important for some practical aspects of this important crop.

It is, for example, evident from only a qualitative understanding of the control from above system that a key element is the species of ant that nests in the shade trees and that, if those shade trees are eliminated , the whole control structure will be dramatically interrupted. Questions also arise about generality. Does this model system reflect something more general about the structure of control from above, or does it simply reflect interactions of this one particular system? First, most terrestrial systems have a spatial component involved, and framing the spatial component as one in which a subsystem operates to effectively create a spatial pattern in which other subsystems may operate is likely to apply frequently. Indeed, the idea of a predator–prey system generating a Turing pattern may be increasingly appreciated as more research programs interrogate the idea . Second, population dynamics unfolding on this space are likely to be nonlinear, and this nonlinearity will frequently be of the form that critical transitions lead to an alternative equilibrium within hysteretic zones, which may be multiple and constrain the herbivores above which control is being exerted . Third, the idea that multiple herbivores have their own suite of controlling factors is almost certainly true, but the idea that there will be connections, even if weak, with other sub-components of the control from above, is likely to be characteristic. These three generalities encompass the complex systems topics of Turing pattern formation, critical transitions, hysteresis, chaos, basin boundary collisions, trait-mediated indirect interactions, and scale-dependent spatial processes, all of which are exemplified in our model system, and certainly may be embedded in other systems of control from above. The message is not that these particular topics are essential but, rather, that control from above is not the one-dimensional process frequently imagined of a predator guild preying on a prey guild but, instead, a complex community of predators and parasites and diseases that interact with one another in complicated ways to eventually generate a self-organized system that exerts effective control over the herbivory. Much as one might say that the vertebrate circulatory system is responsible for bringing oxygen to each cell in the body, one might similarly simplify and say that natural enemies in the coffee agroecosystem are responsible for the regulation of potential pests. However, it is the heart, the veins, the arteries, exchanges across membranes, strawberry gutter system and so forth that tell the real story of how the delivery of oxygen to our tissues actually happens. It is a complex system, the details of which are certainly of interest to health and healing. Similarly, in our agroecosystem example, the subsystem that creates large-scale pattern sets the stage for a subsystem involving a predator and a disease that affect regulation of one pest, whereas the community structure of ants determines the efficiency of their predacious activities on a second pest and the disease that helps regulate the first pest is an antagonist to the third pest. This is all to say that yes, it is control from above, but that control is delivered through the ecological complexity of the community of natural enemies. It is misleading to suggest that listing the natural enemies and merely identifying them as such is sufficient. It is only through the lens of the reality of its state as a complex system that we may gain full appreciation of the ecological principle of top-down control, which then can be fully exploited in attempts to aid the management of this important agroecosystem. There is something of a conundrum in this narrative.

Although it is clear that knowledge of all the ecological complexity could inform practical decisions that producers might want to make, is such detailed knowledge really necessary to provide useful advice to the farmer? If ecological knowledge of the particular system is primitive, could well meaning agroecological advisors give advice that will have unintended negative consequences? Post-WWII industrial agriculture enthusiasts embraced DDT and other pesticides creating the well-known pesticide treadmill that haunts us still today. Indeed, that is one of the issues that caused many environmentally conscious analysts to call for the science of ecology to be more actively embraced by agricultural planners. However, ecology is complicated. Secondary consequences cannot necessarily be predicted short of detailed study and the normal rules of thumb extrapolated from a few experiments or extralocal traditions could backfire. Perhaps the famous medical practitioner’s oath primum non nocere makes sense in agriculture as well. As farmers seek solutions to perceived problems on their farms, agroecologists rightly wish to use the science of ecology to help. However, frequently , ecological knowledge of the particular system is not very well understood because it is only recently that agroecological advocates have begun to break into the mainstream, and the basic research required to understand some of the vexing problems the farmers face has yet to be done. It is therefore common to use a few rules of thumb: avoid monocultures, don’t poison your natural enemies, maintain healthy soil, and so on. Such rules of thumb, on the basis of perceived ecological rules, for the most part make sense and probably conform well to the admonition primum non nocere. However, it is worth remembering the dust bowl, pest resurgence following pesticides, ocean dead zones, and other consequences that we live with today because a previous generation of farm advocates, equally sincere in their desires to help farmers, were prematurely confident in the ability of their tools to help the farmer.There are a growing number of examples of a positive relationship between diversity and ecosystem service. 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 .

The BLS estimates that Colorado’s unemployment rate in December 2017 was 3.0 percent, while Denver’s unemployment rate was 2.9 percent . Earlier in 2017, the state unemployment reached a record low of 2.3 percent. This is among the lowest unemployment rates recorded by any state in recent decades. The other six metropolitan statistical areas tracked by the BLS averaged an unemployment rate of 3.4 percent. Fort Collins had the lowest unemployment rate at 2.5 percent. Only two cities had an unemployment rate greater than the national unemployment rate of 4.1 percent—Grand Junction and Pueblo . Personal income growth among state residents reached nearly 8 percent in 2014, but growth slowed over the next two years. This trend reversed in 2017 as personal income growth increased to 5.4 percent. This growth rate exceeds the national rate by more than 2 percentage points . According to the OSPB, per capita income and wage growth in Colorado over the past year also outpaced the national figures. With regard to party registration in Colorado, voters were nearly evenly divided among Democratic, Republican, and unaffiliated categories at the time of the 2016 election. According to voter registration data from the Secretary of State’s office, the state had nearly 3.3 million active voters in November 2016. A plurality of these voters registered as unaffiliated , hydroponic nft while the share of Democratic and Republican were nearly equivalent. In February 2018, the number of active voters decreased relative to November 2016 by about 1.7 percent.

This may be partially attributable to controversy surrounding President Donald Trump’s Commission on Voter Fraud, which made data privacy a concern after the commission requested, “voluminous information on voters, including names, addresses, dates of birth, political affiliations and the last four digits of Social Security numbers, along with voting history” . Fifteen months after the 2016 election, the proportion of unaffiliated voters in the state increased to 36.3 percent, while the share of Democrats and Republicans decreased to 31.1 percent and 30.8 percent, respectively . This change is likely driven by primary election reforms approved by voters in the 2016 election. Voters overwhelmingly approved Proposition 107, which adopted a presidential primary in lieu of the existing caucus system, and Proposition 108, which allowed unaffiliated voters to participate in the party primary of their choice. Previously, unaffiliated voters were prohibited from participating in any primary elections or caucus meetings. Because this reform allows unaffiliated voters to participate in the primary of their choosing, it appears that a substantial number of Coloradans changed their party registration status to take advantage of this new opportunity. Colorado’s economic trajectory remains generally positive. In late March, the Governor’s Office of State Planning and Budgeting released its revised economic forecast. The report summarized the condition of Colorado’s economy by stating, “Colorado’s economy is on solid footing with strong employment growth and expectations of an ongoing expansion. New business formation continues to grow, while Colorado oil production is at record levels. Although much of the state’s economic growth has occurred along the Front Range, stabilizing farmland values and increases in energy prices and production have recently supported rural areas as well. Looking forward, higher costs of living and tight labor market conditions are expected to constrain further growth through the forecast period” .

The OSPB characterized the 3.1 percent increase in General Fund revenue in the 2016–2017 fiscal year as“modest,” while projecting a larger revenue increase for the 2017–2018 fiscal year of 12.9 percent. According to the OSPB, the revenue forecast for the 2018–2019 fiscal year is projected to grow from $11.6 to $12.0 billion. The more substantial increase during the 2017–2018 fiscal year is attributable to “strong economic growth, a rebound in corporate income tax receipts, robust investment income gains, and federal tax changes” . Regarding the latter, the $1.5 trillion tax reform package signed into law by President Trump in December 2017, among other things, lowered individual income tax rates and nearly doubled the standard deduction for individuals and families. Increasing the standard deduction makes it likely that more tax returns would be filed using the standard deduction instead of itemized deductions. This, combined with reduced tax rates, mean that individuals are likely paying less in federal taxes despite having a larger taxable income. Because Colorado state taxes are 4.63 percent of each individual’s federal taxable income, the state projects to receive greater tax revenue while most state residents can expect to pay less in federal taxes. This is particularly notable in Colorado where TABOR requires any tax increases to go before the electorate for approval in a general election. Accordingly, while the state income tax rate remains unchanged, the tax cut at the federal level in effect imposes a tax increase at the state level as a result of many tax returns reporting a greater taxable income. Most of the state’s General Fund revenue comes from individual and corporate taxes. The OSPB reports that income tax with holdings increased by more than 9 percent over the past year . Partly because of the new federal tax law, the OSBP claims that there is a “high degree of uncertainty surrounding the forecast for individual income tax collections” . While individual income tax revenues increased by 3.6 percent in the prior fiscal year, the state projects further increases in excess of 13 percent in the current fiscal year. Income tax revenue is projected to grow by an additional 1.7 percent in the next fiscal year.

Further good news regarding state revenue collection is that corporate income taxes are projected to grow by 38.6 percent in the current fiscal year after a 21.9 percent decrease last year. This would be the first time in the last five years that corporate tax revenues increased. Likewise, sales tax revenues are projected to grow by 9.6 percent in the current fiscal year and 4.8 percent the following year . Part of this increase in sales tax revenue is attributable to the increased special sales tax on recreational marijuana purchases, which increased from 10 percent to 15 percent following the passage of Senate Bill 17-267 in 2017. According to the OSPB forecast, individual income taxes constitute $7.65 billion of the expected $11.6 billion in general fund revenue for the 2017–2018 fiscal year. Sales and use tax revenue are projected at $3.5 billion. Corporate income tax revenue is expected to provide an additional $0.71 billion . These three revenue sources constitute 95 percent of total General Fund revenue. State revenues were relatively stable around the $10 billion mark over the past three years. The $11.6 billion revenue estimate for the upcoming fiscal year represents a 12.6 percent increase, which would be the largest growth in state revenue since 2005 when revenues increased 13.1 percent. Such an increase would be similar in magnitude to the percentage of lost revenue that occurred during the Great Recession . Since 2009, individual income tax revenue has increased each year, hydroponic channel although not in a strictly linear pattern. Sales and use tax revenue has also increased each year over the past decade. Corporate tax revenue has exhibited greater volatility. Since the Great Recession when corporate income tax revenue fell to less than $300 million, corporate taxes rebounded over the next five years to greater than $700 million in the 2013–2014 fiscal year. The OSPB cites global economic factors, such as a strong dollar and decreases in oil, gas, and other commodity prices as the catalysts for the three-year decline in corporate tax revenue beginning in 2014. After falling 21.9 percent in the third year of this recent decline, corporate tax revenue is estimated to increase by 38.6 percent in the current fiscal year. In addressing how federal tax reform may affect state corporate tax revenue, the OSPB projects continued growth in corporate tax revenue, but cautions that “future increases will be constrained by higher business costs, especially for employee compensation, which will reduce profit margins and result in lower tax liabilities” . Taxes from the state’s legal marijuana market continue to grow. According to data released by the Colorado Department of Revenue, total marijuana sales surpassed $1.5 billion in 2017 . Of this total, $1.09 billion in sales came from the retail market, while medical marijuana sales were approximately $0.42 billion. Table 2 reports annual marijuana sales and tax revenue data. Sales have increased each calendar year since the retail market began operation on January 1, 2014, but the growth rate has gradually declined each year. In 2014, marijuana sales totaled nearly $680 million. This figure increased by 45.7 percent in 2015 to $990 million. Sales increased by 31.3 percent and surpassed the $1 billion mark for the first time in 2016 to reach a total of $1.3 billion. Total sales in 2017 amounted to $1.5 billion, which represents a 15.3 percent increase. If the trend continues, Colorado could expect to see sales numbers plateau since the growth rate has decreased by an average of 15 percentage points each year. Sales data through September 2018 indicate sales of nearly $1.16 billion. The monthly sales average for 2018 puts the state on track for an annual marijuana sales total of about $1.54 billion, which would be the largest sales amount to date and constitute a slight increase of 2.4 percent from 2017. State revenue from the medical and retail marijuana markets in the form of taxes and fees reached nearly $250 million in 2017. This is a 27.8 percent increase from 2016 following a 48.5 percent increase in tax revenue from 2015 to 2016. During the first 10 months of 2018, the state reported tax and fee revenues of $223 million. A linear projection of tax revenue for the remainder of the year suggests that the annual tax revenue would reach nearly $268 million, an increase of about 8 percent from the prior year. The largest annual increase in marijuana taxrevenue occurred in the second year after retail sales became legal when tax revenue nearly doubled . Increasing sales have driven greater tax revenue, and the state legislature modified the marijuana tax structure in the prior session with the passage of Senate Bill 17-267. From January 1, 2014 through June 30, 2017, retail marijuana sales were subject to the state’s 2.9 percent sales tax and a special 10 percent sales tax in addition to local sales taxes.

Beginning on July 1, 2017, marijuana sales are exempt from the state sales tax and are instead taxed at a special tax rate of 15 percent. A 15 percent excise tax also applies to retail marijuana sale from cultivation facilities to dispensaries for manufacturers. According to the Joint Budget Committee, marijuana tax revenue from the most recent fiscal year was allocated as follows: 49.4 percent to the marijuana tax cash fund, 39 percent to several K-12 education funds, 6.7 percent to local governments, and 4.9 percent to the General Fund.Relative to last year’s budget, Governor Hickenlooper’s budget request for the 2018– 2019 fiscal year is much more optimistic. This positive tone is a product of a good economic climate and the successful passage of a major budgetary reform in the prior session. Transitioning hospital provider fees into a government enterprise fund made these funds TABOR exempt. In the 2016–2017 fiscal year, hospital provider fee revenue was $654.4 million. In future years, these funds do not count toward the TABOR revenue cap. The governor emphasized the importance of this reform by noting that “The passage of S.B. 17-267 has materially and positively changed the State’s financial outlook compared with one year ago, when the request had to close a $500 million funding gap in the General Fund” . Beyond this important budgetary reform, Governor Hickenlooper also lauded the strong upward trajectory of the state’s economy by claiming, “Colorado’s economy continues to outperform nearly every state and the national economy overall” . Statewide unemployment remains low and job creation numbers are strong—approximately 53,000 new jobs are projected for 2018. As the state’s population continues to grow, Hickenlooper’s budget request reflects spending priorities to address increased demand for certain state services. K-12 spending is proposed to increase by $84.6 million, which represents an increase of $343.38 per student. According to state estimates, the 178 school districts in Colorado currently serve the educational needs of more than 865,000 students.

DNA quality was verified by pulsed-field gel electrophoresis. DNA fragments longer than 50 Kb were used to construct a 10× Gemcode library using the Chromium instrument and sequenced at HudsonAlpha Institute for Biotechnology on a HiSeqX system with paired-end 150 bp reads. Approximately 95 Gb of 10X Chromium library data was sequenced . To increase sequence diversity and depth, three separate mate-pair libraries were constructed with 2–5 Kb, 5–7 Kb, and 7–10 Kb jumps using the Illumina Nextera Mate-Pair Sample Preparation Kit. In addition, two additional size-selected Illumina genomic libraries, ∼470 bp and ∼800 bp, were sequenced. The ∼470 bp and ∼800 bp libraries were made using the Illumina TruSeq DNA PCR-free Sample Preparation V2 kit. The ∼470 bp library was designed to produce ”overlapping libraries” after sequencing with paired-end 265 bp reads on an lllumina Hiseq2500 system, producing ”stitched” reads of approximately 265 bp to 520 bp in length. The 800 bp library was sequencedon an Illumina HiSeq2500 system with paired-end 160 bp reads, while the MP libraries were sequenced on an Illumina HiSeq4000 system with paired-end 150 bp reads. A total of ∼433 Gb of additional Illumina sequencing data were generated . Illumina library construction and sequencing was conducted at Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.The genome of ”Draper” was assembled using the DeNovoMAGIC software platform , hydroponic gutter which is a de Bruijn graph-based assembler designed for higher polyploid, heterozygous, and/or repetitive genomes.

The Chromium 10X data were utilized to phase, elongate, and validate haplotype scaffolds. Four Dovetail Hi-C libraries were prepared as described previously  and sequenced on an Illumina HiSeq X system with paired-end 150 bp reads to a total of 90.7X physical coverage of the genome . The de novo genome assembly, raw genomic reads, and Dovetail Hi-C library reads were used as input data for HiRise, a software pipeline designed specifically for using proximity ligation data to scaffold genome assemblies. Illumina genomic and Dovetail Hi-C library sequences were aligned to the draft input assembly using a modified SNAP read mapper. The separations of Dovetail Hi-C read pairs mapped within draft scaffolds were analyzed by HiRise to produce a likelihood model for genomic distance between read pairs, and the model was used to identify and break putative misjoins and to make joins to close gaps between contigs.Plant Thissue samples were collected from blueberry cv. Draper grown in the growth chamber . For the fruit developmental series, three biological replicates each of berries at seven developmental stages were collected from cv. Draper in a field at the Horticulture Teaching and Research Center, Michigan State University, in July 2017. All plant Thissues were immediately flash frozen in liquid nitrogen, and total RNA isolation was performed using the KingFisher Pure RNA Plant kit . Isolated total RNA was quantified using a Qubit 3 fluorometer . RNA libraries were prepared according to the KAPA mRNA HyperPrep kit protocol . All samples were submitted to the Michigan State University Research Technology Support Facility Genomics core and sequenced with paired-end 150 bp reads on an Illumina HiSeq 4000 system .The draft genome of V. corymbosum cv. Draper was annotated using the MAKER annotation pipeline. Transcript and protein evidence used in the annotation included protein sequences downloaded from A. thaliana and UniprotKB plant databases, V. corymbosum ESTs from NCBI, and transciptome data assembled with StringTie from different blueberry Thissues .

A custom repeat library and Repbase were used to mask repetitive regions in the genome using Repeatmasker. Ab initio gene prediction was performed using gene predictors SNAP and AugusThus. The resulting MAKER Max gene set was filtered to select gene models with Pfam domain and annotation edit distance <1.0. The filtered gene set was further scanned for transposase coding regions. The amino acid sequence of predicted genes was searched against a transposase database. The alignment between the genes and the transposases was further filtered for those caused by the presence of sequences with low complexity. The total length of genes matching transposases was calculated based on the output from the search. If more than 30% of gene length aligned to the transposases, the gene was removed from the gene set. Furthermore, to assess the completeness of annotation, the V. corymbosum Maker standard gene set was searched against the BUSCO v.3 plant dataset . Genes were annotated with pfam domains using InterProScan v5.26–65.0 .To identify and classify repetitive elements in the genome, LTR retrotransposon candidates were searched using LTR harvest and LTR finder  and further identified and classified using LTR retriever. A non-redundant LTR library was also produced by LTR retriever. Miniature inverted transposable elements were identified using MITE-Hunter . MITEs were manually checked for target site duplications and terminal inverted repeats and classified into super families . Those with ambiguous Target Site Duplication and Terminal Inverted Repeats were classified as ”unknowns.” Using the MITE and LTR libraries, the V. corymbosum genome was masked using Repeat masker. The masked genome was further mined for repetitive elements using Repeat modeler. The repeats were then categorized into two groups: sequences with and without identities. Those without identities were searched against the transposase database; if they had a match, they were considered a transposon.

The repeats were then filtered to exclude gene fragments using Prot Excluder and summarized using the ‘fam coverage.pl’ script in the LTR retriever package. The assembly continuity of repeat space was assessed using the LLAI deployed in the LTR retriever package. LAI was calculated based on either 3 Mb sliding windows or the whole assembly using LAI = /Total LTR-RT length. For the sliding window estimation, a step of 300 Kb was used . To account for dynamics of LTR retrotransposons, LAI was adjusted by the mean identity of LTR sequences in the genome based on all-versus-all blastn search, which was also performed by the LAI program .Illumina adapters were removed from the raw reads using Trimmomatic/0.33, and trimmed reads were filtered using FASTX Toolkit. After quality assessment using FastQC , the filtered reads were then aligned to the V. corymbosum genome using STAR. For the samples that were usedfor annotation, transcript assembly was performed de novo using StringTie. Counts of uniquely mapping reads were generated through HTSeq for all 35 RNA-seq datasets . Multi-mapping reads were excluded from the analysis except for the tandem gene expression analysis. Differential gene expression analysis was performed using the DESeq2 pipeline across fruit developmental stages with three biological replicates per developmental stage . Gene expression values were derived by calculating the fragments per kilobase per million reads mapped values using the standard formula for FPKM /gene length in kilobases [Kb]. To construct the gene co-expression network, genes that were not expressed or very weakly expressed in 30 or more conditions were first excluded from the analysis. The count data was then transformed into variance stabilized values using the variance stabilizing transformation function in DEseq. Pairwise correlations of gene expression were calculated using Pearson correlation coefficient and mutual rank using scripts available for download from the project’s data repository. MR scores were transformed to network edge weights using geometric decay function; five different co-expression networks were constructed with x set to 5, 10, 25, 50, and 100, respectively. Edges with PCC <0.6 or edge weight <0.01 were excluded. For each network, modules of coexpressed genes were detected using ClusterONE v1.0 using default parameters, u planting gutter and modules with P value > 0.1 or quality score <0.2 were excluded. The results from all co-expression networks were then combined by collapsing modules into metamodules of nonoverlapping gene sets.Total antioxidant capacity of Thissues from the fruit developmental panel was analyzed using the ORAC assay. Briefly, ∼20–30 mg of frozen ground fruit Thissue was measured for Thissue samples prior to extraction. Sample extractions were performed on ground Thissue using 1.8 mL of ice cold 50% acetone. Samples were vortexed and then put on a shaker for 5 minutes at room temperature. Samples were then centrifuged at 4◦C for 15 minutes . The ORAC assay was performed in a 96-well black microplate using the FLUOstar OPTIMA microplate reader . Each reaction well contained 150 μL of 0.08 μM fluorescein and 25 μL of 75 mM phosphate buffer , Trolox standards , or diluted sample extracts. For blueberry Thissue samples, 1:80–1:20 dilutions were used. Upon loading all appropriate wells, the 96-well microplate was put into the microplate reader and incubated for 10 minutes at 37◦C. Following incubation, 25 μL of 150 mM AAPH was added to each well, and fluorescence measurements began immediately. Fluorescence measurements were taken for 90 seconds per cycle for 70 cycles until the fluorescent probe signal was completely quenched.

The total antioxidant capacity of a sample was calculated by subtracting the AUC from the blank curve from the AUC of the sample curve to obtain the net AUC. Using Trolox of a known concentration, a standard curve was generated , and the total antioxidant capacity of each sample was calculated as Trolox equivalents. Each sample was run twice for two technical replicates. The coefficient of variation between technical replicates was required to be less than 0.20. Biological replicates were run for all Thissues in the fruit developmental series.Berries from ”Draper” were collected as described above. Approximately 100 mg of each frozen ground sample was resuspended in extraction solvent in a 2 mL tube . Ground Thissue was immediately mixed thoroughly to prevent thawing during extraction and to prevent metabolism of analytes by enzymes in the samples. All tubes were spun down for 10 minutes at 13,000 × g to pellet protein and other insoluble material. Then, 1 mL of supernatant was transferred to an autosampler vial. Anthocyanin content was evaluated by LC-MS as follows: 5 uL of sample extract were separated using a 10 minute gradient on a Waters Acquity HSS-T3 UPLC column on a Waters Acquity UPLC system interfaced with a Waters Xevo G2-XS quadrupole time-of-flight mass spectrometer . Column temperature was maintained at 40◦C, and the flow rate was 0.3 mL/min with starting conditions of 100% solvent A and 0% solvent B . The gradient was as follows: hold at 100% A for 0.5 minutes, ramp to 50% B at 6 minutes, then ramp to 99% B at 6.5 minutes, hold at 99% B to 8.5 minutes, return to 100% A at 8.51 minutes, and hold at 100% A until 10 minutes. Mass spectra were acquired in positive ion mode electrospray ionization over m/z 50–1500 in continuum mode using a data-independent MSE method that acquires data under both low and high collision energy conditions with the high collision energy setting using a ramp from 20–80 V. Capillary voltage was 3 kV, desolvation temperature was 350◦C, source temperature was 100◦C, cone gas flow was 25 L/hr, and desolvation gas flow was 600 L/hr. Correction for mass drift was performed using continuous infusion of the lock mass compound leucine encephalin. Anthocyanins and other related flavonoids were identified based on accurate mass and fragmentation pattern. Peak areas were determined using Quanlynx within the Masslynx software package . Relative anthocyanin content was calculated for each sample using the formula: reported peak area of the compound/peak area of internal standard/weight of extracted Thissue .Cardiovascular disease remains the leading cause of mortality in the United States, and after decades of decline, is rising coincident with the increase in obesity, insulin resistance, and diabetes that characterize cardiometabolic risk. Notwithstanding hereditary predisposition, reduction in identified, modifiable lifestyle risk factors can reverse CMR and CVD. It is estimated that 45.4% of all cardiometabolic deaths in the United States due to heart disease, stroke, and diabetes are associated with sub-optimal intakes of 10 dietary factors. Fewer than 1% of American children and adolescents meet full recommended metrics of heart healthy nutrition, falling especially short of recommended intake in the categories of fruits, vegetables, fiber and essential fatty acids. Intensive pediatric lifestyle interventions for obesity are effective in achieving significant reduction in body mass index but do not elicit stable changes in nutrition habits in children and adolescents. These studies suggest a critical need for developing innovative tools to improve diet quality in youth. We have previously shown that twice daily consumption for two weeks of a whole food based nutrient bar composed of a blueberry, dark chocolate, red grape, and walnut matrix, soluble and insoluble fiber, with supplemental vitamins, minerals and essential long chain fatty acids, significantly increased high density lipoprotein cholesterol , due primarily to a 28% increase in large HDL particles, in generally healthy and insulin sensitive lean and overweight adults.

This condition can cause a feedback loop in which contact between bacteria and epithelial cells leads to dysregulation of mucosal immune response. This contact can lead to a bacterial biofilm, formed when bacteria attach themselves to the surfaces of the aqueous environment in the gut and begin to secrete substances that allow them to affix onto the epithelium. 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 prolifteration 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, bato bucket 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, 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 lifte style 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 lifte style. 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 life style. 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 life style 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 prolifteration 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 Thissue 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 lowgrade 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, dutch bucket hydroponic 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.More than three quarters of all plant viruses are transmitted by insects , and information regarding key biological traits of vector-borne pathogens is needed to inform effective control strategies. For example, knowledge of transmission efficiency can aid in predicting rates of pathogen spread . Another key parameter in estimating the rate of appearance of newly diseased hosts is the pathogen incubation period, the time between initial infection and when symptoms become evident. Despite the importance of transmission efficiency and incubation period with respect to the development of disease management strategies, data are often not available and, when available, are usually derived from research performed under artificial conditions such as greenhouse environments. Grapevine leaf roll-associated virus 3 , in the genus Ampelovirus, family Closteroviridae, is the primary virus species associated with grapevine leaf roll disease in vineyards of wine growing regions worldwide . GLRaV-3 can cause interveinal reddening and downward rolling in red berried grape varieties , inhibits photosynthesis, decreases vine lifespan, and reduces fruit yield and quality . GLRaV-3 is one of the most common and detrimental viruses of grapevines, and has led to economic losses of 25 % or more . Spread of GLRaV-3 in vineyards and vector-borne transmission in controlled laboratory studies were first documented in South Africa , and since then GLRaV-3 spread in vineyards and transmission by several mealybug species have been documented in wine growing regions worldwide . Although multiple grape-colonizing mealybug species transmit GLRaV-3, estimates of vector transmission efficiency vary both among and within mealybug species . GLRaV-3 is transmitted in a semi-persistent manner with no latent period required between acquisition and inoculation by vectors; transmission can occur after access periods of as little as one hour, and reaches a maximum after access periods of 24 hours . First instar mealybugs are the most efficient vectors, and mealybugs lose the ability to transmit GLRaV-3 four days after being removed from an infected source .

Each experimenter tested half of the days. We used high quality rewards that would be easily visible to the subjects. Blueberries were not part of their daily diet but were sometimes presented as enrichment in puzzle feeders and were highly desirable for all gibbons housed at the GCC. The apparaThus was composed of a plastic folding table with a square wooden plank clamped to the top. At one end of the plank a transparent plastic bin was taped so that it could be lifitted up or hang down. Te bin, at rest, would hang down and remain unmoved on the top of a wooden ramp. A hole big enough to ft blueberries was drilled on the back side of the bin so that when at rest on the ramp, the experimenter could place five blueberries into the bin. A thin purple rope was tied to the far end of the plastic bin and was routed back to the opposite end of the wooden plank. This was set up so that pulling on the purple rope would reliably lift the plastic bin, so blueberries could fall down the wooden ramp and be easily accessible for subjects to obtain. Te extreme end of the rope was attached to the mesh of the enclosure. To allow reaching and pulling the rope, we attached a small, handheld, opaque white handle . At the right tension, pulling on the handle would reliably lift the plastic bin. Te handle could contain a single blueberry inside depending on the condition presented. We used two handles of the same dimensions and appearance to avoid contamination of blueberry leftovers after the trial. Te table with wooden plank would be set up at a distance so that it could not be grabbed by subjects and the ramp was placed underneath so that blueberries would roll down and land in front of the enclosure gate.

E2 would then distract the two subjects to an opposite or adjacent side of the subjects’ enclosure with a handful of cereal pieces while E1 tied the end of the purple rope with the handle onto the mesh gate of the enclosure, roughly at the experimenter height, blueberry packing boxes approximately 2 m to the right or left. Te distance and location of the rope was kept constant for all trials of each dyad; however, because the enclosures differed in layout, the rope would go to the most convenient side. This way, we ensured that the rope had proper tension to be pulled by gibbons and lift the plastic bin as well as be distant enough from the ramp so that a subject could not easily pull on the rope and obtain food from the ramp at the same time.Individual solo pre-testing of the mechanism of the apparaThus was not possible because the separation of the days was prohibited. However, gibbons had had experience with ropes before as part of their enrichment and several individuals had participated in pilot sessions where they had to pull from different ropes and handles. Tree conditions were tested: direct food test condition, indirect food test condition and no food control condition. In the direct food test condition, the following procedure was performed. E1 would place five blueberries in the plastic bin on the apparaThus. To gain the attention of the subjects, E1 would call the subjects names and show the food, if they were not already focused on the food/experimenter. Once both subjects had observed the five blueberries placed in the plastic bin, E1 would squeeze a single blueberry on top of the handle, so that the blueberry would be clearly visible. Te rope and handle would be set up so that the handle was just far enough from the enclosure in order for subjects to need to pull on the rope to obtain access to the handle and blueberry. Consequently, pulling the rope would also lift the plastic bin and drop five blueberries down the ramp, accessible to subjects. Te experimenter would also call the names of the subjects when placing the single blueberry in the handle.

A choice was recorded when one of the subjects pulled the rope. If no subject pulled the rope within 90 s, the trial ended and was recorded as no pull. If an experimenter error was made , up to 3 repetitions of the trial would be completed. Environmental conditions such as rain would also end test sessions to be continued the next day. In the indirect food test condition, there was no single blueberry placed in the handle. To compare conditions, we followed the same procedure as in the direct food test condition. Instead of inserting a blueberry inside the handle, we approached it with the first close and then we touched it with the fingers. In the no food control condition, no blueberries were used in the trial. In order to control for time and actions, we used the same procedure of calling the subjects and touching both the box and the handle.Two cameras on tripods recorded footage concurrently. One was placed to the side of the experimenter in order to capture a wide view of the trials, specifically to show the positions of the subjects, their choices and if they obtained blueberries. Te other was placed close to the ramp to accurately count the quantity of blueberries obtained by each subject. For all trials we coded the act of pulling or not pulling and the ID of the puller and non-puller . We also coded the number of blueberries each subject ate and whether the actor subject ate the blueberry from the handle. Next, we coded whether a passive subject was present in front of the ramp or within one meter from it at the moment the plastic bin was lifted and at the moment the actor arrived at the release location. Additionally, we coded instances of cofeeding and displacements. Cofeeding was coded when individuals feed within a distance of 1 m of one another. Displacements occurred when an individual left her spot due to the partners’ arrival. Additionally, we calculated the latency to pull from the start of the trial until the individual releases . All analyses were conducted with R statistics . We used Generalized Linear Mixed Models to investigate gibbons’ choices . Covariates were z-transformed. Every full model was compared to a null model excluding the test variables. We controlled for session and trial number in all our models. We controlled for the length of the dyad in models 1 to 3 given the larger dataset compared to models 4 to 6. In addition, in model 3 we included individuals’ age and sex as control predictors.

When the comparison between the full and the null model was significant, we further investigated the significance of the test variables and/or their interactions. We used the “drop1” function of the lme4 package to test each variable significance including interactions between test predictors. Non-significant interactions were removed and a new reduced model was produced when necessary. A likelihood ratio test with significance set at p<0.05 was used to compare models and to test the significance of the individual fixed effects. We ruled out collinearity by checking Variance Infation Factors . All VIF values were close to 1 except for age and length of dyad in model 3. Te two variables were slightly collinear . For every model we assessed its stability by comparing the estimates derived by a model based on all data with those obtained from models with the levels of the random effects excluded one at a time. All models were stable. We also fitted a mixed-effects Cox proportional hazards model to analyze gibbons’ latencies to act. For this purpose, we used the “coxme” function from the coxme package. Te results of Model 2 are reported as hazard ratios . An HR greater than one indicates an increased likelihood of acting and an HR smaller than 1 indicated a decreased hazard of acting. In addition, to obtain the p-values for the individual fixed effects we conducted likelihood-ratio tests.Drosophila suzukii Matsumura is an economic pest of small and stone fruit in major production areas including North America, Asia and Europe . Female D. suzukii oviposit into suitable ripening fruits using a serrated ovipositor. This is unique compared to other drosophilids, including the common fruit fly, D. melanogaster, package of blueberries which oviposit into overripe or previously damaged fruit. Developing fruit fly larvae render infested fruit unmarketable for fresh consumption and may reduce processed fruit quality and cause downgrading or rejection at processing facilities. In Western US production areas, D. suzukii damage may cause up to $500 million in annual losses assuming 30% damage levels, and $207 million in Eastern US production regions [9]. Worldwide, the potential economic impacts of this pest are staggering. Pesticide applications have been the primary control tactic against D. suzukii both in North America and in Europe. The most effective materials are those that target gravid females, including pyrethoids, carbamates, and spinosyns. These applications are timed to prevent oviposition in susceptible ripening host crops. In the Pacific Northwest, many growers have adopted scheduled spray intervals of 4–7 days. This prophylactic use of insecticide is unsustainable as growers have a limited selection of products and modes of action. This could ultimately lead to D. suzukii becoming resistant and may cause secondary pest problems because of negative effects on beneficial organisms. Furthermore, production costs have increased substantially in crops where D. suzukii must be managed. Effective sampling methodology for D. suzukii is lacking despite extensive efforts to improve trap technology or determine effective fruit infestation sampling protocols. Theoretically, traps to capture adult flies should aid growers in the timing of spray applications so that insecticides could be used more judiciously. Traps baited with apple cider vinegar or a combination of sugar-water and yeast are currently used to monitor adult D. suzukii flight patterns. However, without standard methods for trapping or management thresholds based on trap count data, it is questionable how much is gained by establishing and monitoring traps in crops.

Establishing, monitoring, and maintaining traps is very labor intensive and the costs do not justify the benefits for many growers. Historically, trap data has not provided a reliable warning against D. suzukii attack, especially for susceptible crops in high-density population areas where considerable oviposition can occur in short time periods. Currently, no significant differences are found in any traps used for monitoring D. suzukii given differences between crops and environments where traps have been tested. Monitoring fruit infestation levels to guide management may also be impractical. Furthermore, by the time larvae are detected in the fruit, it is too late for management action and damage has already occurred. No detailed studies could be found using monitoring for fruit infestation for this pest, and precision of sampling methodology is currently unavailable. Degree-day , or phenology models, are standard tools for integrated pest management in temperate regions and are used to predict the lifte stages of pests in order to time management activities and increase the effectiveness of control measures. Degree-day models work best for pests with a high level of synchronicity and few generations. Our data suggest that D. suzukii has short generation times, high reproductive levels, and high generational overlap compared to other dipteran fruit pests. Given this lift history, stage-specific population models represent an alternative and potentially more applicable tool for modeling pest pressure. Pest population estimates may be greatly improved by employing additional tools such as mark recapture and analytical or individual-based models. The ability to describe and forecast damaging pest populations is highly advantageous for fruit producers, policy makers, and stakeholder groups. Many such studies have been directed at forecasting populations of medically important insect species. The major factors affecting survival, fecundity and population dynamics of drosophilids include temperature, humidity, and the availability of essential food resources. Therefore, an improved understanding of the role of temperature on D. suzukii may provide for a better understanding its seasonal population dynamics. In this paper, we present a population model for D. suzukii that represents a novel modification of the classic Leslie projection matrix, which has proven to be one of the most useful age structured population models in ecology, with applications for diverse organisms including plants, animals, and diseases.