The LR and ST decreased leaf area index and increased canopy porosity

These treatments are provided visually in Figure 1.In the second experiment, individual grapes from different cluster positions were collected from two cultivars grown in a commercial vineyard in Oakville, CA in 2017. Cabernet Sauvignon grapevines and Petit Verdot grapevines were 21 and 9-years old, respectively. The exposure of each individual grape was estimated with fish-eye lens photography from the grape perspective pointing the zenith. The images were processed in R . After applying a thresholding condition to the blue channel of all images, they were converted into binary pixels . Thus, the percent of binary pixels capturing the sky was used to calculate the percentage of canopy porosity as reported previously . Then, those berries were collected at harvest, and their flavonoid content was analyzed with reversed-phase high performance liquid chromatography.The experiment was conducted in 2019 in Oakville, CA with row orientation NW-SE. The vineyard was spaced 2 m × 2.4 m with Cabernet Sauvignon grapevines on 110R root stock. The grapevines were trained to a vertically shoot-positioned system with a cordon height 96 cm above vineyard floor, trained to a bilateral cordon, and pruned to 1-bud spurs. Plants were irrigated weekly with 2-drip emitters per vine, with the capacity to deliver 3.8 L of water per hour. The experiment was designed as a randomized complete block with three canopy management practices: removal of 5 to 6 basal leaves on the NE side ; thinned to 24 shoots per vine ; and a combination of LR and ST and an untreated control ,square plant pots with four replicates each consisting in 5 grapevines, 3 of which were sampled and the 2 on distal ends were treated as border plants.

The ST and LR treatments were applied on 11 June 2019. Harvest commenced when the berry TSS reached to ca. 24°Brix on 23 September . The sampling time points were as follows: 2 weeks before veraison , veraison , 2 weeks after veraison , 3 weeks after veraison , 5 weeks after veraison , and harvest , were chosen to cover the response of the berry metabolism to cultural practices and the concomitant increase in exposure.Leaf area index was measured on 21 June to characterize grapevine canopy growth and converted into leaf area on by a smartphone based program, VitiCanopy, coupled with an iOS system . The gap fraction threshold was set to 0.75, extinction coefficient was set to 0.7, and sub-divisions were 25. A “selfie-stick” was used for an easy access to place the device about 75 cm underneath the canopy. The device was positioned with the maximum length of the screen being perpendicular to the cordon, and the cordon being in the middle of the screen according to previous work . In each experimental unit, three images were taken to capture half canopy of each vine, and analyzed by the software. The relationship between leaf dry mass and area was determined on a sub-sample of leaves of different sizes using a leaf area meter . Total leaf area was calculated by defoliating one grapevine per treatment replicate after harvest and using the regressive relationship between leaf dry mass and leaf area. At harvest, clusters were manually removed, counted, and weighed on a top-loading balance. Leaf area to fruit ratio was calculated by dividing leaf area with crop weight. Dormant pruning weight was collected during the dormant season ; and crop load was calculated as the ratio between yield per vine and the pruning mass of each vine. Labor operations costs and gross income per hectare were calculated based on yield and net returns per hectare and methods presented elsewhere . Anthocyanin productivity was calculated as reported by Cook et al. .

At each sampling point and experiment, 55 berries were randomly collected from the middle of each treatment-replicate and kept on ice until they were measured. Berries were weighed, and mean berry mass was determined as the average mass of the counted berries. These berries were used to determine the total soluble solids , the pH, and the titratable acidity . TSS was measured as °Brix, with a digital refractometer . The juice pH and TA was determined with an autotitrator using sodium hydroxide to titrate to an end point of pH 8.3, and it was expressed as g•L−1 of tartaric acid.For each sampling point in each experiment, 20 berries were collected, gently peeled, and berry skins were freeze-dried . Dried tissues were ground with a tissue lyser . Fifty mg of the resultant powder was extracted in methanol: water: 7 M hydrochloric acid to simultaneously determine flavonol and anthocyanin concentration and profile as previously described Martınez-Lüscher et al. . Briefly, extracts were filtered and analyzed using an Agilent 1260 series reversedphase high performance liquid chromatography system coupled to a diode array detector. Separation was performed on a reversed-phase C18 column LiChrospher® 100, 250 mm × 4 mm with a 5-µm particle size and a 4-mm guard column of the same material at 25°C with elution at 0.5 ml per minute. The mobile phase was designed to avoid co-elution of anthocyanins and flavonols consisted in a constant 5% of acetic acid and the following gradient of acetonitrile in water: 0 min 8%, at 25 min 12.2%, at 35 min 16.9, at 70 min 35.7%, 65% between 70 and 75 min, and 8% between 80 and 90 min. The identification of flavonoid compounds was conducted by determining the peak area of the absorbance at 280, 365, and 520 nm for flavan-3-ols, flavonols and anthocyanins, respectively. Identification of individual flavan-3-ols, anthocyanins, and flavonols were made by comparison of the commercial standard retention times found in the literature. Commercial standards of epicatechin, malvidin-3-O-glucoside, and quercetin-3-Oglucoside were used for the quantification of flavan-3-ols, anthocyanins, and flavonols, respectively.

The determination of proanthocyanidins was performed using an Agilent HPLC-DAD after an acid catalysis in the presence of excess phloroglucinol , with minor modifications described in Martınez-Lüscher et al. .The 3-isobutyl-2-methoxypyrazine was quantified by a stable isotope dilution assay using headspace solid phase microextraction coupled to a gas chromatograph and a mass spectrometer as described Chapman et al. and Koch et al. with some modifications. Briefly, 20 berries per treatment-replicate from Experiment 3 were randomly collected from the clusters of three vines in the middle of each treatment-replicate on both side of the canopy, by cutting the pedicel with a pair of scissors and frozen at −80°C until analysis. Pedicels were removed by hand and berries were placed in 50 ml conical tubes. 10 ml of pure water and 100 ml of deuterated IBMP isotope were added into the tube. Then, samples were ground with a tissue homogenizer Power Gen 1800D and centrifuged at 3000 rpm for 10 min. 10 ml of the supernatant was pipetted into 20 ml SPME vials containing 3 g of sodium chloride.Statistical analyses were carried out using the R-Studio version 3.6.1 for Windows. All data were subjected to Shapiro-Wilk’snormality test . Correlations between variables were calculated with the Pearson’s test by using the same software. Segmented regression analysis was used to determine the point of inflection the in the relationship between increasing exposure and the berry skin anthocyanin and flavonol content with “segmented” 0.5-0.3 R package . Data were normally distributed and, subsequently, were submitted to an analysis of variance to assess the statistical differences between the treatments applied in each experiment performed. Means ± standard errors were calculated, and when the F value was significant , a Duncan’s new multiple range post hoc test was executed using “agricolae” 1.2-8 R package . When data were not normally distributed, a Kruskal-Wallis test was conducted. Percentage data were transformed according to the suggestion of the most likelihood test,plastic pots for planting into arcsine root square before ANOVA or Kruskal-Wallis tests.The growing season of 2017 was warmer and drier compared to the reference data for the same period within the last 20 years . Thereby, average daily temperature was 4°C higher and rainfall was 18 mm less. Grape berry mass differed significantly depending on the degree of exposure . Overexposed berries were the smallest due to overexposure resulting in dehydration thereby reducing berry mass. Neither total soluble solids nor titratable acidity changed regardless of the degree of exposure to which berries were subjected. However, the juice pH of the Exp+ Deg+ and Exp+ Deg++ berry must was greater compared to Exp− and Exp+ Deg− berries. Berry skin flavonoid content and composition were also affected by the degree of exposure . The berry anthocyanin content of Exp− was similar to Exp+ Deg−. However, overexposed berries resulted in berry anthocyanin content that was 70% and 90% lower when compared to the Exp− berries. Grape berry exposure to solar radiation not only affected the anthocyanin content but also modified the ratio between the tri- and di-substituted anthocyanins leading to a less stable profile in all treatments with exposed berries. Likewise, berry skin flavonol content and composition were strongly affected by the degree of exposure to solar radiation. Therefore, in Exp+ Deg− flavonol content was two-fold greater than Exp−, albeit they abruptly decreased in overexposed grapes where flavonol content was 25% and 50% lower when compared to Exp− berries. Furthermore, in overexposed berries the proportion of kaempferol and quercetin significantly increased while the proportion of myricetin decreased. Regarding proanthocyanidins in berries, mild exposure did not affect their content in Exp+ Deg− compared to Exp− berries.

However, greater solar exposure decreased proanthocyanidin content in berries but to a lesser extent compared to Exp−. Finally, the content of flavan-3-ols was severely reduced in Exp+ Deg++ berries .The analyses performed on single berries from two varieties confirmed the obtained response in anthocyanins and flavonols in Cabernet Sauvignon . Thus, exposure affected the accumulation/degradation of these flavonoids. Exposed berries from the East side of the canopy decreased 8%and 36% of the anthocyanin content in Cabernet Sauvignon and Petit Verdot, respectively. Thus, Petit Verdot seemed to be more sensitive to higher level of solar exposure and degraded anthocyanins. Overexposed berries of Cabernet Sauvignon resulted in an 87% decrease of the berry skin anthocyanins when compared to the interior berries . Berry skin anthocyanins and increasing exposure showed a significant trend below the 22% of kaempferol . Conversely, analysis of the segmented regression on Petit Verdot berries did not show a clear trend below the 3.2% of Kaempferol and after the point of inflection, anthocyanins started to degrade . Regarding flavonol content, no differences were observed between cultivars . Conversely, when exposure increased to ca. 60% the content of flavonols in exposed berries of both canopy sides and in both cultivars; the overexposed berries had the lowest flavonol content . Thus, our data revealed a strong positive relationship between the berry skin flavonols and the percentage of kaempferol until 8.6% of kaempferol proportion for Cabernet Sauvignon and 7.2% Petit Verdot . However, beyond these thresholds, flavonols started to degrade, and there was an indirect relationship between the flavonol content and the percentage of kaempferol for both cultivars, this relationship being significant only for Cabernet Sauvignon .The weather conditions during the execution of this experiment were highlighted by greater maximum daily temperatures when compared to the reference period . This was more prominent during the driest months . Moreover, global solar radiation received at the experimental site was to ca. 200 W m−2 greater than the total solar radiation recorded within the reference period . The combinatory effect of LR and LT treatments caused a 58% reduction of LAI and a 45% increase of canopy porosity . However, neither leaf area nor pruning mass showed significant differences between treatments. On the other hand, yield components were mostly affected by the shoot thinning treatments . Thus, shoot thinned vines showed lower number of clusters, yield, and Ravaz Index , and increased leaf area to fruit ratio per vine as expected. The extent of yield reductions was 55% and 47% for ST and LRST vines, respectively . Berry mass was not significantly affected by canopy management practices during the berry ripening although vines subjected to LRST tended to result in smaller berries . The most influential effects observed on berry chemistry were due to shoot thinning treatments . Therefore, shoot thinned vines had greater total soluble solids and lower titratable acidity from mid-ripening to harvest. However, no significant effect was observed on the must pH . Shoot thinned grapevines had higher anthocyanin content at veraison . However, we did not measure any changes to anthocyanin content at harvest as affected by the canopy management practices applied.

These analyses were also run separately for both the experimental and control groups

For instance, to measure the relative strength of automatic associations between the BII bipolar dimensions of cultural harmony and cultural blendedness with self-related words, participants were asked to complete the following tasks. During one block of trials, participants had to categorize “self” words with words that depict the “Harmony” concept pole of the BII dimension on one side and “other” words with words that represent the “Conflict” concept pole of the BII dimension on the other side. In a second block of trials, “self” words shared the same response as the “Conflict” pole of the BII dimension and “other” words shared the same response option as the “Harmony” pole of the BII dimension. The second IAT followed the same logic in that participants had to discriminate between words that represent the “Blended vs. Distance” dimension of BII, paired with words that differentiate between “self vs. other” concept pair. In total, participants completed seven blocks of trials. Each block included 20 practice trials and 40 test trials. The order of blocks was randomized across participants. For each bicultural participant, the software randomly determined the order in which the seven blocks were completed. This procedure limits the influence of order effects on the obtained results. Explicit measures. After completing the two IATs,square plastic planter participants filled out the battery of acculturation and outcome measures described in Study 1. The implicit measures were administered first. The opposite order might have produced more noise in the implicit data due to fatigue. Please see Study 1 for a description of the explicit measures .

Data screening of test trials showed an overall error rate of 5.6% and a mean response latency of 901 ms for the IAT that assessed the conflict versus harmony dimension of BII. Furthermore, there was an overall error rate of 8.1% and a mean response latency of 919 ms for the IAT that assessed the blendedness versus distance dimension of BII. For the experimental condition, data screening of test trials showed an error rate of 5.5% and a mean response latency of 934 ms for the IAT that assessed the conflict versus harmony dimension of BII. There was an overall error rate of 7.2% and a mean response latency of 954 ms for the IAT that assessed the blendedness versus distance dimension of BII. For the control condition, there was an overall error rate of 5.7% and a mean response latency of 866 ms for the IAT that assessed the conflict versus harmony dimension of BII. Finally, there was an overall error rate of 9.1% and a mean response latency of 881 ms for the IAT that assessed the blendedness versus distance dimension of BII. Taken together, these results suggest that participants had little trouble completing the IATs. Similarly to Study 1, any outliers of extremely fast or slow responses were noted and excluded during data screening. Based on the criterion developed by Greenwald et al. , there were a total of 6 participants eliminated from the study. See Study 1 for how the IAT D effect is calculated. In Study 2, for the Harmony vs. Conflict IAT, a positive score indicated that the Self + Harmony association was stronger than the Self+ Conflict association. A negative score indicated that the Self + Conflict association was stronger than the Self+ Harmony association. Forthe Blendedness vs. Distance IAT, a positive score indicated that the Self + Blendeness association was stronger than the Self+ Distance association. A negative score indicated that the Self + Distance association was stronger than the Self+ Blendedness association.

Two one-sample t-tests were performed in order to examine if the two IAT D means differ from 0 . For the Harmony versus Conflict IAT, results indicated that the sample mean of .396 was significantly greater than 0, t=9.60, p<.001. This result suggested that overall participants implicitly identified more strongly with being a harmonious bicultural relative to being a conflicted bicultural. For the Blendedness versus Distance IAT, results indicated that the sample mean of .270 was significantly greater than 0, t=7.95, p<.001. This result suggested that overall participants implicitly identified strongly with being a blended bicultural compared to being a distant bicultural. Finally, a paired sample t-test was performed to examine the difference between these two groups and results suggested there to be a significant difference between the harmony vs. conflict IAT and blendedness vs. distance IAT, t=2.20, p=.024. This result suggested that Mexican American participants implicitly showed a stronger self-attachment to harmony relative to self + blendedness association. An independent sample t-test was performed to examine if there was a difference in IAT D effect between the experimental and control conditions for both dimensions ofBII. Results indicated that for the harmony versus conflict dimension of BII, there was no significant difference in the IAT D effect between the control condition and experimental conditions, t=.645, p=.520. For the blendedness versus distance dimension of BII, there was no significant difference in the IAT D effect between the control and experimental conditions, t=1.38, p=.171. A second independent sample t-test was performed to examine if there was a difference in the explicit BII scores between the experimental and control conditions for both dimensions of BII. Similarly to the implicit measures, results indicated that for the harmony versus conflict dimension of BII, there was no significant difference in the explicit scores between the control condition and experimental conditions, t=.113, p=.910.

For the blendedness versus distance dimension of BII, there was no significant difference in the explicit scores between the control condition and experimental conditions, t=1.16, p=.248. Taken together, these results suggested that the manipulation did not work. First, correlation analyses were performed to examine the overall pattern among the two IATs . Results indicated that there was no significant relationship between the Harmony vs. Conflict IAT and the Blendedness vs. Distance IAT , r=-.07, p=.46. Next correlational analyses were performed to examine the relation between explicit BII measures and both IATs. Overall, results showed that there was only one significant correlation between the implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . This result suggested that the more Mexican American participants explicitly selfidentified as being a blended bicultural, the less they implicit self-identified as being a harmonious bicultural. The rest of the results indicated that there were no other significant relationships among the other three pairings: implicit and explicit conflict versus harmony dimension of BII , implicit and explicit blendedness versus harmony dimension of BII , and the implicit blendedness versus distance BII dimension with the explicit BII dimension of harmony versus conflict . Even though the experimental manipulation did not work, the aforementioned relationships were examined separately for the experimental and control conditions. Reason being is that these correlations will help to explain the discrepancy in the results in the general discussion section. Results indicated that there was no significant relationship between the harmony vs. conflict IAT and the blendedness vs. distance IAT for both the experimental and control groups . Next correlational analyses were performed to examine the relation between explicit BII measures and both IATs. Similarly to the overall pattern of results, for the control group, there was a significant correlation between the implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . This result was consistent with the overall correlation; however, the association was stronger. In regards to the experimental group,square plastic plant pot there was no significant correlation between implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . The rest of the results indicated that there were no other significant relationships among the other three pairings for both the experimental and control groups . To further explore the validity of the implicit BII measure, additional correlations were run to assess the overall relationship between the two IATs and a battery of explicit acculturation and outcome measures. Interesting enough, there were no significant correlations between the implicit BII measures and the battery of explicit acculturation and outcomes measures with the exception of two correlations. Results indicated a marginal correlation between implicit BII dimension of blendedness versus distance and the explicit acculturation strategy measure of separation and explicit U.S. Identification . These correlations suggested that the more Mexican American participants implicitly self-identified as being a blended bicultural, the less they explicitly endoresd the separation strategy and identified with U.S. culture. The same correlations were also run separately for both the experimental and control groups. Results indicated the same pattern of correlations found in the overall correlation patterns, however differed by either the experimental or control groups . Overall, these correlational analyses indicated that there is little to no relationship between the implicit BII measure and the battery of acculturation and outcome measures including the explicit BII measure. Participants were categorized into two groups based on their explicit BII scores. First, participants received two BII scores for blendedness and harmony. A median split was performed on the two BII scores in order to determine the high versus low groups for each BII dimension. For both BII dimensions, the median score was 4.0. Any participant that scored below the median was categorized as being a conflicted or distant bicultural, whereas any participant that scored at the median or higher was categorized as being a harmonious or blended bicultural.

Based upon these categorization criteria, results from the explicit data indicated that 51% of participants were categorized as high blendedness and 57% were categorized as high harmony, while 49% were categorized as low blendedness and 43% were categorized as low harmony. Participants were then categorized into two groups based on their implicit IAT D scores for comparison purposes. First, participants received two implicit IAT D scores for blendedness and harmony. A median split was performed on the two implicit IAT D scores in order to determine the high versus low groups for each BII dimension. For the harmony vs. conflict dimension of BII, the median score was .459. For the blendedness vs. distance dimension of BII, the median score was .263. Any participant that scored below the median scores of each BII dimension was categorized as being a conflicted or distant bicultural, whereas any participant that scored at the median or higher of each BII dimension was categorized as being a harmonious or blended bicultural. Based upon these categorization criteria, results from the implicit data indicated that 52% of participants were categorized as high blendedness and 51% were categorized as high harmony, while 48% were categorized as low blendedness and 49% were categorized as low harmony. Upon comparing the categorizations based upon the explicit and implicit data, results indicated that the categorizations for high versus low blendedness were roughly identical. However, categorization results based on the explicit and implicit data showed some discrepancy between the high versus low harmony groups. These results indicated that the Mexican American participants tend to assess their blended bicultural identities at both levels of awareness with little variation; however tend to assess their harmonious bicultural identities across two levels of awareness with a little more variation. To further examine the validity of the implicit BII measures, four independent sample tests were performed to examine the overall differences between explicit high and low blendedness and harmony groups on the two IAT measures . Results indicated that there was a significant difference between the explicit high and low blendedness groups on the harmony versus conflict IAT measure, t=-2.23, p=.027. This result suggested that Mexican American participants who explicitly selfidentified as being high in blendedness, implicitly self-identified weaker with harmony compared to those explicitly low in blendedness. Results further indicated that there was no significant difference between the explicit high and low blendedness groups on the blendedness versus distance IAT measure, t=1.31, p=.194. Results for the high versus low explicit harmony groups showed that there was no significant difference between the high and low harmony groups on the harmony versus conflict IAT measure, t=-.526, p=.600. Results further indicated that there was no significant difference between the explicit high and low harmony groups on the blendedness versus distance IAT measure, t=-1.75, p=.083. For the experimental condition, results showed that that there was no significant difference between explicit high and low blendedness and harmony groups on the two IAT measures .

Fewer epochs will also be tested to see how early-stopping the model from training will perform

Technical improvements for this project include developing a stronger data augmentation technique. Instead of using the set transform method which artificially augments the data set, using another package that can actually create the separate images and add them to the data set instead would be interesting to see how it would perform. More Hyper-parameter fine-tuning could be done such as exploring the learning rate and adding an optimizer. More Epochs should be tested in order to see how the model will perform over a greater period of time. Another idea is to explore more the Training-Validation-Testing splits chosen for the data. Exploring the performance between different splits could show how to better improve the classification model. To achieve our expected agricultural need of feeding 10 billion people by 2050, we must prioritize minimizing crop loss wherever possible. More research is needed to help develop more tools to assist crop growers with preventing crop loss. The study “Mobile phone use is associated with higher smallholder agricultural productivity in Tanzania, East Africa” by Amy Quandt et al. looks into the relationship crop growers have with their cell phones as agricultural tools to help increase crop yields. “A key result is the positive association between phone use for agricultural activities and self-reported agricultural yields” . Cell phones are increasing accessibility to technological tools that help with agriculture. These technologies for assisting with crop loss will not only be utilized by commercial crop growers or the average hobbyist and enthusiast as well. Whether crop growers use a ViT image classification model or a convolutional neural network image classification model, or another type of machine learning architecture is used,25 liter plant pot more research is needed to help develop tools to assist crop growers worldwide in eradicating crop loss everywhere!

Variation in bitter taste sensitivity has long been recognized as an important determinant of diet and health. By shaping behaviors such as diet choice and smoking habits, it exerts downstream effects on health measures such as body mass index, cardiovascular function, hormonal processes, and possibly even cancer susceptibility . Much interest stems from the fact that bitter sensitivity varies profoundly from person to person and is highly heritable . This has spurred efforts to detect gene mutations shaping responses to specific compounds, with the aim of better understanding the mechanistic underpinnings of taste–health connections. A consistent finding as these efforts have progressed is that mutations in TAS2R genes, which encode G protein-coupled receptors controlling the initial stages of the bitter perception process, are major contributors . This issue of Chemical Senses features a new study of TAS2R38, which is famous for its role in shaping PTC sensitivity . Here, Risso et al. investigate associations between mutations in TAS2R38 and taste responses to fruit from a little known tree found in southeast Asia, Antidesma bunius. Risso et al. ask, does variation in TAS2R38 predict bitter taste perception of A. bunius fruit, as it does in PTC? The short answer is, yes. However, the association is the opposite of PTC’s: mutations associated with high PTC sensitivity are associated with low A. bunius sensitivity and, conversely, mutations associated with low PTC sensitivity are associated with high A. bunius sensitivity. The pattern is striking, and it is more than a novelty. It bears on our understanding of not just PTC and A. bunius perception, but bitter perception in general. Though little known outside the region, A. bunius is a familiar sight in south and southeast Asia, and into the Malay archipelago, the Philippines, Borneo, Papua New Guinea, and most regions of Melanesia and Micronesia. A. bunius goes by many common names, most commonly bignay or bignai, Chinese laurel, salamander tree, or variants of these .

It is a leafed evergreen with characteristics similar to those of oak, with a large central trunk and limbs branching above, and heights reaching 30 m . It is frequently cultivated as an ornamental due to its attractive appearance, ability to provide shade, and yield of edible fruit. A. bunius fruit is small , round, consists of a single seed surrounded by a thin layer of pulp, and grows in clusters like grapes . The fruits ripen at different rates, giving maturing clusters a striking appearance with white, red, and black berries. A. bunius fruit is generally not eaten raw due to its sourness and astringency, but it is a popular ingredient in sweetened, cooked, or fermented products such as jellies, juices, and wine. A. bunius tea, another popular product, is derived from the tree’s bark.Henkin and Gillis evaluated subjects’ responses to 2 solutions: PTC at saturation in water and juice pressed from A. bunius fruits. Subjects’ responses to PTC were consistent with previous studies, with 68% of subjects reporting bitterness and 32% reporting no taste . Patterns of response to A. bunius were different, with 15% of subjects being responders and 85% being non-responders. Strikingly, responses to PTC and A. bunius were negatively associated. Of the 115 PTC responders, none were A. bunius responders; however, of the 25 A. bunius responders, none were PTC responders. Henkin and Gillis concluded from this that bitter perception of PTC and A. bunius are mediated by related factors, probably on a genetic level, although the specific mechanism accounting for this remained speculative. Risso et al.’s new study capitalizes on current understanding of the molecular genetics of bitter perception to revisit the A. bunius puzzle. It is now firmly established that the inheritance of PTC sensitivity is controlled principally by 2 alleles at a single locus, TAS2R38 . Thus, it seemed likely that these might account for the patterns observed by Henkin and Gillis. To find out, Risso et al. frst replicated Henkin and Gillis’ earlier taste tests. Perception was ascertained in subjects evaluating 2 solutions: PTC and A. bunius juice. Risso et al. then went farther, obtaining DNA sequences from TAS2R38 in subjects. These allowed, for the frst time, a test of whether the specific mechanism underlying variability in PTC perception also accounts for variation in A. bunius perception.

Risso et al.’s results are consistent with those of Henkin and Gillis and shed new light on the mechanisms underlying the PTC/A. bunius relationship. Risso et al. found that taste responses to PTC are indeed predictive of responses to A. bunius: only 11% of PTC responders were A. bunius responders, whereas 16% of A. bunius responders were PTC responders. Thus, there is an unambiguous inverse relationship between sensitivity to PTC and sensitivity to A. bunius. Risso et al.’s data further show that variation in TAS2R38 does show an association with A. bunius sensitivity, and it is strong. More than 30% of Risso et al.’s subjects harbored the TAS2R38-PAV/PAV genotype, yet none were A. bunius responders; conversely, 100% of A. bunius responders harbored TAS2R38-AVI. These results are consistent with the longstanding hypothesis that perception of both PTC and A. bunius is mediated by alleles of TAS2R38, with PAV conferring PTC sensitivity and AVI conferring A. bunius sensitivity. They are also consistent with computational structure-function analyses suggesting that the A262V mutation causes a shift in ligand specificity, but does not disable the receptor . Thus, the simplest explanation for Risso et al.’s findings is that A. bunius harbors an agonist compound specific to AVI, much as PTC is an agonist of PAV, and homozygotes can only perceive one compound or the other while heterozygotes can perceive both . Although the findings of Henkin and Gillis and Risso et al. only pertain directly to perception of PTC and A. bunius, they have implications for bitter perception in general. Most TAS2Rs are responsive to multiple substances, and it is already known that PAV mediates responses not just to PTC, but to a constellation of related compounds as well . If AVI is a functional receptor,black plastic plant pots it would be remarkable if were mediating responses to just a single compound found in relatively obscure plant. What is it mediating responses to? The obvious strategy for answering this question is to take the approach of and systematically test AVI for responses to libraries of compounds in vitro. A sensible starting point would be to focus on compounds already known to be present in A. bunius, which are receiving attention for their bio-active properties . Evidence that both of TAS2R38’s common alleles contribute to bitter responses also raises the prospect that similar patterns occur in other TAS2Rs. TAS2R genes are highly diverse, harboring signifcantly more variation than average for the human genome . In a study analyzing genetic diversity in all known TAS2R genes in 55 subjects, Kim et al. found an average of 6 coding haplotypes per locus. In larger sample, found that TAS2R38 alone has >20 coding haplotypes. If divergent functionality among TAS2R alleles is the norm rather than the exception, or even merely common, it would point to the presence of major phenotypic variation arising from effectively unlimited combinatorial diversity. An additional point made by Risso et al. is that evidence for functionality of AVI provides an explanation for signatures of balancing natural selection at TAS2R38. If PAV enables perception of one set of compounds, and AVI enables perception of another, then heterozygotes should be able to perceive both. This could provide a selective advantage to heterozygotes, resulting in the maintenance of both alleles human populations. Evidence that AVI is functional also explains an intriguing but little discussed aspect of variation in TAS2R38, which is that while coding variants of AVI do exist, they are found only at low frequencies, and no profound mutations such as premature stop codons or frame shifts have been reported on the AVI background .

Both of these observations are consistent with the AVI sequence being conserved by selective processes, which could only occur if it has some type of function. It is crucial to recognize that while the simplest explanation for Risso et al.’s findings is that AVI is a functional receptor, it is not the only mechanism through which AVI might mediate taste responses to A. bunius. A compelling alternative is protein–protein interaction. Protein–protein interactions such as heterodimerization are ubiquitous among members of the GPCR super family, and frequently alter the function of the participating molecules . Indeed, the human umami and sweet receptors are both GPCR heterodimers: TAS1R1+TAS1R3 and TAS1R2+TAS1R3, respectively . One explanation for the association of AVI with A. bunius perception is that AVI interacts with a second TAS2R, forming a heterodimer responsive to A. bunius constituents. In this scenario, AVI would be functional, but as a cofactor rather than a receptor. Support for this possibility comes from computational and experimental evidence that the A/V and V/I mutations abolish TAS2R38’s activation by ligands, but do not have major effects on the protein’s overall structure . Thus, while the present findings suggest that AVI is acting as a receptor for constituents of A. bunius, they do not demonstrate it defnitively. Isolating AVI’s function will require identifcation of the specific compounds involved and establishing their interactions. The possibility that the AVI allele is mediating responses to unknown substances suggests that caution should be taken in efforts to understand associations between TAS2R variation and responses to complex aspects of diet and other orosensation driven behaviors. In particular, it raises questions about the directionality and strength of genotype–phenotype associations. In the case of TAS2R38, the prevailing focus is currently on the fact that genotype predicts high, medium, and low sensitivity to known agonists, such as goitrogens found in cruciferous vegetables. The new findings raise the question of whether sensitivity to some unknown compound is commensurately increasing, and whether it might be an equally important driver of observed associations. Both could even occur simultaneously, which could weaken or obscure associations. Dissecting such effects, even if just to rule them out, will require substantial effort from all chemosensory perspectives: molecular, psychophysical, and behavioral.Tomatoes may suffer some leaf burn and early stunting but rapidly outgrow these problems and soon surpass plants grown over bare soil. Eggplant tends to be more sensitive and may suffer prolonged injury. We have observed no problems with any cucurbits grown over metalized mulches. Plants, particularly cucurbits, grown over metalized mulches may be more susceptible to frost injury in the late fall. More widespread adoption of the use of UV-reflective plastic mulches in California has not occurred largely because of added costs associated with their use and disposal and a general lack of familiarity with production techniques required for their successful use.

The estimation of GC from the coancestry matrix differed between founders and ancestors

These results highlight the power and accuracy of diploid Mendelian exclusion analysis methods for pedigree authentication , intellectual property protection, and quality control monitoring of germplasm and nursery stock collections in octoploid strawberry using subgenome-specific DNA markers. The application of these approaches was straightforward because of the simplicity and accuracy of subgenome-specific genotyping approaches in octoploid strawberry populations . The development and robustness of SNP genotyping platforms has facilitated the application of standard diploid genetic theory and methods in octoploid strawberry, including the exclusion analysis methods applied in the present study . The power and accuracy of these methods were rigorously tested and affirmed in a court of law where DNA forensic evidence was pivotal in proving the theft of University of California intellectual property by the defendants in a 2017 case in US District Court for the Northern District of California captioned The Regents of the University of California v California Berry Cultivars, LLC, Shaw, and Larson . The DNA forensic approaches and evidence applied in that case are documented in a publicly available expert report identified by case number 3:16- cv-02477 .We estimated that 80-90% of the individuals in the California and Cosmopolitan pedigree networks were extinct . Using SNP array-genotyped individuals preserved in public germplasm collections as anchor points, we searched for evidence that the allelic diversity transmitted by extinct founders had been “lost.” This is a difficult question to answer with certainty; however, the findings reported here,drainage pot combined with the findings of Hardigan et al. , suggest that genetic diversity has been exceptionally well preserved in domesticated populations.

Using SNA and PCAs of H, we did not observe structural features in sociograms or PCA plots that were indicative of the loss of novel ancestral genetic diversity . The kinship or numerator relationship matrix was estimated for the entire pedigree of genotyped and ungenotyped individuals . For the present study, 1,495 historically important and geographically diverse UCD and USDA F. ananassa individuals were genotyped with high-density SNP arrays . The genomic relationship matrix was estimated for the genotyped individuals and combined with the A matrix to estimate the H matrix for the entire pedigree . The global H matrix was partitioned as needed for subsequent analyses . PCAs of the H matrices yielded two-dimensional visualizations of genetic relationships that were remarkably similar in shape and structure to sociograms for the California and Cosmopolitan populations . We observed distinctive differences in the shapes and structures of the sociograms and PCA plots between the populations . The pattern in the Cosmopolitan population was a characteristic of pervasive admixture among individuals across geographies . We observed a strong chronological trend in the California population but not in Cosmopolitan population . We observed a mid-twentieth-century bottleneck in the California population , in addition to a bottleneck pinpointed to approximately 1987-1993 when the California population became closed. We discovered that 48 founders contributed 100% of the allelic diversity to the California population from 1987 onward . Hardigan et al. showed that even though nucleotide diversity had been progressively reduced by bottlenecks and selection, a significant nucleotide diversity has persisted in the California population but was found to be unevenly distributed across the genome.Our genealogy search did not uncover pedigree records for F. ananassa cultivars developed between 1714 and 1775, the 61-year period following the initial migration of F. chiloensis ecotypes from Chile to Europe .

The scarcity of pedigree records from the eighteenth century was anticipated because the interspecific hybrid origin of F. ananassa was not discovered until the mid-1700s . “Madame Moutot” was the only cultivar in the database with ancestry that could bedirectly traced to one of the putative original wild octoploid progenitors of the earliest F. ananassa hybrids that emerged in France in the early 1700s . Although the genealogy primarily covers the past 200 years of domestication and breeding , ascendants in the pedigree of the cultivar “Madame Moutot” traced to “Chili de Plougastel” , a putative clone of one of the original F. chiloensis subsp. chiloensis plants imported from Chile to France by the explorer Ame´de´e-Franc¸ois Fre´zier . These plants were carried aboard the French frigate “St. Joseph,” delivered by Fre´zier to Brest, France , and shared with Antoine Laurent de Jussieu, a botanist at the Jardin des plantes de Paris. According to de Lambertye , the Fre´zier clone was widely disseminated and cultivated in Plougastel near Brest and interplanted with F. virginiana . Hence, some of the earliest spontaneous hybrids between F. chiloensis and F. virginiana undoubtedly arose in the strawberry fields of Brittany in the early 1700s . The French naturalist Bernard de Jussieu, the brother of Antoine Laurent de Jussieu and a mentor of Antoine Duchesne—“the father of the modern strawberry”—brought clones of the original Fre´zier F. chiloensis plants to the Jardins du Chaˆ teau de Versailles where Duchesne unraveled the interspecific hybrid origin of F.  ananassa . The next earliest F. chiloensis founders appear to be a California ecotype identified in German breeding records from the mid-1800s and an anonymous ecotype in the pedigree of the French cultivar “La Constante” from 1855 . The origins and identities of the earliest F. virginiana founders of F.  ananassa remain a mystery because their migrations from North America to Europe in the early 1600s and subsequent intracontinental migrations were not well documented . The oldest F. virginiana individuals identified in historic documents and pedigree records were “Large Early Scarlet” , “Old Scarlet” , and “Hudson Bay” , all extinct .

We identified 30 anonymous F. virginiana and 76 anonymous F. chiloensis founders in the pedigree records. These individuals were assigned unique alphanumerical aliases to facilitate the reconstruction of the genealogy; e.g., FV22 is the alias for an anonymous F. virginiana founder and FC71 is the alias for an anonymous F. chiloensis founder in the pedigree of “Madame Moutot” .Once the interspecific hybrid origin of F.  ananassa became widely known , domestication began in earnest with extensive intra- and interspecific hybridization, artificial selection, and intra- and intercontinental migration . These forces shaped the genetic structure of the F.  ananassa populations that emerged in Europe and North America, and ultimately migrated around the globe . Over the next 250 years, horticulturalists and plant breeders repeatedly tapped into the wild reservoir of genetic diversity, especially wild octoploid taxa native to North America . There are numerous narrative accounts of what transpired, especially in Europe, North America, and California , but none have painted a holistic picture of the complicated wild ancestry and dynamic forces that shaped genetic diversity in F.  ananassa. We identified 1,438 founders in the genealogy of cultivated strawberry . Here and elsewhere, “founders” are individuals with unknown parents, whereas “ancestors” are ascendants that may or may not be founders . The terminal nodes in the pedigree networks are either founders or the youngest descendants in a pedigree . Of the 1,438 founders, 267 were wild species and 1,171 were F.  ananassa individuals . Because the F.  ananassa founders are either interspecific hybrids or descendants of interspecific hybrids, the number of wild species founders could exceed 268. One of the challenges we had with estimating the number of wild species founders was the anonymity of ecotypes that were used as parents before breeders began carefully documenting pedigrees . We could not rule out that some of the anonymous wild species founders in the pedigree records might have been clones of the same individuals, drainage planter pot which means that the estimated number of wild species founders reported here could be inflated. As interspecific hybridization with wild founders became less important and intraspecific hybridization became more important in strawberry breeding, the proportional GC of wild founders to the gene pool of cultivated strawberry decreased . This seems paradoxical because 100% of the alleles found in F.  ananassa were inherited from wild founders, but increasingly flowed through F.  ananassa descendants over time—wild octoploids numerically only constituted 14% of the founders we identified . Several trends emerged from our analyses of genetic relationships and founder contributions. First, inbreeding has steadily increased over time as a consequence of population bottlenecks and directional selection . Second, the California population was significantly more inbred than the Cosmopolitan population . These results were consistent with the findings of Hardigan et al. from genome-wide analyses of DNA variants and population structure. They found selective sweeps on several chromosomes in the California population, which was shown to be unique and bottle necked. Finally, the relative number of founder equivalents has decreased over time, consistent with the increase in inbreeding over time .

The primary gene pool of cultivated strawberry is comprised of eight cross-compatible, interfertile octoploid taxa: F. chiloensis subsp. chiloensis, F. chiloensis subsp. lucida, F. chiloensis subsp. pacifica, F. chiloensis subsp. sandwicensis, F. virginiana subsp. virginiana, F. virginiana subsp. glauca, F. virginiana subsp. grayana, and F. virginiana subsp. platypetala , seven of which were found in pedigree records . The only primary gene pool taxon not found in the pedigree records was F. virginiana subsp. grayana. We identified 112 F. chiloensis, 65 F. virginiana, and 1,171 F. ananassa founders, which constituted 95% of the founders and were estimated to have contributed 99% of the allelic diversity to global, California, and Cosmopolitan F.  ananassa populations . Even though wild species from the secondary gene pool constituted 6% of the founders and 30% of the wild species founders identified in pedigree records, they were estimated to have contributed < 0:1% of the allelic diversity in the global F.  ananassa population . While the assignment of F. chiloensis and F. virginiana subspecies to the primary gene pool was unequivocal and uncontroversial, the assignment of non-octoploid Fragaria and Potentilla species to secondary or tertiary gene pools, as per the definitions of Harlan and de Wet , was tenuous because evidence for the inheritance of alleles from exotic donors among inter-ploidy hybrid offspring with cultivated strawberry was not always clear from genealogical and breeding records. We lumped the non-octoploid Fragaria and Potentilla into the secondary gene pool solely because they were recorded as ancestors of F.  ananassa individuals , which implied that interspecific, intergeneric, and inter-ploidy hybrid descendants inherited alleles transmitted by secondary gene pool donors. However, the genetic proof was not always clear or available. One or more of the species assigned to the secondary gene pool might belong in the tertiary gene pool , a distinction of negligible practical importance. The secondary gene pool founders in the genealogy were nearly always parents of orphans or other isolated individuals in short dead-end pedigrees that have not materially contributed allelic diversity to important cultivated strawberry populations or cultivars. The exotic founders have included decaploid F.  vescana and pentaploid F.  bringhurstii individuals . Although cited as important genetic resources for strawberry breeding , the secondary gene pool species have had a limited utility because of the range of biological challenges one encounters when attempting to introgress alleles from exotic donors through interspecific, intergeneric, and inter-ploidy hybrids, e.g., reproductive and recombination barriers, ploidy differences, meiotic abnormalities, and hybrid sterility . Genetic variation in the secondary gene pool has not been needed to drive genetic gains or solve problems in strawberry breeding. As highlighted earlier, Hardigan et al. showed that genetic diversity is massive in the primary gene pool and has not been eroded by domestication and breeding on a global scale, even though it has been significantly reduced and restructured in certain populations, e.g., the California population. The profound changes and restructuring in the California population over time, as previously noted, were clearly evident in the sociograms and PCAs of the pedigree–genomic relationship matrices . Because the California population has been the source of numerous historically and commercially important cultivars, we hypothesize that intense selection and population bottlenecks have purged a high frequency of unfavorable alleles compared to many other populations, thereby yielding an elite population with lower genetic diversity than the highly admixed Cosmopolitan population .We used coancestry, betweenness-centrality , and out-degree statistics to estimate the GC of founders and non-founders to genetic variation within a population and identify the most prominent and important ancestors in the genealogy of cultivated strawberry . For founders, GC was estimated by the mean coancestry or MK between each founder and cultivars within a focal population .

Dietary sulfite primarily originates from preservatives in processed and dried food as well as beverages

More comprehensive human intervention studies will be essential in the future to provide insight into the potential influence of dietary polyphenols and their aromatic bacterial metabolites on intestinal microbial communities and their activities.Probiotics are defined as viable microorganisms that, when consumed in sufficient amounts, confer a health benefit on the host.To date, most of the commonly used probiotics are limited to strains of certain Lactobacillus and Bifidobacterium species . Survival during passage through the GI tract is generally considered as the essential feature for probiotics to preserve their active functions in the colon. Indeed, the probiotic strains must overcome biological barriers, including resisting gastric and bile acid secretion and tolerating intestinal lysozyme and toxic metabolites produced during digestion . Various studies found that at least a fraction of probiotic bacteria can be detected in stool for between 1 and 3 weeks after consumption . Probiotic Lactobacillus strains were also found to adapt for survival in the gut and possess gut-inducible genes that are responsive at different sites in the intestine. Interestingly, provision of the probiotic Lactobacillus plantarum to mice fed a Westernstyle diet and to humans resulted in similar gene expression profiles of this strain.As probiotics are delivered via various food vehicles, the complex food matrix should also be viewed as an important factor that may alter the probiotic activity in the gut. To date,pots with drainage holes only a few animal and clinical studies have addressed the functional roles of food on probiotic-conferred health benefits.

The mechanisms of probiotic effects on health are only partially understood but likely function either directly through interactions with host intestinal epithelial and immune cells or indirectly by modulating the indigenous intestinal microbiota. In regard to the latter, several studies have concluded that probiotic consumption does not result in global modifications of the intestinal microbiota in healthy individuals.However, probiotics might confer modest but significant changes to the functional activities of local intestinal bacterial populations. When examined at the meta-transcriptional level, intake of a probiotic fermented milk was associated with the upregulation of microbial genes corresponding to plant polysaccharide metabolism.Similarly, administration of probiotics was shown to induce crosstalk between the probiotics from the diet and the individual bacterial species in the gut and might induce competition for limited substrates that results in fluctuations tof the metabolic profile of the host.The gut microbiome of healthy adults is highly resilient , where the stable native microbiota prohibits the succession of microbes from the diet.In addition, the effect of probiotics on the gut microbiome appears to differ depending on host phenotypes such as age, health status, and chronic conditions. For example, the infant gut microbiome is highly diverse and dynamically changes during development and therefore may be easily influenced by the consumption of probiotics . In individuals with irritable bowel syndrome , probiotic consumption resulted in an increase in the numbers of Bacteroidetes in the intestine.Moreover, intake of two Lactobacillus strains by diet-induced obese mice altered microbial composition and decreased expression of inflammatory genes in the adipose tissue while increasing levels of fatty acid oxidation in the liver.Further studies are needed to investigate the effects of assorted probiotic supplements on the gut microbiome with respect to various host life stages and phenotypes.The premise behind substituting sugar with artificial sweeteners is to maintain the palatability of food at the same time as lowering energy intake.

However, a sufficiently high ingestion of non/low-digestible sugar substitutes stimulates the growth of gut microbiota and can induce transitory diarrhea in humans.In particular, the great proportion of non/low digestible sugar substitutes that reach the distal intestine are subject to fermentation by the colonic microbiota, offering approximately 2 kcal/g of energy.Although discovering and characterizing these compounds within foods is relatively new, it is of interest to note that many of these food ingredients are common in our daily diet. For example, the disaccharide alcohol maltitol is considered a common replacement for sucrose. Urinary and fecal excretions of sorbitol and maltitol after 24 h in conventional rats were shown to be minimal compared with germ-free rats.Likewise, maltitol consumption significantly increased production of SCFAs in addition to nine tested fecal microbes after a 6 week trial, including bifidobacteria, Bacteroides, Clostridium, lactobacilli, eubacteria, Atopobium, Fusobacterium prausnizii, Ruminococcus flavefaciens, and R. bromii. A 12 week administration of Splenda, composed of 1.1% of the artificial sweetener sucralose, increased fecal pH and reduced the amount of fecal bifidobacteria, lactobacilli, Bacteroides, clostridia, and total aerobic bacteria in a rat,whereas isomalt, a widely used low-energy sweetener, was considered to be bifidogenic in a human study.Overall, artificial sweetener fermentation by gut microbiota remains either unexplored or poorly documented, some of which are highlighted in a review by Payne et al.Azo compounds are widely used as coloring agents in foods, beverages, and food packaging.In addition, azo polymer coatings have been specifically designed for colon-selective drug delivery due to the presence of pH-sensitive monomers and azo cross-linking agents in the hydrogel structure. Indeed, azo dyes can be metabolized under anaerobic conditions by intestinal microbial processes and, as a result, produce the reductive cleavage products aromatic amines .

The majority of the toxic effects of azo dyes are exerted through aromatic amines produced by their colonic degradation.Raffi et al. reported that isolated intestinal bacteria in an anaerobic culture system were able to decolorize the dyes in the supernatant, suggesting that some of the azoreductase activities are extracellularly released.Xu et al. demonstrated a variable degree of efficiency in the reduction of Sudan azo dyes and Para Red by 35 prevalent human intestinal microbes in vitro.In contrast, Sudan azo dyes and their metabolites selectively inhibit the growth of some human intestinal microorganisms,which may suggest a potential impact on gut microbiome after long-term exposure. In summary, although there are tantalizing glimpses into the effect of azo dyes on microbes in vitro, more data from animal and human studies are keenly awaited.In the colon, sulfur is present in either inorganic form or organic form .The human GI tract poorly absorbs sulfate, and there is little sulfatase activity in the mucosa of the GI tract; therefore, free sulfate in the colon is likely to be of dietary origin.Dietary sulfate drives the activity of sulfate-reducing bacteria that couple oxidative phosphorylation with reduction of sulfate to produce sulfide.The total inorganic sulfur intake is much higher in the Western diet in comparison to a typical African rural diet.Highly processed foods that are high in sulfate include bread, soy flour, dried fruits, and brassicas, as well as sausage, beers, ciders, and wines.Sulfur-containing amino acids such as cysteine can be found in dietary protein and are a source of sulfur for colonic sulfate-reducing bacteria Desulfovibrio desulfuricans. Native Americans who consume a diet high in resistant starch and low in animal products harbor significantly distinct sulfate-reducing bacterial populations and more diverse and different methanogenic archaea than Americans consuming a typical Western diet.Substrate competition for hydrogen among methanogenic archaea, sulfate-reducing bacteria, acetogenic bacteria, and otherspecies likely occurs in the colon.Because hydrogen is an essential component for the survival of colonic methanogens, removal of the substrate terminates methanogenesis. Given an adequate supply of sulfate, sulfate-reducing bacteria that are more abundant in the right colon out compete methanogenic archaea for H2 due to their higher substrate affinity to produce hydrogen sulfide ,an end-product of dissimilatory sulfate reduction.As a result, the mucosal microbiome may be shaped in part through the availability of toxic sulfide compounds and the differential susceptibility of mucosalistic microbes to the toxins.Furthermore, the activity of methanogenic bacteria can also be disrupted by bile acids.In brief, methane production was thought to occur only when sulfate-reducing bacteria were not active.If sulfate is limited and hydrogen is in relative excess, methanogenic bacteria or perhaps acetogenic bacteria will become essential.Therefore, the levels of sulfate present in the colon are critical for determining which bacterial group gains a better survival advantage.Many people consume alcoholic beverages; however,drainage pot few studies exist on the effect of alcohol consumption on the gut microbiome of healthy individuals. For individuals who consume alcohol to excess, abnormal gut microbiota and bacterial overgrowth can potentially initiate or worsen alcoholinduced impaired gut barrier function and contribute to endotoxemia in patients with alcoholic fatty liver disease.

Yan et al. demonstrated a 3 week acute effect following alcohol administration in mice that resulted in bacterial overgrowth, as well as an expansion of Bacteroidetes and Verrucomicrobia bacteria while decreasing Firmicutes, with no difference observed after only 1 day or 1 weekChronic alcohol consumption induces changes in gut community profiles. For example, daily alcohol consumption for 10 weeks in a rat alters the colonic mucosa-associated bacterial microbiota fingerprint pattern.Similarly, chronic ethanol feeding for 8 weeks increased fecal pH and decreased abundance of both Bacteriodetes and Firmicutes phyla with a remarkable expansion of Proteobacteria and Actinobacteria phyla in mice.In a human trial, chronic alcohol consumption resulted in the alteration of the mucosa-associated colonic bacterial composition in a subset of alcoholics, with lower median abundances of Bacteroides and higher Proteobacteria. Furthermore, measurement of serum endotoxin suggests a change in microbial function, rather than abundance, which may lead to increased levels of gut-derived pro-inflammatory factors in chronic alcohol consumption. It is noted that the inability to detect clear differences between alcoholics with and without liver disease suggests that chronic alcohol consumption, rather than the disease physiology, is the most important event that appears to alter microbiota composition.It is now well established that host diet alters the gut microbiome. Changes in the gut microbiota composition are also considered an important factor in health and disease. Dietary assessment has provided us with a window to discover a way to reconfigure the gut microbiome. In this regard, the nutritional manipulation of the gut microbiome serves as a basis for formulating therapeutic approaches that are feasible and acceptable to the general population as a promising way to promote health in the era of personalized nutrition and medicine. Understanding the impact of foods and nutrients on host− microbe coevolution supports the essential role of a mutualistic relationship for intestinal homeostasis, but there remain challenges for nutritionists and scientific investigators alike to determine the “ideal” diet. This review collectively maintains the emerging view that diet supports a specific bacterial community structure and further suggests that a suboptimal dietary composition/quality may promote the development of diseases through introducing intestinal microbial dysbiosis. Major shifts in intestinal microbial composition are often observed when dietary differences between groups are extreme. Only a few population-wide studies are available to date, but some of them support a role of food diversity as a potential mechanism for altering gut microbial diversity. Although it is difficult to determine the causality of observed fecal microbiota shift with respect to many lifelong changes, generally, an adequate control over influential factors is important for the success of clinical studies to eliminate the drastic effects of unnecessary confounding variables. Many of the studies reviewed here rely on the assumption of equivalence between the term “fecal microbiome” and “intestinal microbiome”. Further studies are necessary to elucidate more clearly the exact impact of the selection of different diets on qualitative changes in the gut microbiota. Some nutrients that have been studied, such as dietary fiber, are a possible option for the maintenance of intestinal homeostasis and improvement of gut health, whereas others may contribute an opposite effect. Therefore, future research must be focused on looking to improve the effectiveness of diets with an underlying long-term “targeted approach” that allows improvement of intestinal microbial composition and functional activities. In other instances, when dietary differences are small and on a short time scale, gut microbiota changes are not as obvious, but that is not to say that changes do not occur. An alteration of the gut microbiota at lower taxonomic levels is still likely to have important functional consequences for the host. Notably, gut microbiota varies dramatically from individual to individual in lower taxonomic levels. Even small dietary changes may have impacts on the gut microbiota and altered metabolic activities in the microbial profile that are not easily detected by the phylogenetic/taxonomic methods. Metabolic alterations induced by diet may result in varying the microbial capability of synthesizing substances in the intestinal tract. It appears that measurement of bacterial enzyme activities may be a more sensitive indicator of diet induced changes in the gut microbiota than taxonomic-based methods.

CNGs may have also been degraded during juice preparation due to native β-glucosidases

The total levels of CNGs measured here are much lower than CNG concentrations found in European or American elderberry. In a study of European elderberries evaluated at various growing locations and altitudes found that sambunigrin levels range from 0.08 ± 0.01 to 0.77 ± 0.08 µg g-1 . 6 A nearly 10-fold difference in concentrations between elderberry samples highlights the variation on CNG levels due to differences in growing conditions and environmental factors like sun exposure and temperature fluctuations. Furthermore, evidence of CNGs degrading with thermal processing has been evaluated in European elderberry products: when sambunigrin levels were measured in raw and cooked elderberry juice and other products, heating of elderberry juice reduced the level of sambunigrin, from 18.8 ± 4.3 mg kg-1 to 10.6 ± 0.7 mg kg-1 . 1 Liqueur, tea, and spread also had significantly lower CNG concentrations as compared to the raw and cooked juice. American elderberry was evaluated for concentration of CNGs in the seeds, juice, skin, and stem of two genotypes: Ozone and Ozark.60 Elderberry juice was prepared by thawing previously frozen berries in a plastic bag and gently pressing to release juice. The juice of these elderberries contained amygdalin, dhurrin, prunasin/sambunigrin , and linamarin. Total concentrations of these four CNGs was 4.01 µg g-1 in Ozone and 3.66 µg g-1 in Ozark elderberries. The levels of amygdalin and prunasin/sambunigrin were almost equal in Ozone but in Ozark,vertical gardening in greenhouse prunasin/sambunigrin levels were much higher than amygdalin . These concentrations are much higher than the levels found in the present study, as raw blue elderberry juice had a total CNG concentration of only 0.737 µg g-1 .

Because CNGs are formed from phenylalanine, it is possible that the blue elderberry had limited stock of this key material to create CNGs. An alternative reason may be that blue elderberry may have less expression of the genes needed to form CNGs like sweet almonds compared to bitter almonds.A future study should investigate the impact of freeze thaw cycles on the activity of β-glucosidase in elderberries because elderberries are frequently frozen before processing because they can spoil quickly if only refrigerated. Two cooking temperatures were investigated to understand the impact of temperature on the degradation rates of the phenolic compounds in blue elderberry juice. The pH and soluble solids were evaluated for the five juice replicates to ensure the juices were similar for the cooking process. The average pH value of the juices was 3.76 ± 0.11 and the average Brix reading was 16.2 ± 1.1%. The major phenolic compounds in elderberry juice were measured via HPLC-DAD and include 5-hydroxyprogallol hexoside , which is a novel phenolic compound tentatively identified for the first time by Uhl et al. 202239 chlorogenic acid, rutin, isorhamnetin-3-O-glucoside, cyn 3-sam, and cyn 3-glu. Whereas levels of cyn 3-sam and cyn 3-glu decreased to 82.2 ± 6.9 % and 79.3 ± 6.3 %, respectively , more than 98% of the original concentration of 5-HPG, rutin, isorhamnetin-3-O-glucoside and chlorogenic acid remained after two hours. At the higher cooking temperature , the anthocyanins again experienced significant degradation, retaining only 33.2 ± 4.6 % and 36.8 ± 5.5 % of the original concentration after cooking two hours . In a separate study of the thermal stability of elderberry juice, 15% of cyn 3-sam and cyn 3-glu were retained in juice as compared to control juice.

Szalóki-Dorkó, et al. demonstrated that the more complexly glycosylated anthocyanins cyn 3-sam is more stable during thermal process as compared to cyn 3-glu.The results of our study are similar to Oancea et al. which showed after 90 min at 100 °C, total anthocyanin content degraded 58 %.However, that study also observed an increase in total phenolic and total flavonoid content after 60 min, followed by a gradual decrease, which was not observed herein. If sample vials were sealed well to protect from any loss of moisture, this increase in concentrations may be due to the release of phenolic compounds bound to the cell well or other polysaccharides, which can be released with the assistance of pectinase treatments.The main flavonols in blue elderberry, rutin and isorhamnetin glucoside, were stable during the thermal processing, retaining 100.5% and 99.3%, respectively, of their original concentration even at 95 °C . The high retention rates of rutin and isorhamnetin glucoside match literature reports for the thermal stability of these compounds, which show that rutin has a strong thermal stability at acidic pH. More than 80% of the starting concentration was retained after five hours of cooking at 100 °C at pH 5.148 Our results do not agree with another study in which rutin had an activation energy 107.3 kJ/mol, and the half-life values at 70 and 90 °C were 19.25 and 1.99 h, respectively; however, the rutin was in an aqueous solution at pH 6.6.Other compounds present in blue elderberry juice, in addition to a lower pH, could cause synergistic effects to improve stability of rutin in the present study. Limited information on the thermal stability of isorhamnetin glucoside was found, though a study of black currant juice stability found that during long-term storage at room temperature and at 4 °C, isorhamnetin glucoside concentrations did not change significantly during the 12-month period. In the same study, rutin did not change significantly during storageThe main phenolic acid in blue elderberry juice, chlorogenic acid, was also thermally stable.

This result was unexpected, as another study on the thermal stability of chlorogenic acid in a complex with amylose showed a significant decrease in content after 10-15 minutes, depending on the temperature.Their results also showed that a 10 °C increase in temperature results in a 2.5-fold increase in the rate of degradation of chlorogenic acid. It can be beneficial to maintain levels of chlorogenic acid in anthocyanin-rich matrices, as shown in black carrot extract where chlorogenic acid increased absorbance of cyanidin-based anthocyanins at pH 3.6 and 4.6 due to intermolecular co-pigmentation.Overall, our results show that blue elderberry juice behaves similarly to anthocyanin-rich matrices, in that longer processing at higher temperatures degrades anthocyanins. The two main anthocyanins in blue elderberry, cyn 3-sam and cyn 3-glu, behaves similarly during processing, degrading at about the same rate at 72 °C and 95 °C. Furthermore, the other major phenolic compounds like rutin, isorhamnetin, and chlorogenic acid, were highly stable and can withstand the thermal processing. Our study into the effects of thermal processing on the phenolic composition and cyanogenic glycoside content in blue elderberry juice showed that the main anthocyanins present degrade faster at higher temperatures but other important phenolic compounds like rutin and isorhamnetin 3-glucoside are more thermally stable, retaining over 90% of their original concentrations even after two hours at 95 °C. Furthermore, neoamygdalin and sambunigrin were measured in the blue elderberry juice, which were in lower concentrations compared to European and American elderberry. Perched in the hills above Monterey Bay, the UC Santa Cruz campus looks out on the rich farmland of the Pajaro and Salinas Valleys, home to some of the most successful and productive organic farming operations in the country. UCSC’s own 25-acre farm, managed by the Center for Agroecology and Sustainable Food Systems, has been training organic farmers for nearly four decades. Yet until a year ago, students eating in the campus dining halls seldom had a choice of organically grown food. Today, all five UCSC dining halls and the University Center’s Terra Fresca restaurant serve certified organic produce every day of the week. Growers from the seven local farms that make up the Monterey Bay Organic Farmers Consortium —including UCSC’s farm—pool their produce through the Agriculture and Land-Based Training Association in Salinas to sell to UCSC Dining Services. ALBA’s contract to provide locally grown organic produce is a first among the UC system’s 10 campuses. This transition didn’t come easily. It’s the result of several years of collaboration and hard work by students, staff, and local growers, as well as some fortuitous timing. Thanks to these efforts, UCSC is now positioned to be a national model for a growing movement called “farm-to-college,” which, like the K-12 farm-to-school movement, is bringing fresh,greenhouse vertical farming local produce to student dining halls through direct relationships between farmers and educational institutions. Farm-to-school or farm-to-college arrangements help farmers get more of the food dollar, benefit local economies, and give students access to locally produced, fresh food. Several features distinguish UCSC’s Farm-to-College project: a consortium of organic growers was formed to supply produce to the campus dining halls; sustainable food purchasing guidelines were developed; and education is incorporated from the campus farm fields to the dining halls.

In this article we’ll discuss the history of the farm-to-college work at UCSC, describe some of the strategies and obstacles involved in changing the University’s purchasing practices, and report reactions from participating farmers and campus chefs. We’ll also talk about the key role that students across the UC system are now playing in a campaign to create sustainable food systems at all of UC’s campuses, and offer advice on how other campuses can implement such efforts.In the winter of 2003, UCSC’s Students for Organic Solutions brought together diverse stakeholders of the campus food system at the annual Campus Earth Summit to discuss how to create sustainable change in the system, including the advantages of purchasing organic produce from local farmers. This grassroots effort was largely unsuccessful in garnering support from Sodexho—the largest food and facilities management services company in North America—which was then under contract to provide all the food to UCSC campus dining halls. Sodexho was at the same time dealing with its own challenges. UCSC’s Students for Labor Solidarity—unhappy with the company’s labor practices—had organized to “dump Sodexho” in conjunction with campus labor unions. After a six-month student campaign the UCSC administration ended its 30-year contract with the company in June 2004, enabling Dining Services to contract directly with suppliers for the first time. This transition to an “in-house” service structure opened a crucial avenue to work with the university administration in designing a more sustainable food system. Early in this process, conversations between members of the Center for Agroecology and Sustainable Food Systems and Dining Services director Alma Sifuentes brought staff of Dining Services to the UCSC Farm, an important step in introducing the concept of sustainability to the campus food system. Sifuentes also helped catalyze the effort to bring organic, Fair Trade coffee to campus through the Community Agroecology Network .Several months of meetings followed the 2004 Earth Summit as members of campus and community organizations came together as the Food Systems Working Group to craft the details of a purchasing guidelines proposal. Included were representatives from the Center for Agroecology and Sustainable Food Systems, Community Alliance with Family Farmers, Comercio Justo, the Community Agroecology Network , Students for Organic Solutions, and the Education for Sustainable Living Program —all of whom brought expertise in various aspects of sustainable agriculture and food systems. Under these guidelines, preference is given to price-competitive bids from the primary food vendor that meets the greatest number of criteria. For the local organic contract, all produce must be grown within 250 miles of Santa Cruz and be certified organic. In selecting a local organic produce vendor, preference is given to price competitive bids that are “worker supportive” as defined in the guidelines. In May 2004, the Food Systems Working Group formally presented these guidelines to UCSC’s Dining Services. Students for Organic Solutions also continued to build support for bringing local organic food to the dining halls by putting on educational classroom presentations and organic “taste tests” for students. Timed to coincide with the presentation of the guidelines, a campaign spearheaded by Comercio Justo and CAN generated over 2,000 postcards from students to Dining Services in support of the guidelines’ adoption. Honoring the guidelines, Dining Services selected the local distributing company Ledyard as the prime food vendor in 2004. The sole source organic produce contract with the Monterey Bay Organic Farming Consortium began in late summer 2005 after a year-long struggle to find a way to include “worker supportive” as a criterion in selecting a vendor. During the process, FSWG found that “worker supportive” could not be used as a criterion under UC purchasing regulations because, unlike organic and local, employment practices are not regarded as a characteristic of food. In order to qualify for a sole source contract, local organic farmers formed a consortium and agreed to make their farms available for organic farming and food system research conducted under the auspices of the Center.

Future chapters will focus on evaluating the blue elderberry and elder flower for their composition

European elderberry has been studied for its antioxidant, antimicrobial, anti-inflammatory, anticancer, immunomodulatory, and antidiabetic properties, as well as neuroprotection and cardiovascular protection in vitro and in vivo. These activities have been mainly attributed to the phenolic compounds like cyanidin 3-glucoside and cyanidin 3- sambubioside, but some other compounds have been shown to be bioactive as well, including terpenes, lectins, pectin, peptides, and malic acid. Using data from randomized, controlled clinical trials, a recent review found that elderberry could reduce symptoms from upper respiratory viral infections, providing support for the use of elderberry supplements by consumers to combat colds and flus without the use of antibiotic medicine.In a more unique application, elderberry and elder flower extracts have both shown to be effect in combatting gingival inflammation using a topical herbal patch and elder flower tea, respectively.A study of the mechanism of cyanidin 3-glucoside to treat against the influenza virus showed that elderberry extract had some inhibitory effect during the early stages of virus cycle with stronger impacts during post-infection. The mechanism proposed was that the elderberry extract blocks viral glycoproteins which prevent the virus from attaching or entering cells to replicate, and increases expression of IL-6, IL-8, and TNF. Inflammatory modulating activity of elderberry and elder flower extracts have been investigated.Results showed that quercetin, rutin, and kaempferol are strong inhibitors of nitric oxide production,25 liter pot and metabolites from phenolic degradation including caffeic acid and 3,4-dihydroxyphenylacetic acid were also strong inhibitors without cytotoxicity.

Only a few studies have been done on the bioactivity of S. nigra ssp. canadensis. In one, the fruit was evaluated for anticancer properties, which showed chemo-preventative activity by inducing quinone reductase and inhibiting cyclooxygenase-2, as well as inhibiting ornithine decarboxylase. These activities are attributed to flavonoids and lipophilic compounds. Another study evaluated two Canadian cultivars of this subspecies evaluated the antiproliferative efficacy of the fruit and flowers on glioma and brain endothelial cells and results showed that elderberry and elder flower extracts inhibited the proliferation of cells under normoxic and hypoxic conditions. The elderberry extracts performed the best and the bio-activities were attributed to the synergistic work of cyanidin 3-sambubioside-5-glucoside and rutin content of the berries, though the rutin concentration in the flowers still had beneficial effects. Blue elderberry has only been evaluated as antioxidant activity using the ABTS assay, which indicated that this subspecies has 11.62 ± 0.38 mM Trolox kg-1 FW, roughly one third of S. nigra ssp. nigra evaluated in the same study, where all fruit samples were grown in Slovenia.Further work on elucidating the biological activity of this subspecies through in vivo assays and preferably clinical trials should be explored, especially using blue elderberry plants growing in North America to support its use in supplements. Elder flowers have also been evaluated for their biological activities. A review of antioxidant activity in S. nigra ssp. nigra flowers has recently been published 2 , including ABTS, DPPH, FRAP and CUPRAC assays, therefore it will not be re-summarized here. In general, the data showed that elder flower has higher levels of antioxidant activity compared to the elderberry. Similarly, elder flower extracts had higher nitric oxide inhibition compared to elderberry extracts in vitro.

Elderflower is antidiabetic by increasing insulin-dependent glucose uptake, diuretic, treat respiratory infections, antiviral. While phenolic compounds like flavonols are presumed to be the most active compounds, pectic polysaccharides are also bio-active in elderberry and elder flower, inducing complement fixing and macrophage stimulation.Flowers of the blue elderberry have been evaluated for their antioxidant activity using the ABTS assay, which showed they have 44.87 ± 0.54 mM Trolox kg-1 DW, significantly less than flowers of S. nigra ssp. nigra . Aqueous extracts of wild elder flowers of this subspecies were also found to have neuroprotective effects, especially related to Parkinson’s disease, by increasing the antioxidant response mediated by Nrf2 in cortical astrocytes and improving mitochondrial function in neurons.Unfortunately, that study did not include any growing information about the elder flowers or the concentration of the phenolic compounds in the extract, which would have helped other researchers replicate and expand on the results. While there have been promising studies on the impact of elderberry and elder flower extracts to combat illness and disease, more in vivo studies and clinical trials should be performed to better understand the mechanisms of the bio-activity as well as to determine which compounds are responsible for the bio-activity, particularly in the lesser-known subspecies canadensis and cerulea. This can better inform people involved with the cultivation of elderberry to select for varieties that have the compounds of interest. The market for herbal supplements has been growing in the recent decade and immune system-supporting supplements had a huge spike in sales during the COVID-19 pandemic.

Elderberry products are a popular option of alternative medicine in hopes of improving and protecting health.Beverages are a popular use of the elderberry, including syrup or other tonics made by soaking the berries in water or alcohol. It can also be found as an ingredient in various kombuchas, juices, energy drinks, wine, and tea. Elderberry is typically mixed with a variety of other ingredients, including but not limited to ginger, honey, echinacea, and other spices.More recent products using elderberry include gummies typically marketed as health supplements, lozenges, tablets, and powdered berries especially as part of a drink mix. Elderberries are also frequently used in jams and jellies. Pomace, the byproduct of juicing, has been studied for its benefits when incorporated into other products just as baked goods.Beyond its potential for bio-active products to benefit consumers, elderberry can also be used as a natural food dye due to the high concentration of anthocyanins, which can be used in place of artificial red or purple food dyes, particularly in acidic foods. Its application in edible films has recently been investigated, explored various bio-polymers that could retain the phenolic compounds of elderberry in the film so that they can remain active to protect foods Active edible films can be an effective solution to reduce plastic packaging and food waste due to spoilage.Cosmetic and skin care applications are also an area of interest, and current products on the market that include elderberry include lip color, toner, face mask, and Epsom salt. Herein, the data available on the other elderberry subspecies of interest are summarized to provide a basis of the expected composition as well as information to compare the subspecies for their composition. Elderberries have a high amount of water, at about 80%. The main sugars in elderberry are glucose and fructose, with some small amounts of sucrose. Sorbitol was also measured, which was very minor compared to the other three sugars and was seen in the highest concentrations in the wild elderberry. Citric acid is the main organic acid in elderberry, with malic acid the next highest acid. Small amounts of shikimic, tartaric, and fumaric acid have been measured in elderberry as well. Only data on European elderberry is available for micro-constituents such as vitamins, minerals, fatty acids, and amino acids. Vitamins found in elderberry include various B vitamins, vitamin C, and vitamin E.The main minerals are magnesium, calcium, and potassium.Because studies of these micro-nutrients have only been performed on the European elderberry, it is important for further work to include other subspecies, including the American and blue elderberry so that better comparisons can be made. An important group of bioactive compounds found in fruit and vegetables is phenolic compounds,raspberry cultivation pot which consist of one or more phenolic groups . Types of phenolic compounds include phenolic acids and flavonoids; flavonoids can be further separated into groups such as anthocyanins, flavonols, flavan-3-ols, and flavones. Phenolic compounds may have some biological activity, although bio-availability can be very low. A common, albeit imperfect, way to measure phenolic content of elderberries is using a colorimetric method like Folin-Ciocalteu which can measure a complex that forms between phenolic compounds and molybdenum-tungsten at 765 nm. Because this method measures all reducing agents in the matrix, reducing sugars and ascorbic acid will also react and increase the absorption thus inflating the total phenolic content . Standard curves are typically constructed using gallic acid, hence the units for TPC are gallic acid equivalents . TPC in European elderberries can vary greatly but reported values include 461 ± 121 49 and 683 ± 49.

In American elderberry, TPC has been reported to be 390 ± 56 50, 593 ± 70. One study has included blue elderberry grown in Slovenia, which had a TPC of 416 ± 31. However, because of the imprecise nature of this assay, it is important to identify and measure the concentration of each phenolic compound present whenever possible, the results of which is explored in the following sections.Anthocyanins are water-soluble pigments in plants, and they give elderberries their bluepurple hue. Total monomeric anthocyanin content is typically measured using the pH differential method, which takes advantage of the change in light absorption of anthocyanins in solutions with different pH and the unit is typically cyanidin glucoside equivalents . European TMA content of European elderberry can range from 170 ± 12 to 343 ± 11 mg CGE 100 g -1 FW. In American elderberry, the range of TMA content is 354 ± 59 to 595 ± 26 mg CGE 100 g -1 FW 52 and 106 ± 2 to 444 ± 14 mg CGE 100 g-1 FW. Analysis of the phenolic compounds via high performance liquid chromatography with UV-Visible light detection or with mass spectrometry have elucidated a variety of molecules present in the European elderberry. Anthocyanins, a type of flavonoid and popular for their red to blue pigments, are of high interest in elderberry. Most studies have found that cyanidin -based anthocyanins are the dominant type in European and American elderberry, including cyn 3-O-sambubioside -β-Dglucopyranoside and cyn 3-O-glucoside. Cyn 3-sambubioside-5-glucoside and cyn 3,5- diglucoside are also commonly seen in the elderberry. The American elderberry has a more unique anthocyanin profile with high presence of acylated anthocyanins compared to the European elderberry, including cyn 3-O-coumaroyl-sambubioside-5-O-glucoside , cyn 3-Ocoumoaryl-sambubioside. These acylated anthocyanins may be more stable during processing, but the authors found that cyn 3-O-coumaroyl-sambubioside was the least stable anthocyanin during storage , whereas cyn 3-O-cou-sam-5- O-glu and cyn-3-O-sam-5-O-glu were more stable. Another major type of phenolic compound in elderberry is flavonol glycosides, which include rutin , isorhamnetin 3-O-glucoside or 3-O-rutinoside, and kaempferol 3-O-rutinoside. Rutin has frequently seen to be the most concentrated flavonol in European elderberry, and often the most concentrated phenolic compound of any present. 8 S. nigra ssp. canadensis also contains higher levels of rutin than other flavonols.Other flavonol glycosides present in elderberry include kaempferol and isorhamnetin derivates, such as kaempferol-rutinoside, isorhamnetin-rutinoside, and isorhamnetin-glucoside. Phenolic acids are also present in high amounts in elderberry, including chlorogenic acid isomers , p-coumaric acid, sinnapic acid, cinnamic acid, and ferulic acid. Flavan-3-ols found in elderberry include -catechin, -epicatechin, and procyanidins than those detected in elderberry juice, found to be 18.8 ± 4.3 mg kg-1 in raw juice and 10.6 ± 0.7 mg kg-1 in cooked elderberry juice, suggesting that thermal processing can reduce CNG levels in elderberry products. American elderberries have been evaluated for their concentrations of CNGs. These include amygdalin, sambunigrin , linamarin, and dhurrin. Specifically, the Ozone and Ozark genotypes were evaluated, giving better insight into how CNG concentrations may be impacted by plant genetics. While the total concentrations of the four CNGs in the two American elderberry genotypes were somewhat similar , the composition of which CNGs made up that total were quite different: Ozone elderberries had similar levels of amygdalin and sambunigrin while Ozark elderberries had much higher levels of amygdalin than sambunigrin . The flavor profile of elderberries is an important factor in the consumer sensory experience with elderberry products. Two of the most common compounds identified as drivers of elderberry aroma identified in multiple studies of the berries or elderberry juice are β-damascenone and dihydroedulan. Nonanol was also identified as a key volatile compound contributing to the characteristic elderberry aroma, while ethyl-9-decenoate was found to be important for the characteristic elderberry aroma by another study. While these volatile compounds can be key to the unique aroma, they are not typically the most concentrated compounds. Studies have found the most concentrated compounds to be linalyl acetate, linalool, phenylacetaldehyde, benzaldehyde, hexanal, 2- and 3-methyl-1-butanol, nonanal and benzaldehyde. However, comparing concentration of compounds across studies can be difficult due to differences in sample preparation, extraction method, and method parameters, to name a few important factors.

Folklore has many stories about the healing power of the elderberry and elder flower

Due to the barrier created by type IV enzymes in the free-living condition , horizontal transfer involving Frankia in the soil is likely limited to other actinobacteria whose genomes similarly lack methylation , many of whom are endophytes . Inside the host, however, Frankia is likely more receptive to genes from other endophytic taxa as well. Combined, these factors could result in the preferential acquisition of genes involved in growth and host-microbe interactions in planta. In legume symbioses, exudates from hosts into their rhizospheres have been proposed to promote the conjugative transfer of symbiosis genes from a donor group of rhizobia to others, broadening the range of symbionts available to the host . Down-regulation of type IV restriction genes in actinorhizal nodule symbioses could be another mechanism that enhances horizontal transfer of genes related to interactions with plants by making the recipient Frankia more susceptible in the endophytic environment. M. tuberculosis showed much lower transcription of its annotated type IV methyladenine targeting restriction enzyme than other actinobacteria. M. tuberculosis expresses an adenine methyltransferase in hypoxic conditions that regulates the expression of genes likely involved with survival during macrophage infection . For this reason it is likely that M. tuberculosis responds to methylated DNA differently than other actinobacteria; indeed electrotransformation of M. tuberculosis can be readily achieved with methylated plasmids replicated in E. coli DH5α , suggesting that methylated DNA is not digested in M. tuberculosis. In this study derivatives of broad host-range plasmid pSA3 were capable of replication in F. alni. This shows that the broad host-range origin is capable of replication in Frankia and supports its use as a vector for the manipulation of Frankia spp. The parent plasmid of pSA3, pIP501,grow bucket replicates in a very broad range of bacteria including Streptomyces lividans and E. coli indicating the potential for transformation of additional actinobacteria with these plasmids.

The expression of the egfp gene of plasmid pIGSAFnif was up-regulated in N media compared with expression in N media, at proportional levels to the expression of the nifH nitrogenase gene , demonstrating for the first time that expression of reporter genes can be manipulated in Frankia. This transformation system resulted in the ability to visualize the expression of nitrogen fixation genes in vitro by fluorescence microscopy . Interestingly, fluorescence was detected in both the spherical portion of the vesicle as well as in the stalk that connects to the hyphae, suggesting that nitrogen fixation genes are expressed in both parts of the vesicle. Previous studies have shown that the vesicle envelope is deposited around the stalk as well as the spherical part of the vesicle , supporting the observation that nitrogen fixation can occur in the stalk. Although the fluorescence observed when egfp was expressed under the control of the F. alni nif cluster promoter was predominantly in the vesicles, some fluorescence was occasionally observed in hyphae under nitrogen-fixing conditions whereas in N media there was no observable fluorescence . This suggests that there can be condition-dependent expression of nif genes in the hyphae as well as the vesicles induced by nitrogen limitation. Frankia spp. in symbiosis with members of the Casuarinaceae have been reported to fix nitrogen in hyphae, since no vesicles are differentiated ; this pattern correlated with the formation of a lignified host cell wall in the symbiotic tissue that likely reduces oxygen partial pressure . In liquid culture, there may be zones of low pO2 that develop in portions of a Frankia hyphal colony where nitrogen fixation could be induced. Frankia spp. in symbiosis have been suggested to be more autonomous than rhizobial microsymbionts due to their ability to control the flow of oxygen with the formation of vesicles, and due as well to the expression of more metabolic pathways in the micro-symbiont in symbiosis. These factors potentially allow Frankia to be more metabolically independent from their hosts .

The development of genetic tools for the manipulation of Frankia will allow further exploration into these and other distinctive molecular aspects of actinorhizal symbioses, which will, in turn, further inform analyses of the evolution and diversity of root nodule symbiosis. The transformation methods presented here should be applicable for genetic experiments in other Frankia strains. Because plasmid pIGSAF has a broad host-range origin of replication and expresses egfp under the control of a constitutive promoter, the plasmid is likely to be usable in other strains as well. Even in the absence of selection, plasmid pIGSAF was found to be stable in F. alni cultures for at least 3 weeks and cultures continued to show fluorescence after at least 4 weeks . Three to 4 weeks is a time period that sufficiently spans the stages of nodulation and early nitrogen fixation in a broad-spectrum of hosts. This includes Alnus glutinosa with F. alni ACN14a , and Casuarina cunninghamiana , Discaria trinervis , Shepherdia argentaea , and Datisca glomerata . This suggests that transformants can be used to inoculate plants to study of the role of Frankia and its interactions with hosts during nodule establishment and symbiosis. In future this system could be modified using recombination or site-specific integrases to anchor genes within the genome. Differential regulation of reporter genes such as egfp can be used to localize the expression of genes identified by genomics and transcriptomics in specific Frankia cell types, in different growth conditions, and in symbiosis. Replicating plasmids may also enable the study of gene function by constitutive expression of selected genomic genes, by promoter switching or by knock-down experiments expressing anti-RNAs to genes of interest . Circumventing the natural restriction systems of Frankia will also increase the transformation rate of non-replicating plasmids and enable higher efficiency recombination, which can be combined with CRISPR systems, for gene knock-out experiments as attempted by Kucho et al. . While this manuscript was in review a separate method for the transformation of Frankia spp. utilizing conjugation with a methylation-positive E. coli was reported by Pesce et al. . Conjugative transfer has been shown to evade recipient restriction systems , thus presumably allowing Frankia spp. to circumvent the type IV restriction barrier identified in this study.

Nevertheless, the transformation efficiency of Streptomyces spp. by conjugation has been shown to increase over 104 -fold with unmethylated DNA . Thus, in addition to enabling the transformation of Frankia spp. by electroporation, our analysis of restriction systems in Frankia spp. can be further utilized to improve the transformation efficiency of conjugative transfer to Frankia spp. through the use of methylation-deficient E. coli donors. Optimized transformation efficiency will be crucial for future studies involving the generation of recombinants including gene knock-outs. Elderberry is a part of the Viburnaceae family and grows all over the world, including Europe, North America, and Asia.Due to the vast geographic and morphological variety within Sambucus, there have historically been many species within the genus. However, a reorganization by Bolli reclassified some of the most common species under Sambucus into subspecies of S. nigra. More recently, elderberry was moved out of the Adoxoaceae family, which had already been changed before when elderberry was taken out of the Caprifoliaceae family. These changes have impacted the three subspecies most of interest in this work: the European elderberry S. nigra ssp. nigra; the American elderberry S. nigra ssp. canadensis; and the blue elderberry S. nigra ssp. cerulea .However, due to wide acceptance of this naming scheme for the subspecies, it will be used through this work to align with the current naming, but previous works cited may use the former species names. Furthermore, some sources refer to the entire plant as an “elder”,dutch bucket for tomatoes while others refer to the plant as “elderberry”, which is also used to denote the fruit of the plant. In this work, “elderberry” is used to discuss the plant as well as the fruit. “Elderflower” is used to refer to the blossoms of the plant. European elderberry is the most well-studied and widely used subspecies of elderberry in the market. This subspecies grows throughout the European continent, including countries such as Slovenia, Portugal, and Austria. The fruit and flower have been studied for decades for their composition and bio-activity, and while elderberry and elder flower are not new ingredients to the market, they have garnered more attention in the last several years as consumers look for more natural remedies and supplements to support their health. This has been especially true during the COVID-19 pandemic, in which elderberry became a popular ingredient in immunity-supporting supplements. Thus, investigating other elderberry subspecies like the blue elderberry, the focus of future chapters, allows for farmers in the United States to capitalize on this demand, but more information is needed on this particular plant if it is going to be used in consumer products. There is a long, rich history of the use of different parts of the elderberry plant by many cultures. For example, the wood has been used for kindling and musical instruments. Indeed, the name of the plant is derived from various ancient words related to instruments. The flowers and berries have been used in a variety of beverages, foods, and other herbal supplements.\

The plant itself has been revered by many cultures, with a story about the “Elder Mother” living within the plant would protect those near the plant. It was even expected to ask the Elder Mother for the berries or flowers before taking them; without permission, she may seek revenge. The leaves, branches, flowers, and berries were believed to have protective powers for a home and the leaves were also used during burial rituals by some Celtic people. The personification and deep reverence for the elderberry show the importance of the plant through generations. Hippocrates and Pliny the Elder both wrote about elderberry and its medicinal properties. Tribes indigenous to North America used flowers and fruit for medicinal and beverages. Berries were also used as a natural dye for baskets and branches were used to make musical instruments. Elderberry is a perennial, deciduous plant native to many regions of the northern hemisphere. Elderberry plants are neither tree nor bush, as the plant sends new canes up each season, which without pruning, can lead to a large, shrub-like plant that can be several meters tall and wide. They prefer to grow in sunny, riparian climates with moist, well-drained soil, though subspecies in North America can be drought-tolerant. While pruning even down to the ground level of the elderberry can improve yield and accessibility for harvesting, there is a limitation on pruning of the blue elderberry in the Central Valley of California. Due to the threatened status of the Valley Elderberry Longhorn Beetle , which lives only in the elderberry, branches larger than one inch in protected areas should not be pruned or removed from a growing site.Elderberry shrubs typically produce small white flowers with five petals in the spring, though the elder flowers of the blue elderberry are a creamy yellow color. Small, dark blue-purple berries ripen in the summer in large clusters called umbels or cymes, though there are examples of subspecies that have some variation to these morphologies, such as the blue elderberry that has a white bloom on the berries, causing the berries to look blue, and S. racemosa, which are red.Variation can also occur within a subspecies due to growing conditions, such as soil type, precipitation, and temperatures, as well as a key differentiation tool: cultivars or genotypes. There are established cultivars or genotypes of the European subspecies , such as Sambu or Haschberg, as well as of the American subspecies , like Bob Gordon or Wylewood. Cultivars can have more consistent growing patterns, such as blooming or ripening all at once, and desired chemical compositions, such as increased anthocyanins, thus are more desirable to use in large scale growing of elderberry for commercial use. Blue elderberry does not have any established genotypes to date. If commercial interest in this subspecies continues to expand, effort should be made to develop cultivars with consistent quality and improved harvest ability, which is hampered right now due to flowers and berries ripening throughout a season, instead of a smaller window of time like the American and European subspecies. Indeed, starting this work can help increase the commercial interest viability of the blue elderberry. A primary driver in interest in the composition of elderberry and elder flower is for their potential health benefits. Several reviews have recently been published on this topic; thus, it will not be explored in depth here.

The LDD operation is based on distributed waste heat from SOFC that powers the servers

The B-number and soot yield are fundamentally robust parameters that may be used in the future as means to classify the flammability of a given warehouse commodity, to strengthen the level of confidence in determining the flammability of a commodity, and to increase the effectiveness of warehouse fire protection and suppression applications. Additionally, the results of this study are useful for the application of sprinkler activation and determining the amount of sprinkler suppression that is necessary as a fire grows larger.Electricity consumption projections place data centers at up to 13% of global electricity demand in 2030 due to the expected growth in the production and use of electronic devices, cloud services, and computer networks. Cooling infrastructure accounts for up to 40% of the total energy delivered to a data center. With business and society relying so much on data centers, there is a greater need for reliable and clean electric power for data centers. Solid Oxide Fuel Cell systems have the potential to provide more reliable and cleaner electrical load-following characteristics compared to other technologies while enabling dynamic operation and control. High temperature exhaust of SOFC can be used to run a bottoming cycle such as cooling system which makes it an attractive integrated system for data center applications. However, cost and durability are major challenges associated with SOFC technology. On the other hand, the biggest challenge for using hydrogen as an energy carrier for SOFC is the very high pressure or very low temperature required for its storage, transmission, and distribution,nft growing system which makes the need for a more dense liquid energy carrier like ammonia inevitable. This dissertation, first, focuses on evaluating the integrated system concept and assesses the achievable air conditioning from SOFC waste heat.

To explore the feasibility of thermally integrating SOFC with liquid desiccant dehumidification , a spatially resolved physical model developed in MATLAB is used to simulate the operating characteristics of this SOFC system. A corresponding physical model is developed to simulate the liquid desiccant air conditioner for dehumidification. This research evaluated SOFC systems for powering demand of a single server rack to powering a row of servers . The LDD operation is based on distributed waste heat from SOFC that powers the servers. This research indicates whether waste-heat based cooling and dehumidification could power the servers and maintain server operating temperatures and humidity in the safe range for different weather conditions. It calculated the yearly storage capacity required for each location to meet the demand of the data center for the entire year. Next, the performance and degradation of a 1.5kW commercial system, that is proposed for source of power and cooling of servers, is evaluated under steady state and dynamic load cycling conditions for over 6000 hours. The degradation rate and performance characteristics of the SOFC system is analyzed to determine the long-term performance and durability of SOFC system under dynamic condition. Finally, to analyze and compare the degradation of single cell SOFC directly fed with ammonia , externally reformed ammonia and pure hydrogen , three durability tests are conducted on anodesupported SOFC. Electrochemical impedance spectroscopy and scanning electron microscopy are conducted to study the performance losses during operation and to observe the microstructure changes of the cell after testing. The rapid growth of internet use, cloud computing and data-driven machines and services is increasing the electric power consumption and carbon footprint of data centers. Data center electricity demand was around 200TWh in 2018.However, due to the expected growth in the production and use of electronic devices, cloud services, and computer networks, electricity consumption projections place data centers at up to 13% of global electricity demand in 2030.

As shown in Figure 1 in the best-case scenario data center electricity consumption doubles in the next 10 years. Associated with this massive electricity consumption are greenhouse gas and criteria pollutant emissions due to the use of conventional fossil energy resources to power data center electric loads. In 2020, the information and communications technology sector represented 2.3% of global GHG emissions, 28.8% of which were associated with data centers. In addition, as a result of the COVID-19 pandemic, dependency upon internet technology, and cloud services, data center demands are only increased further. Data centers will use around 3–13% of global electricity in 2030 compared to 1% in 2010. In order to meet the emissions reduction targets imposed by many IT companies like Microsoft, the power supply for data centers must come from renewable energy sources. The trend of using renewable power is being used widely and likely many data centers can be run with low GHG and pollutant emissions, even if they do not find ways to reduce their absolute electricity usage.In a traditional data center connected to the electric grid, less than 35% of the energy from the fuel source that is supplied to the power plant is delivered to the data center. Power plant generation losses and transmission and distribution losses are the most significant inefficiencies in data center. Figure 2 shows the process of power loss through the transportation and distribution network of the electric grid starting from the fuel source up to the power supplied to the consumer. It is evident that the largest inefficiency is from the power generated at the power plant level with additional losses associated with the transmission and distribution to the data center, where the data center receives roughly 30% of the total energy that could have been supplied ideally from the fuel source. There are further losses associated with the infrastructure required for daily reliable operation systems. The additional power consumed by the cooling, lighting, and energy storage, means approximately less than 17.5% of the energy supplied to the power plant is ultimately delivered to the servers. Information Technology equipment and cooling infrastructure are the two major power consumers. As shown in Figure 3 cooling infrastructure is a large electricity consumer in the data center and can account for up to 40% of the total energy delivered to the data center. Cooling also represents the biggest slice of the total cost in a data center.

With more capacity and higher density there is an increased need for energy-efficient cooling of the IT equipment. While data centers need cooling to protect servers and other equipment, an additional challenge is humidity control. Too much humidity can cause corrosion of metal parts of the servers leading to short circuiting of electronics. On the other hand, low humidity allows the servers to develop electrostatic charges that can cause damage to sensitive equipment. According to Uptime Institute, electric power outages are the main causes of the increasing outage trend in data centers. According to the Eaton Blackout Tracker, the US experienced more than 3,500 utility power outages in 2017, the vast majority of which were attributed to faults in the transmission and distribution system. This number represents a 62% increase in outages from a decade ago. In 2018, a storm interrupted grid power to Microsoft’s San Antonio Azure data center, knocking cooling systems offline, damaging a significant amount of equipment, and bringing down Active Directory and Visual Studio Team Services for almost 24 hour. In some areas, rising temperatures are driving up the cost of data centers. In other areas, extreme rainfall and flooding have damaged equipment, and prevented the fuel deliveries which are so critical to the traditional back-up power solutions. And power costs continuously increase. The global cost of power for data centers is expected to increase 80% in the next five years. At 35% of total costs,vertical hydroponic nft system electric power continues to represent the largest portion of data center operating costs. Every power generation system that supplies a data center must comply with stringent reliability and availability constraints to ensure 99.9999% server uptime. With business and society relying so much on data centers, and data centers growing more and more, there is a greater need for reliable and clean electric power for data centers. Our solution is using small scale Solid Oxide Fuel Cell for rack level power generation, which is capable of delivering uninterrupted, 24×7 power that is resilient and clean and eliminates the need for back up generation and is also able to provide high quality heat to run a liquid desiccant dehumidification system to provide cooled and dehumidified air for servers. Generating power on-site, at the point of consumption, rather than centrally, eliminate the cost, complexity, interdependencies, and inefficiencies associated with electrical transmission and distribution. Providing the required cooling for servers through liquid desiccant dehumidification run by high quality exhaust of SOFC has the potential to decrease the power consumption of data centers by up to 40%.In this research, first, I investigate the integration of rack level fuel cell powered servers with Liquid Desiccant Dehumidifier technology that can be dynamically dispatched to produce electricity and cooling in various amounts to meet power and air conditioning demands of data centers. This thesis focusses first on evaluating the integrated system concept and to assess the achievable air conditioning from SOFC waste heat. To explore the feasibility of thermally integrating SOFC with LDD, a spatially resolved physical model developed in Matlab is used to simulate the operating characteristics of this SOFC system.

A corresponding physical model is developed to simulate the liquid desiccant air conditioner for dehumidification. This study considers SOFC systems capable of powering a 1. single server rack and the operation of an LDD for cooling and dehumidification of that same rack, and 2. SOFC and LDD systems designed for a row of 20 servers. The analysis will indicate whether waste-heat based cooling and dehumidification is capable of powering the servers and maintaining server operating temperatures and humidity in the safe range for different weather conditions. Even though SOFC technology offers several advantages such as fuel flexibility, high efficiency, and zero criteria pollutant emissions, cost and durability are major challenges associated with current SOFC technology. Durability of SOFC technology is a key aspect for its commercialization and long-lasting deployment in different applications. Dynamic operating conditions have considerable effects on the long-term performance and durability of SOFC systems. On the other hand, while many studies have focused on green hydrogen produced through electrolysis from sun and wind, as a clean fuel for fuel cells, the biggest challenge for using hydrogen as an energy carrier is the very high pressure or very low temperature required for its storage, transmission and distribution, which makes the need for a more dense liquid energy carrier like ammonia inevitable. I propose that ammonia made in a sustainable way can serve as a sustainable, low-cost, and high-density energy carrier and the fuel for SOFC systems in the Future.In the second part of this research, I first evaluate the performance and degradation of a 1.5kW Alternating Current commercial SOFC system that is proposed for source of power and cooling of servers under steady state and dynamic load cycling conditions for over 6000 hours. I monitored and analyzed the degradation rate and performance characteristics of the SOFC system to determine the long-term performance and durability of SOFC system under dynamic operating conditions. Second, I evaluate the effect of ammonia as fuel on SOFC performance. I study and compare the degradation of an SOFC single cell fed with fed with ammonia , externally reformed ammonia and pure hydrogen . The goal of this thesis in to evaluate the integration of SOFC with Liquid Desiccant Air Conditioning for efficient, reliable, and grid-independent data center power and cooling. The integrated system will supply electricity and cooling to data center applications. This configuration offers the potential for high energy efficiency, environmental and economic benefits. The integrated concept is shown in Figure 4. The SOFC generates electricity from natural gas which is used directly for powering a rack of servers. The SOFC thermal exhaust will be used to produce hot water which is used for regenerating the liquid desiccant. Concentrated liquid desiccant will be stored and is used for dehumidifying the air when there is a cooling demand. The integrated system is expected to have high efficiency, low emission and provide reliable power and cooling for data center applications. This integrated configuration eliminates grid connection and any transmission line for powering servers as well as significantly decreasing the electric power used for providing cooling to servers.Most traditional data centers get their primary electricity from utility electric grid.

Three previous studies have attempted to quantify the economic cost of the SWD invasion

Due to concerns of flavanol monomer epimerization during cocoa production which might yield substantially less bioactive -catechin from naturally occurring -epicatechin the specific concentrations of catechin and epicatechin enantiomers of thinned clusters and cocoa powders are also provided in Table 2 using chiral chromatography to facilitate future epidemiological study designs.The same trend was observed for Chardonnay fractions as the less mature seed had the highest flavanols and procyanidins compared to its more mature dark seed fraction . However, for the Chardonnay seedless fractions, the dark fraction had a significantly higher amount than the light fraction . Ivanova et al. have found that the total content of catechin, epicatechin, and procyanidin dimers B1- B4 in Chardonnay and Merlot grown in R. Macedonia were significantly higher in seeds rather than in skins and pulp at veraison. Our data on flavanols and procyanidins DP 1–2 are in accordance with their findings as the highest content was found in Chardonnay seeds , followed by Pinot noir seeds , Chardonnay seedless , and Pinot noir seedless . Overall, 2.2-fold and 1.2-fold variations of DP 1–2 were found in Chardonnay and Pinot noir thinned cluster fractions, respectively. Previous studies also showed that flavanol monomers in white and red grapes slow down or stop accumulating from veraison to ripening while procyanidin dimers B1-B4 increase slightly until the intermediate phase . These all indicated that grape thinned clusters at veraison could be richer sources of monomeric and oligomeric flavanols and procyanidins compared to grapes during berry formation and berry ripening.

With the increasing interest in utilizing specific bioactive catechin and epicatechin enantiomers,hydroponic bucket mainly -epicatechin and -catechin, in epidemiological studies , we separated catechin and epicatechin enantiomers using chiral chromatography and presented the data in Table 2. Like grapes, the predominant forms of flavanol monomers in natural cacao beans are -epicatechin and -catechin. However, Payne et al. have found that various processing techniques used in cocoa production, such as fermentation and roasting at over 70°C, significantly decrease the total catechins amount and generate significant amounts of -catechin from -epicatechin epimerization, respectively. The Dutch processing is widely used in cocoa production where the cocoa is treated with an alkali solution to reduce the acidity and to intensify the chocolaty flavor in the final powder . Compared to natural cocoa powders, Dutch processing also caused a greater loss in both epicatechin and catechin according to Payne et al.As -catechin has been shown to have pharmacological effects including antimicrobial , antioxidative , and had about five times higher bioavailability than -catechin , thinned clusters could complement cocoa ingredients—a small portion of grape thinned cluster as an ingredient would likely make a positive impact on the -catechin and total catechins content of cocoabased products.Drosophila suzukii , also known as the spotted wing drosophila , is a vinegar fly originating from Southeast Asia. SWD was first detected in North America in August 2008 in Santa Cruz County, California, where it was observed infesting strawberries and caneberries.In 2009, SWD was detected in Washington, Oregon, and Florida. By 2010, SWD was detected in Utah, Mississippi, North Carolina, South Carolina, Wisconsin, and Michigan in the United States, and Alberta, Manitoba, Ontario, and Quebec in Canada.

Recent trapping indicates that SWD can be found in virtually any region of North America where host fruit are available. A coincidental invasion of SWD with a genetically distinct population has also been observed in Europe, with initial detections in both Spain and Italy in 2008, followed by its spread throughout the continent. In North America, SWD is primarily a pest of berries and cherries. In Europe, it is reported to also damage a number of stone fruits and grapes. Unlike native vinegar flies in North America and Europe, female SWD possess a serrated ovipositor that can pierce the skin of healthy, soft-skinned fruits to lay eggs. These eggs quickly develop into larvae, which consume the fruit and render it unmarketable. The only other Drosophila species known to oviposit in sound, marketable fruit is Drosophila pulchrella Tan. This species is native to Japan.1 Growers have attempted to mitigate crop damage risk by applying additional insecticide, harvesting more frequently, performing field sanitation, and implementing trapping programs to detect SWD populations. These management practices are costly and many growers still face significant yield losses from SWD infestations. Raspberry producers are perhaps the most affected by SWD’s invasion among California commodities, although producers of blueberries and cherries have experienced substantial losses too. Strawberry producers have experienced lower damage rates and primarily on the lower-value fruit produced for processing. SWD-related losses in these industries vary by year and crop depending on management practices, weather conditions, time of the year, and geographic location. A primary motivation for focusing on the California raspberry industry is that California accounts for the majority of raspberry production in the U.S. and the raspberry industry accounts for the majority of economic losses due to SWD among berry crops.A second motivation is the magnitude of change in pest management practices; few of the SWD control practices used by raspberry producers were needed to prevent injury from other pests prior to its establishment.

Economic losses in the California raspberry industry include the cost of managing SWD and the value of the fruit lost due to SWD infestations despite management efforts. First, we compute the cost of the chemical management programs and the labor-intensive sanitation practices implemented to mitigate SWD-related yield losses. Second, we calculate the industry level yield losses due to infestation. These components form an estimate of the full economic cost of SWD’s invasion into California raspberry production.In 2013, raspberries were estimated to be the twenty-seventh largest crop in California by value of production. The United States is the third largest producer of raspberries in the world, producing 91,300 tonnes, after the Russian Federation and Poland, which produce 143,000 and 121,040 tonnes, respectively. Across all counties, California’s raspberry production was worth an estimated $239 million according to the United States Department of Agriculture’s National Agricultural Statistics Service , and $437 million according to California County Agricultural Commissioners’ Reports.The difference in these estimates reflects that the NASS data report cash receipts to producers while the Agricultural Commissioners’ Reports estimate the total value of production. Figures 1, 2, 3, and 4 plot California raspberry hectares, production, yield per hectare, price per kilogram, and the total cash receipts between 2004 and 2013.Note that raspberry hectares multiplied by yield per hectare is equivalent to production, and production multiplied by price per kilogram is equivalent to total cash receipts. Four counties account for virtually all commercial raspberry production in California: Ventura, Santa Cruz, Santa Barbara, and Monterey.In 2014, Ventura County produced approximately 52% of California’s raspberry crop by value, $241 million, on 1,873 hectares. Raspberries are the third most valuable crop in Ventura County.9 Santa Cruz County produced approximately 28% of California’s raspberry crop by value, $131 million, on 979 hectares. Raspberries are the second most valuable crop in Santa Cruz County.10 Santa Barbara County produced approximately 10% of California’s raspberry crop by value, $45.2 million, on 591 hectares. Raspberries are the ninth most valuable crop in Santa Barbara County.Monterey County produced approximately 10% of California’s raspberry crop by value, $45 million, on 316 hectares. Raspberries are the sixteenth most valuable crop in Monterey County.Table 1 summarizes California raspberry production by county.Counties are listed from north to south along the Pacific Coast. Figure 5 identifies these berry-producing regions with a stylized map of California.Most commercial raspberry plantings in California have had an 18-month lifespan. The crop is planted in the winter and then harvested twice, first in the fall following planting and then in the subsequent summer. Both harvest seasons last approximately three months, with crews harvesting fruit every three days on average. Variations in harvest frequency depend on yields and pest management activities. Yields are low at the beginning and end of a harvest season,stackable planters and peak near the middle of a season. Pesticide applications may require an interval of time, depending on the particular pesticide, before normal harvesting activities can resume. This period is known as the pre-harvest interval , and it is determined by the U.S. Environmental Protection Agency. Occasionally, low yields are realized during the harvest season due to crop damage resulting from weather, pest activity, or other external factors. The summer harvest is typically larger than the fall harvest.Organically produced raspberries represent a significant share of total California raspberry production.

In 2008 and 2011, California’s organic raspberry production was valued at $11.4 million and $8.98 million, respectively, according to the USDA-NASS. In 2012, 408 hectares of California raspberries were organically managed according to the University of California Agricultural Issues Center. Raspberry prices vary throughout the year, but on average organic raspberries are sold at a price premium. In 2015, the national average retail price of organic raspberries over the entire year was $3.52 per six ounce tray according to the USDA Agricultural Marketing Service. The average retail price of conventional raspberries over the same period was $2.55 per tray. The average California terminal market prices for organic and conventional raspberries were $3.29 and $1.97 per tray, respectively. 16 California raspberries are a major export crop. In 2013, the combined category of raspberry, blackberry, mulberry, and loganberry exports was the twentieth largest export crop category by value in California. Raspberries account for the majority of the production volume and the total value of this category. This California export category was valued at $157 million, and accounted for approximately 85% of total US fresh and processed raspberry, blackberry, mulberry, and loganberry exports. 84% of these exports are received by Canada, 6% by Japan, and 5% by the European Union.The presence of SWD has clearly increased production costs and caused yield losses for California raspberry producers through a variety of channels. However, these studies occurred within one or two years of the first SWD infestations in North America when information on the pest was still sparse and management techniques were rapidly evolving. We can improve on these original estimates now that much more is known about SWD biology, risks, and management. We briefly review these original studies before establishing new estimates of the economic cost of SWD in the California raspberry industry. Walsh et al. 1 and Bolda et al. 6 are the first studies to estimate the economic cost of SWD. These studies utilize yield loss estimates and observations for strawberries, blueberries, raspberries, blackberries, and cherries in California, Oregon, and Washington in conjunction with production data to calculate revenue loss estimates for each state and crop pairing. Walsh et al.1 assume a yield loss of 20% for all the listed crops in these states. As a result, the study estimates a total of $511 million in potential damages annually due to SWD. Bolda et al.6 continue the analysis by assuming the maximum reported yield losses of 40% for blueberries, 50% for blackberries and raspberries, 33% for cherries, and 20% for processing strawberries. The study concludes that potential revenue losses across these states and crops could be as large as $421.5 million given current prices.Goodhue et al. refine these estimates of lost revenue for the California raspberry and strawberry industries by including potential price responses into their estimates. This additional assumption reflects that as the production of raspberries and strawberries decreases, the prices of these products may increase in response. The interaction between production and price is quantified with the inverse own-price elasticity of demand for each crop. The elasticity predicts the percentage change in price of a good in response to a 1% increase in quantity demanded. Drawing upon elasticity estimates established in prior studies, the authors conclude that SWD-induced yield losses could decrease California raspberry and processed strawberry revenues by up to 37% and 20%, respectively. The authors also evaluate the cost of different SWD-targeting insecticide applications and the cost of a specific conventional raspberry pest control program in California’s Central Coast region. The insecticide material and application costs are estimated to be $825.33 per hectare. However, these chemical applications may also provide incidental control of other pests. This implies that the estimate represents an upper bound of the potential chemical control costs associated with SWD.The revenue loss and management cost estimates in these prior studies can be substantially improved using current information about SWD-induced yield losses and management practices. Fruit losses due to SWD and SWD management costs have decreased over time as researchers and producers have developed and implemented better techniques for reducing crop losses.