Month: November 2024

The signature raspberry flavor comes from aromatic volatiles, mostly composed of a mixture of ketones and terpenes . α-Ionone and β-ionone are carotenoid-derived aromatic volatiles that are mostly responsible for floral notes in fruit ; these compounds usually intensify as raspberries ripen. Also, α-terpineol, which has a sweet, flowery aroma was found to have a positive correlation with sweetness in our study. Aromatic volatiles become prominent during fruit ripening and tend to increase towards senescence, ultimately developing the aroma and flavor for the fruit . Guichard reported that in raspberries all the terpenes and sesquiterpenes concentrations significantly increased during ripening with an increase in α -ionone followed by a slight increase in β-ionone. In our research, α-ionone concentration increased over time in air and 5 kPa atmosphere storage, but decreased in raspberries stored in 15 kPa atmosphere, perhaps due to slowing of further ripening. α-Terpineol, limonene, linalool and hexanoic acid also decreased 3-4-fold with increasing CO2 concentration in storage. Linalool, α-terpineol, limonene and hexanoic acid showed increases in concentration with time in air storage. In our study, the aromatic volatiles were mostly associated with raspberries stored in lower CO2 atmospheres . This may be largely due to little or no inhibitory effects on further ripening in these atmospheres. Ripening of fruit is usually accompanied by softening and production of flavor and aroma volatiles Some fruity/floral volatiles are known to enhance the perception of sweetness . Volatiles such α-ionone, linalool, square pot and α-terpineol have a sweet floral aroma . This may explain why we observed a positive correlation of sweetness with these particular volatiles in our study.

While raspberries held in higher CO2 atmospheres had lower concentrations of aromatic volatiles, most, but not all, of the differences can be explained by ripening inhibition. High CO2/low O2 atmospheres also restrict enzyme activity, diminishing generation of certain organic volatiles, and reducing the effects of ethylene on CA-stored produce . Off-flavor’s association with low CO2 atmosphere storage may be related to the concentration of limonene which was higher in low CO2 stored raspberries and positively correlated with off-flavor. Elmaci et al. also reported an association of off-flavor with increasing percentage of limonene during storage of mandarins. It is possible that off-flavor was also linked to development of decay or leakiness because the rate of decay and leakiness was higher in fruit stored in low CO2 atmospheres due to the lack of fungistatic conditions or inhibition of metabolism. However, raspberries stored in 8 kPa atmosphere performed better in sensory evaluations in terms of raspberry flavor, juiciness, and sweetness. Raspberries stored in air or 5 kPa atmosphere lost almost all their sensory quality by 10 days. Selection of modified atmospheres for raspberries should be based on the storage time and desired quality. While 15 kPa atmosphere prolonged shelf life the longest, 8 kPa atmosphere prolonged shelf life to 10 days while maintaining sensory quality. Based on these findings, modified atmosphere conditions can be formulated and applied during transportation to further investigate the impacts on quality under commercial conditions. Also, synthesis of volatile compounds and associated gene expression as effected by high CO2 atmospheres would be an interesting area for further exploration.

Grapevine leaf roll-associated viruses are among the most consequential pathogens affecting grapevine and have considerable economic impact . GLRaVs are diverse and belong to the family Closteroviridae, with six species and numerous strains in three genera . Grapevines are often infected with several of these viruses simultaneously . Given their impact and global distribution, efforts to manage the spread of GLRaVs, characterize their effects, and understand the interaction between the vine and GLRaVs have been undertaken. Generally, plant responses to viruses include numerous changes in gene expression, gene regulation, and metabolism . Pathogens and stresses elicit conserved responses from their hosts . Infections with GLRaVs have been associated with poorer fruit quality, lower yield, and leaves that curl, redden, and become brittle. Gene expression studies that implicate regulatory systems in the leaf roll disease phenotype are few in number and have focused on the impact of GLRaV-3, highlighting changes in the expression of senescence-associated and flavonoid bio-synthetic pathway genes . Additional transcriptomic study could help generate novel hypotheses concerning the controls that are fundamental to GLRaV responses . Though common responses might be expected in infected plants given the relatedness of GLRaVs, there is considerable variability in the severity of GLRaV infections. Some GLRaV infections appear without symptoms or are mild , but others cause significant changes in photosynthesis, metabolism, and gas exchange in leaves . Changes in fruit yield, organic and amino acids, titratable acidity, potassium, sugars, and flavonoids are also observed .

These are influenced by host genotype , which virus or combination of viruses is present , and environmental conditions . Leaf reddening, for example, is only observed in red-fruited grapevines . Evidence relating GLRaV responses to rootstock is mixed . In a study of Cabernet Franc vines grafted to different rootstocks, the effect of GLRaV infection on pruning weight depended on rootstock and the largest effects were observed in Kober 5BB-grafted vines . Similarly, fruit yield was influenced by both infection type and rootstock, with Kober 5BB-grafted vines most severely affected by a mixed infection with GLRaV-2, GLRaV-3, and grapevine fleck virus . In another report, Red Globe scion buds infected with a strain of GLRaV-2 were used to inoculate Cabernet Sauvignon plants grafted to 18 different rootstocks; the infection was lethal in plants grafted to several rootstock genotypes, including Kober 5BB . This study used Cabernet Franc grapevines infected with zero, one, or two GLRaVs and grafted to two different rootstocks to identify leaf roll effects in ripening berries that were conserved across experimental conditions, and determine whether or not GLRaV responses could be distinguished in berries from plants grafted to different rootstocks. Grapevines were grown in a single experimental vineyard and evaluated in four consecutive years. Vine growth and several measures of fruit composition were taken in the first two years. Total soluble solids were measured in all four years. RNA sequencing , hormone, and metabolite data were collected from Cabernet Franc berries at four stages during ripening in the third and fourth years. RNA-Seq reads were mapped to the Cabernet Franc genome, which was sequenced in long PacBio reads, assembled using the FALCON-Unzip pipeline, and scaffolded using Hi-C data. The same samples were used to measure the levels of stress and ripening-associated hormones and metabolites. Among these were abscisic acid , jasmonic acid , and salicylic acid . Though many of the GLRaV effects occurred in individual years, a subset of reproducible conserved responses and rootstock differentiating responses were discovered.Cabernet Franc grapevines infected with individual and pairs of GLRaVs and grafted to different rootstocks were studied during grape berry ripening in a dedicated experimental vineyard at the University of California, Davis. Typical grapevine leafroll disease symptoms were observed by mid-ripening . In addition, square plastic planter there was a visible, stark reduction in canopy density and cluster size in GLRaV-1,2 versus GLRaV in vines grafted to Kober 5BB that was not readily apparent in vines grafted to MGT 101-14 with the same infection status . Vine growth, cluster weight, and other measures were collected in 2015 and 2016 . The effect of GLRaV infection on dormant pruning weight, berry weight, pH, and tartaric acid content in 2015 and on moisture content, total anthocyanin content, and titratable acidity in 2016 differed significantly based on the rootstock present . This interaction was significant for malic acid in 2015 and 2016. Significant differences in dormant pruning weight, total cluster weight, and tartaric acid were observed in plants with different GLRaV infection status and rootstock . In contrast, few or no significant differences between GLRaV given the same rootstock were observed for total anthocyanins, moisture content, malic acid content, pH, titratable acidity, weight per berry, or yeast assimilable nitrogen and overwhelmingly in a single year if at all . Overall, GLRaV infection tended to reduce dormant pruning weight and cluster weight. The dormant pruning weights and cluster weights of GLRaV-1,2 was significantly lower than those of GLRaV and other GLRaV ; this was observed for both rootstock genotypes. Significant differences in fruit tartaric acid levels were observed only in 2015 and were between GLRaV-1,3 grafted to different rootstocks and between plants with different GLRaV infection status . In each year except 2015, there was a significant interaction between rootstock and GLRaV infection status in terms of TSS at harvest . This interaction was significant at each other developmental stage in 2017 and at prevéraison in 2018 . Significant differences in TSS at harvest were found between GLRaV and GLRaV in each year except 2017 . Overall, significant reductions in TSS relative to GLRaV were limited to the dual infections and GLRaV-3 . Significant differences were observed between rootstocks in GLRaV 1,2 at every developmental stage, albeit only in 2017 . These data provide limited evidence that different GLRaV infections may or may not affect various aspects of vine growth and fruit composition, some of these differences are rootstock specific, and although some of these effects are observed across years, year-to-year differences may impact whether or not effects Occur.

We used RNA-Seq to sequence the transcriptome of 384 Cabernet Franc berry samples collected from plants grafted to different rootstocks , with different GLRaV infection status, at four developmental stages , and in two consecutive years . Because of the remarkable structural and gene content variability among grape cultivars , we built a genome reference specificallyfor the analysis of these RNA-Seq data. The Cabernet Franc genome was assembled into 504 primary contigs for a total assembly size of 570 Mb. This is comparable to the size of the Zinfandel , Cabernet Sauvignon , Chardonnay , and Pinot Noir PN40024 genomes. In total, 3,085 additional haplotigs were assembled with an N50 of 184 kb . The primary assembly and haplotigs were annotated with 33,563 and 19,146 protein-coding genes, respectively . Ripening was associated with transcriptomically distinct developmental stages. Samples clustered primarily by developmental stage and secondarily by year, though samples at harvest clustered separately . Genes with comparable, significant responses in both years of the study were selected to identify reproducible responses to GLRaVs during ripening. Gene expression in GLRaV was compared to gene expression in GLRaV grafted to the same rootstock at the same developmental stage . In addition, the effects of each GLRaV infection on gene expression at each developmental stage were compared in plants grafted to different rootstocks . On average, 7.1% of the genes differentially expressed between GLRaV and GLRaV were reproduced in both years . This percentage was slightly above average for plants with dual, relatively more severe, infections and below average for individual infections . A subset of 32 genes significantly changed their expression level in two or more GLRaV infection conditions, in both rootstock conditions, and at least one developmental stage . These genes constitute the “conserved” responses to GLRaVs in Cabernet Franc berries during ripening. The majority of these differentially expressed genes are associated with defence, ABA signalling, and cytoskeleton organization and biogenesis . Six of these were genes encoding nucleotide-binding site and leucine-rich repeat-containing proteins; half of these were upregulated. Two F-box genes encoding SNIPER4 were upregulated , as was a gene encoding a hydroxyproline-rich glycoprotein . HRGP and NBS-LRR proteins are associated with pathogen detection . Genes encoding a respiratory burst oxidase protein D , a wall-associated kinase-like protein , and a β-glucosidase 3 were downregulated. RBOHD participates in the production of reactive oxygen species and hypersensitive responses to pathogens . RBOH family proteins are targeted by Snf1-related kinase 2 phosphorylation, a key component of the ABA signalling pathway. Likewise, a WAKL gene in citrus participates in JA and ROS signalling . Among the functions of β-glucosidases are the activation of ABA and SA by freeing them from the conjugates that render them inactive . Several ABA-related genes were among the conserved GLRaV responses, including an upregulated ABC transporter and two downregulated genes, AMP1 and RDA2. AMP1 negatively regulates ABA sensitivity . RDA2 participates in the inhibition of ABA signalling and the promotion of MAPK signalling . Five genes related to cytoskeleton organization were sensitive to GLRaV infection. Only one of these, a myosin VI motor proteincoding gene, was downregulated.

Host plant resistance is the most sustainable option in managing soilborne disease , but like other crops it is believed there is little resistance to southern blight within commercial processing tomato cultivars. However, some resistance is available in the tomato germplasm. The Texas A&M breeding program released several breeding lines that have shown superior resistance to southern blight under field conditions . The mechanism of resistance is associated with the development of secondary tissue on the basal mainstem called the phellem barrier. The six Texas A&M selections 5635M, 5707M, 5719M, 5737M, 5876M, and 5913M were screened for two years in fields infested with A. rolfsii and showed resistance commensurate to a resistant wild accession PI 126432 . Additionally, the six selections showed field resistance to Fusarium oxysporum f. sp. lycopersici W. C. Snyder & H.N. Hansen race 1 including good average plant yields for 5719M and 5876M . The relative susceptibility of commonly grown commercial processing tomato cultivars to southern blight is unknown but would be beneficial for disease management. Grafting is another option for management of soilborne diseases. Disease control by grafting has already shown to be a beneficial alternative to the soil fumigant methyl bromide in Asia and much of Europe . Grafting is a fusion of two plant segments, 25 liter pot the shoot of the plant with desired fruit quality called the ‘scion’ and the root system with desired root traits as the ‘rootstock,’ that functions as a single plant . Grafting is commonly used for perennial crops and has since the early 20th century become a technique for vegetable production in Cucurbitae and Solanaceae species . Grafting to a resistant rootstock has previously been shown to reduce diseases causes by soilborne pathogens and has potential to be a sustainable alternative to fumigants for the control of many soilborne diseases .

In tomatoes, grafting has been used to augment growth under low potassium environments , improve tomato resistance to root-knot-nematodes , and increase tolerance to drought . The main mechanism of disease control by grafted plants is speculated to be by avoidance by having the resistant rootstock come into contact with the pathogen instead of the susceptible scion tissues . Maxifort is an interspecific hybrid of tomato and a wild Solanum species developed as a rootstock for greenhouse tomato . In a study in the southeastern United States, heirloom tomato grafted to the rootstock specific Maxifort exhibited 0 to 5% southern blight incidence whereas incidence in nongrafted plants was 27 to 79% . To our knowledge grafting processing tomatoes to a southern blight-resistant rootstock has not been explored in processing tomatoes in the San Joaquin Valley. Although rootstocks like Maxifort are highly resistant, some plants often develop southern blight symptoms . In our preliminary work, we observed that the graft union was planted below the soil line, possibly rendering the susceptible scion vulnerable to infection by A. rolfsii in the field. To our knowledge, raising the height of the graft union in other crops has yet to be evaluated in processing tomato. The use of resistant rootstock for an annual crop has been studied in fresh-market and heirloom tomatoes for improvement on yield but has yet to be explored for disease resistance for processing tomato in California. The objectives of this study were to: evaluate susceptibility of commercial processing tomato cultivars to southern blight; and evaluate grafting and increased height of the graft union with the resistant rootstock Maxifort for southern blight management in processing tomato.Athelia rolfsii sclerotia were produced in culture media using the oat seed method . The three Athelia rolfsii isolates used were each obtained from a different processing tomato field in Kern County, California in 2017.

Briefly, for each trial the isolates were grown from infested filter paper maintained at – 80ºC, hyphal tipped from mycelium actively growing on potato dextrose agar, and incubated at 25ºC under continuous light for approximately six days. Two plugs from the edge of the purified colonies were inoculated into Erlenmeyer flasks containing oat seeds and 1% water agar that had been autoclaved twice for 60 min on a 24 hr interval. Flasks were then incubated at room temperature for approximately 33 days. The sclerotia grown on oats were moved into sterile 5.7 L plastic containers placed in a biosafety cabinet to dry for approximately 14 days, and sclerotia were separated from oats by pressing the dried oat-sclerotia mixture with a gloved hand over a 2.0 mm and 850 µm sieves. Sclerotia were stored at room temperature in a plastic Ziploc bag until experiment set up. Viability of the inoculum was evaluated by germinating surface disinfested sclerotia on water agar.The susceptibility of 19 commercial processing tomato cultivars to A. rolfsii was evaluated in a greenhouse study in 2018 . In 2019, 19 commercial cultivars and six processing tomato breeding lines from Texas A&M were evaluated. The commercial cultivars were chosen based on highest total yield in California counties affected by southern blight. Treatments consisted of the 19 of these commercial cultivars grown in inoculated soil and a selection of 6 of the 19 commercial cultivars grown in non-inoculated soil as negative controls. The 2018 trial included two hybrid tomato cultivars grown in inoculated soil as positive controls, but were not included in 2019 due to poor germination. The rate of inoculum was 10 sclerotia per 100 cm3 soil based on recommendations by Punja and Rahe . The plants were started from seed using an organic seed starter soil mix in a tray with 200 22 mL, 2.22 cm x 2.22 cm cells. Two seeds were planted per cell.

The trays were placed on a clear plastic-lined chamber in the greenhouse on a warming mat set at 24ºC and misted three times per day for 15 seconds. Emergence began five days post seeding. Eleven days post seeding the trays were moved to an open misting bench where the plants could receive more sunlight, thinned to one plant per cell using sterile metal scissors, and sprinkled with one tablespoon of granular Osmocote Flower and Vegetable fertilizer 14-14-14 per 90 cells on the trays. The Osmocote rate used for germination was recommended by colleagues with tomato germination experience. Three weeks post seeding the plants were transplanted into trays with 36 166 mL, 5.72 cm x 5.08 cm cells to allow for advanced root development. In these larger trays, the soil substrate used was UC Soil Mix III, composed of 50:50 plaster sand:peat moss that was pasteurized at 100ºC for two hours. Inoculation and transplanting occurred five weeks post seeding. The day before inoculation, sclerotia were surface disinfested using 0.5% sodium hypochlorite solution for 1 minute, subsequently rinsed twice in sterile deionized water, and dried with sterile paper towels. The number of sclerotia needed to total 1 g was determined by manually counting, the amount to be added was weighed and incorporated to the top 10.2 cm of soil in 15.2 cm diameter pots to reach the target sclerotia count per 100 cm3 soil. Plants were then transplanted into 15.2 cm , 2.7 L pots with UC Soil Mix III at one plant per pot. Plants were grown in a greenhouse with the temperature set at 33ºC. Temperature data loggers were installed, but in 2018 they malfunctioned. In 2018, 25 liter plant pot the plants were arranged in a randomized complete block design with seven replications across four benches and with six replications across three benches in 2019 oriented east-west, one or two blocks per bench. Blocking was designed to capture potential confounding factors of light, temperature, and watering differences across the different benches. All benches had their own irrigation sub-line connected to a main line. A drip system was installed 15 days post transplanting with one JAIN Twist Weight emitter per pot and was set to water daily for 2 minutes early in the morning. Each plant was fertilized once per week for 3 weeks with 15 mL of a solution containing Jack’s Classic Professional Water Soluble Plant Food 20-20-20 at the recommended rate of 1 tablespoon per gallon of water. The volume of fertilizer was chosen based on observation of adding a volume of liquid that would not leach through the openings of the pots. Four days after the drip system was installed approximately one tablespoon of granular Osmocote Flower and Vegetable fertilizer 14- 14-14 was added around the drip emitter of each pot. The same growing methods from 2018 were used for 2019 with adjustments in using only granular Osmocote Flower and Vegetable fertilizer 14-14-14. The plants were maintained in the greenhouse for 126 days in 2018 and the plants from 2019 were maintained in the greenhouse for 107 days.In 2018, because little disease development was observed in blocks 5 and 6, additional inoculum was added to the inoculated pots in these blocks 77 days after initial inoculum was added. Inoculum for each individual pot was calculated by multiplying the volume of the top four inches of the pots by the rate of inoculum , then divided by the average number of sclerotia from one gram of sclerotia. The sclerotia from all three isolates were evenly mixed. The mixed sclerotia were then weighed to 0.12 g for each individual pot, inoculum per pot were placed in a ziplock bag, then one bag of inoculum was carefully poured around the previously inoculated tomato stem. Plant material for grafting experiments.

The processing tomato cultivars used as scions or non-grafted controls in grafting experiments were Heinz 5608 and Heinz 8504, which are commonly grown in the San Joaquin Valley of California. The hybrid cultivar Maxifort served as the rootstock in grafted treatments. For all greenhouse and field grafting experiments, transplants and grafting were produced by Growers Transplanting Inc. in Salinas, CA using the tube grafting technique with the modification of using a clip that applies minimal pressure on the graft union. Grafting for the high-union grafted treatment consisted of plants with a union approximately 2.54 cm above the standard graft. These high-union grafted plants were produced by stretching the rootstock 2.54 cm to 5.08 cm before the grafting process, applying extra fertilizer to the rootstock, and cutting the rootstock approximately 6.35 cm to 7.62 cm from the plug .Grafting greenhouse experiments. In 2017 a preliminary study was conducted that evaluated two cultivars , two graft treatments , and four inoculum levels in a full factorial treatment arrangement. On June 5, 2017 a single plant was transplanted into each 2733 mL pot with UC Soil Mix III that was inoculated as described above for the cultivar trial and grown in a greenhouse at 32ºC. One-plant pots were arranged in a randomized complete block design with 8 replications across two benches oriented east-west, four blocks per bench. The pots were watered via a drip system beginning 24 days post planting. The plants were fertilized every 2 to 3 weeks with 100 mL of Jack’s Classic Professional Water Soluble Plant Food 20-20-20. The treatment structure was modified based for 2018 and 2019 to include a grafted treatment with a high-union, referred to as ‘tall’. These studies evaluated two cultivars , three graft treatments , and two inoculum levels in a full factorial arrangement . Plants were transplanted into one-plant pots on July 18 in 2018 and April 29 in 2019. Plants were arranged in a randomized complete block design with 6 and 8 replications in 2018 and 2019, respectively, on benches oriented east-west with two or three blocks per bench. The 2018 experiment was conducted in a greenhouse set to 21ºC for 120 days, which was increased to 26ºC for 34 days due to low disease pressure. The 2019 experiment was conducted in a greenhouse set to 35ºC for 83 days. Hobo MX2301 data loggers monitored temperature in the greenhouse and reported the average temperature maximum 38ºC and minimum 15ºC in 2018. In 2018, four days post planting drip irrigation was used to water daily with fertilized water for 21 days before switching to industrial water. After adjusting the drip system, the plants were fertilized once every week then adjusted to fertilizing twice a week with 100 mL solution of Jack’s Classic Professional Water Soluble Plant food. In 2019, approximately one tablespoon of granular Osmocote Flower and Vegetable fertilizer 14-14-14 was added around the drip emitter of each pot. In 2019 additional inoculum was added to the inoculated pots 64 days after transplant to encourage disease development.

Similar results were observed in wines prepared from “Merlot” grapes treated with a racemic mixture of ABA . This treatment resulted in changes in the proportions of anthocyanins, increased total phenol and flavonol content, and increased antioxidant activity . However, it should be considered that application of racemic mixtures of enantiomers may result in a range of plant responses because R-ABA is not found in plants and is less active and less effective than S-ABA. The two enantiomeric forms may have different effects on gene expression and on physiological responses . Anthocyanin accumulation in grape berries during véraison is probably triggered by increased sugar and ABA concentrations in the berry skin, which activate the expression of genes involved in anthocyanin biosynthesis . The activation threshold for genes involved in anthocyanin production was reported to be between 9 and 10◦Bx . S-ABA application at 7 DAV, when anthocyanin biosynthetic genes are normally induced, followed by a second application at 21 DAV, when endogenous ABA concentrations are close to maximal or are beginning to decrease, can upregulate their expression even further or maintain them at a constant level for a longer period of time. These transcription factors are responsive to ABA and are associated with the regulation of the biosynthetic genes CHI, F3H, DFR, LDOX, and UFGT . The transcription factors VvMYBA1 and VvMYBA2 activate anthocyanin biosynthesis in grapevines and are not functional in white grape cultivars . Transcription factors affect the ratio of tri-/dihydroxylated anthocyanins through trans-regulation of flavonoid 3-hydroxylase and flavonoid 30 5 0 -hydroxylase gene expression .

During anthocyanin biosynthesis, F3H is responsible for the hydroxylation of naringenin at position 30 , black plastic planting pots generating dihydrokaempferol, a dihydroflavonol that can be hydrolyzed at position 30 or 50 of the B-ring by the enzymes F30 H or F30 ,50 H, which are responsible for the hydroxylation of the B-ring of flavonoids. F30 H activity promotes accumulationof the cyanidin and peonidin anthocyanin groups, whereas F30 ,50 H activity results in the production of delphinidin and its derivatives petunidin and malvidin. These two enzymes compete in controlling di- and trihydroxylated anthocyanin synthesis . In our study, treatment of hybrid grapes with two applications of 400 mg/L S-ABA primarily favored the accumulation of delphinidin-3-glucoside and malvidin-3-glucoside ; therefore, such treatment decreased the difference between the concentrations of diand trihydroxylated anthocyanins in the grapes. This is consistent with previous results obtained for “Aki Queen” grapes , in which the application of S-ABA stimulated the gene expression of F30 ,50 H relative to F30 H. In addition, the concentrations of petunidin and malvidin increased in the berries, thereby increasing the proportion of trihydroxylated anthocyanins and decreasing the proportions of cyanidin and peonidin anthocyanins relative to the total anthocyanins . In this study, the expression of the main enzymes leading to anthocyanin biosynthesis were analyzed. Future experiments to study changes in expression of F30 H and F30 ,50 H encoding genes are still required to gain a better insight into the impact of exogenous ABA applications on the differential accumulation of specific anthocyanins. Our results indicate that application of S-ABA increased the expression of the UFGT gene and the transcription factors at 28 DAV, but this was not observed for the treatment with only one S-ABA application. Anthocyanin accumulation begins when all genes involved in the biosynthetic pathway are induced, especially UFGT . Anthocyanidins are unstable and are easily degraded to colorless compounds; therefore, before anthocyanins are transported, they must be stabilized by the addition of a glucose residue at position 3 of the C-ring .

The enzyme UFGT catalyzes the final step of anthocyanin biosynthesis, therefore UFGT has been considered by many authors to be a critical enzyme in anthocyanin biosynthesis . Temporary stimulation of gene transcription is believed to be related to a decrease in S-ABA concentration over time. In ‘Crimson Seedless’ grapes, a constant decrease in S-ABA levels with a half-life time of 14.7 days was observed in treated grape berries . The natural decrease in ABA concentration, along with the decrease in S-ABA levels, may, therefore, lead to decreased activity of some genes, depending on the S-ABA concentration in the plant. Expression of the UFGT gene increased considerably 7 days after S-ABA application in ‘Crimson Seedless’ grapes but decreased 3 weeks after treatment, becoming similar to the control . In “Cabernet Sauvignon” grapes treated with ±cis, trans-ABA, expression analysis of anthocyanin biosynthetic genes revealed that the maximum expression levels were only reached 10–17 days after application and that they then rapidly decreased . ABA cis– and trans-isomers differ in the orientation of the carboxyl group at carbon 2. Only the ABA cis-isomer is biologically active, and it accounts for almost all of the ABA produced in plant tissues. However, unlike the S and R enantiomers, the cis– and trans-isomers can be interconverted in plant tissue . Most of the studies on S-ABA involved V. vinifera cultivars were done in temperate zones and testing a single application . In this study, we evaluated the response of a new V. vinifera × V. labrusca hybrid grape cultivar grown in a subtropical area to multiple S-ABA applications. This hybrid often shows lack of color development; therefore, our results confirm the effectiveness of S-ABA to improve the color of ripening berries, even under warm climate conditions. The application of S-ABA to berries of the seedless grape Selection 21 increased the total anthocyanin concentration, changed the proportion of individual anthocyanins, improved their color attributes, and increased the expression of transcription factors and anthocyanin biosynthetic genes.

Two applications of 400 mg/L S-ABA, at 7 and 21 DAV, resulted in the best results in terms of color increment and total anthocyanin concentration, favored the accumulation of trihydroxylated anthocyanins, and increased the expression of transcription factors and of the genes F3H and UFGT. These results not only show that S-ABA is a valuable tool for improving the color of red grapes in warm areas, where color deficiency is frequently observed, but also suggest that S-ABA may be useful in grape breeding programs by permitting the selection and release of new cultivars with natural poor color, but other desirable characteristics such as high yield and resistance to common diseases.Wild birds provide many ecosystem services that are economically, ecologically, and culturally important to humans . One especially important service is suppression of insect populations in agricultural systems . On a global scale, insectivorous birds consume an estimated 400–500 million tons of insects annually and have the capacity to decrease arthropod populations and increase crop yields of both temperate and tropical farms . While these beneficial effects are not always observed , attention has focused on promoting avian diversity and abundance on farms to leverage these benefits . The fact that birds consume agricultural pests does not ensure that they can control them, in the sense of substantially reducing densities of rapidly-growing pests. Here, we evaluate the capacity of birds to suppress agricultural pests, specifically the coffee berry borer, aninvasive pest found in almost every coffee-producing region worldwide. The coffee berry borer is one of the most economically significant pests of coffee worldwide , causing an estimated annual global loss of US $500 million . These small beetles damage coffee crops when a female bores into a coffee cherry and excavates chambers for larvae to grow, consuming the coffee bean. Control of CBB can be accomplished by spraying fungal bio-insecticide Beauvaria bassinia, increasing harvest frequency or continually removing, by hand, over-ripe and fallen cherries, which serve as reservoirs for infestations . The last, and most laborious, control method appears to be the most economically effective In addition to human-mediated control, natural predators such as ants, parasitoid wasps, and nematodes are being explored as potential bio-control agents . Birds have also been identified as a significant biological control agent of CBB . Field experiments in Central America have shown that CBB infestation dramatically decreases when birds are present . For example, Karp et al. reported that bird predation suppresses CBB infestation by 50% and saves farmers US $75– 310/ha per year; another estimate values bird predation at US $584/ha . Suppression is done by both resident foliage-gleaning insectivores, such as rufous-capped warblers , drainage pot and Neotropical migrants like the yellow warbler . Similar to other agriculture systems, avian abundance is higher on farms with heterogenous landscapes in close proximity to native habitat , suggesting low-intensity shade coffee farms are better not only for supporting biodiversity, but also in providing pest mediating ecosystem services . Several lines of evidence support the notion that birds depredate CBB in coffee plantations, and that their effects are biologically significant. Firstly, we know that a variety of bird species consume CBB from assays of avian fecal and regurgitant samples , though the detection rate is quite low . Low detection rates might be due to low consumption rates; detectability of DNA in feces depends on number of CBB eaten, and time since feeding, as well as fecal mass . Secondly, bird and bat exclosure experiments are associated with greater CBB infestation within enclosures . At the same time, it is not clear how birds can effectively suppress CBB at most sites, and throughout the season. Exclosure experiments that report avian suppression appear to be at sites with relatively low CBB infestations , whereas coffee-producing regions with more recent introduction of CBB have infestations of up to 500,000 CBB in a season .

We also do not know whether suppression is effective throughout the reproductive cycle of the CBB, or just when abundances are relatively low. Finally, CBB field traps often capture large numbers of CBB, even in the presence of birds . Consequently, while there is clear evidence that birds consume CBB, the degree to which CBB populations can be suppressed is less clear, particularly because of the species’ population growth potential . Here, we use a CBB population growth model to assess the capacity of birds at naturally occurring densities to reduce CBB populations, as a function of a starting infestation size. We created an age-based population growth model for CBB using data from a life-stage transition matrix published by Mariño et al. . We converted their matrix into a female-only, daily time-step, deterministic Leslie matrix; we could not estimate population growth directly from the original matrix because it did not use a common time step . We incorporated a skewed adult sex ratio to mimic real populations , and added a life-stage for dispersing females, the stage at which CBB are vulnerable to predation by birds. Since the entire CBB lifecycle occurs within the coffee cherry, CBB are vulnerable to predation by birds for a short time window when adult females disperse between plants and burrow into a new cherry . Birds do not eat coffee cherries, with the exception of the Jacu , which is found in southeastern South America. Consequently, we assumed that only adult CBB females are vulnerable to bird predation. With our Leslie matrix, we projected population growth for a closed population during a single CBB breeding season. We projected growth at three levels of initial starting populations of CBB , calculated from published estimates of CBB densities from alcohol lure traps in coffee farms from Colombia, Hawaii and Costa Rica. We then determined the degree to which dispersing female survival rate would have to be decreased to result in a 50% depression in the adult population size at the end of the coffee season at all three infestation levels. Finally, we assessed the plausibility of this degree of CBB suppression by birds as a function of avian energy requirements, reported avian densities on coffee farms, prey composition of avian diets, estimated caloric value of CBB, and the starting population size of CBB females.Coffee phenology is directly related to rainfall patterns that differ among coffee producing regions, leading to distinct seasons, and timing of harvest. Our model assumes environmental conditions of Costa Rica, and thus describe the coffee phenology of this region. In regions of Costa Rica with marked seasonality, coffee flowering is triggered during the dry to wet season transition by the onset of acute precipitation . Areas with relatively consistent rain patterns have more continuous flowering events and a longer harvest season In the Central Valley of Costa Rica, flowering typically begins in March, with three flowering events spread over a month . Flowers are short-lived, lasting only a few days before fruit begin to develop.

The levels of amygdalin and prunasin/sambunigrin were almost equal in Ozone but in Ozark, 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. CNGs may have also been degraded during juice preparation due to native β-glucosidases. A future study should investigate the impact of freezethaw 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 , drainage planter pot 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.1 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 %.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. Because elderberry has predominantly cyanidin-based anthocyanins, protocatechuic acid is typically found as the main degradation product, though phloroglucinaldehyde can also be formed. However, neither protocatechuic acid nor phloroglucinaldehyde were observed in any of the cooked juice samples. Protocatechuic acid dihexoside, which was tentatively identified in an earlier study of blue elderberry did not increase over the cooking period. Caffeic acid, a hydroxycinnamic acid increased up to 108.1% of its initial concentration after 2 hours of cooking at 72 °C, and up to 147.1% after 2 hours of cooking at 95 °C. The levelsof caffeic acid were highly variable, with larger standard deviations that the other phenolic compounds. This is a known metabolite of cyanidin-based anthocyanins,and further work investigating the breakdown of anthocyanins in blue elderberry juice into this phenolic acid can elucidate the pathway to this compound.

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. 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 storage. The 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 maintainlevels 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.The Berry phase has played significant roles in many aspects of physics, ranging from atoms to molecules to condensed-matter systems. As pointed out in Ref., the Berry phase has a profound geometrical origin because an adiabatic and cyclic process of a quantum state is mathematically equivalent to parallel transporting it along a loop, which connects to the concept of holonomy in geometry. Hence, the Berry phase bridges physics and geometry, making it extremely important in the understanding of topological phenomena, such as integer quantum Hall effect, topological insulators and superconductors, and others. The description of the Berry phase relies on the properties of a pure state of a quantum systems at zero temperature. Meanwhile, mixed quantum states, including thermal state at finite temperatures, are more common. Therefore, mixed-state generalizations of the Berry phase have been an important task. Uhlmann made a breakthrough by constructing the Uhlmann connection for exploring the topology of finite-temperature systems. As the Berry holonomy arises from paralleltransport of a state-vector along a closed path, the Uhlmann holonomy is generated by parallel-transporting the amplitude of a density matrix. defined by W = √ρU. Here the amplitude W is the mixed-state counterpart of the wave function, and U is a phase factor. A geometrical phase is deduced from the initial and final amplitudes. However, Uhlmann’s definition of parallel transport is rather abstract and may involve nonunitary processes, complicating a direct and clear physical interpretation. Moreover, plant pot with drainage the fiber bundle built upon Uhlmann’s formalism is trivial, which severely restricts its applications in physical systems.Purification of a mixed state leads to purified state, a state-vector equivalent to the amplitude of a density matrix. The lack of a one-to-one correspondence between the density matrix and its purified states gives rise to a phase factor, similar to the phase of a wave function. In a branch of quantum field theory called thermal field theory, there is a similar structure for describing the thermal-equilibrium state of a system by constructing the corresponding thermal vacuum by duplicating the system state as an ancilla and forming a composite state. It plays a crucial role in the formalism of traversable wormholes induced by the holographic correspondence between a quantum field theory and a gravitational theory of one higher dimensions. Importantly, purified states of a two level system has been demonstrated on the IBM quantum computer while the thermal vacuum of a transverse field Ising model in its approximate form has been realized on a trapped-ion quantum computer. Despite the superficial similarity, a major difference between a thermal vacuum and a purified state is a partial transposition of the ancilla to ensure the Hilbert-Schmidt product is well defined.

In quantum information theory, a partial transposition is closely related to entanglement of mixed states. Importantly, partial transpositions of composite systems have been approximately realized in experiments by utilizing structural physical approximations in suitable quantum computing platforms. Although ordinary observables cannot discern the partial transposition between the purified state and thermal vacuum, here we will show that at least two types of generalizations of the Berry phase to mixed states are capable of differentiating the two representations of finite temperature systems. Among many attempts to generalize the Berry phase or related geometric concepts to mixed states, a frequently mentioned approach was proposed in Ref. Instead of decomposing the density matrix to obtain a matrix-valued phase factor, a geometrical phase is di-rectly assigned to a mixed state after parallel transport by an analogue of the optical process of the MachZehnder interferometer. Hence, the geometrical phase generated in this way is often referred to as the interferometric phase. The interferometric phase has been generalized to nonunitary processes, but the transformations are still on the system only. Moreover, it is essentially different from Uhlmann’s theory since the conceptual structure of holonomy is not incorporated. We will first derive a mixed-state generalization of the parallel-transport condition for generalizing the Berry phase without invoking holonomy. This approach unifies the necessary condition for both the interferometric phase and Uhlmann phase . Two ways to implement the parallel-transport condition based on how the system of interest undergoes adiabatic evolution will be introduced, and they lead to different generalizations of the Berry phase. We will name one thermal Berry phase and the other generalized Berry phase. Importantly, the partial transposition of the ancilla between a purified state and thermal vacuum will be shown to produces observable geometrical effects in both thermal Berry phase and generalized Berry phase. Through explicit examples, the two generalized phases are shown to differentiate the two finite-temperature representations, a task beyond the capability of the conventional interferometric phase or Uhlmann phase. The rest of the paper is organized as follows. Sec. II summarizes the Berry phase in a geometrical framework with an introduction of the parallel-transport condition for pure quantum states. In Sec. III, we review the representations of mixed states via purified states and thermal vacua and then explain the difference of the partial transposition of the ancilla. In Sec. IV, we introduce the thermal Berry phase via generalized adiabatic processes. While the thermal Berry phase can differentiate a purified state from a thermal vacuum, it may contain non-geometrical contributions. In Sec. V, we generalize the parallel-transport condition to involve the system and ancilla and derive the general Berry phase according to the generalized condition. While the generalized Berry phase only carries geometrical information, its ability of differentiating a purified state from a thermal vacuum depends on the setup and protocol. We present examples of the thermal and generalized Berry phases. Sec. VI concludes our study. Some details and derivations are given in the Appendix.While purified states of a two-level system incorporating environmental effects have been simulated on the IBM quantum platform, thermal vacua of the transverse Ising model has been experimentally realized on an ion-trap quantum computer by the quantum approximate optimization algorithm. Moreover, partial transposition of a composite system has been approximately realized on quantum computers with various numbers of qubits.

American elderflower appears to contain a different chlorogenic acid isomer than the European elderflower, which has mainly neochlorogenic acid. Furthermore, 12 cultivars were sampled for the study, which showed high variability in concentration of the two compounds measured. Rutin concentrations ranged from 4637 to 8111 mg kg-1 while chlorogenic acid concentrations ranged from 1180 to 3064 mg kg-1 , showing that key phenolic compounds can be more than double in some cultivars. The concentration of these two compounds did not appear correlated, as the correlation coefficient was only 0.018.While there have been several studies measuring the CG content in elderberries of different subspecies, the data available on elderflower CG content is limited. In fact, only one study has published data on this area to date and it focused on European elderflowers. A study comparing growing locations at multiple altitude levels to determine impact on phenolic compounds and cyanogenic glycosides found that CG concentrations in elderflowers ranged from 1.23 ug g-1 to 18.88 ug g-1 , generally increasing as thealtitude increases. 6 Sambunigrin was the only CG measured and compared to the berries of the same plants in this study, elderflowers contained more CGs than elderberries. Elderflowers from the American subspecies nor the blue subspecies have been analyzed for their CG content. As consumer concern for this toxic group of compounds remains high, it would increase confidence of consumers to utilize the elderflowers of these other subspecies if data was available on the CG concentrations of these flowers.Elderflowers and elderflower products have been investigated for their volatile profile. A direct comparison is difficult to make from the syrups, danish trolley which have other ingredients like sugar or lemons, to the plain flower extracts, but due to the high popularity of elderflower syrups, the results of those studies are included here as well.

In studies of the European elderflower without any additional food ingredients, linalool and linalool derivates, such as -linalool pyranoxide and cis-linalool oxide, have frequently been identified as prominent. The aroma of linalool, the main aroma compound in lavender, can be described as citrus, fruity, floral, and woody. The age of the flower when harvested as well as how the flowers are stored after harvest can greatly impact the volatile profile. As expected from the other data on inter-cultivar variation, the volatile profile is heavily influenced by the cultivar. For example, wild elderflower had twice as much rose oxide and more linalool oxide than the other 12 cultivars. While this could be a challenge for manufacturers that use elderflower in products to have a consistent aroma from batch to batch, it also allows for more selectivity to find a cultivar that matches desired organolepticproperties in the product. American elderflowers have not yet been evaluated for their volatile profile, nor have blue elderflowers.Elderberry and elderflower are becoming more common ingredients and flavoring agents in beverages and food products. However, a vast majority of the products on the market today utilize the European subspecies of this plant due its more established cultivation and a deeper understand of the composition, particularly the phenolic profile, of the fruit and flower. North American subspecies, the American elderberry S. nigra ssp. canadensis and the blue elderberry S. nigra ssp. cerulea, have some information available regarding composition, but further analyses are needed to understand how they may perform in the common applications that European elderberry and elderflower are used in today.As global warming and water scarcity issues continue to impact food systems, fire-resilient and drought-tolerant plants will become more important for supplying nutrient-rich foods. Wildfires throughout the western United States are becoming more common and more serious as seasons are hotter and drier. California has been experiencing unprecedented levels of wildfires, including over 1.9 million acres burned in 2018, over 4.2 million acres burned in 2020, and over 2.5 million acres in 2021.

One native and fire-resilient plant is the blue elderberry , which grows wild throughout the western United States and has become a popular choice to grow in hedgerows. The blue elderberry is drought-tolerant, and the roots of the blue elderberry can survive fires to regrow the next season to continue providing valuable flowers and fruit , making it an ideal choice to plant in regions of California and American West often stricken by wildfires. While European and American elderberries have been studied for decades, there is currently little information on the subspecies native to the western region of North America, S. nigra ssp. cerulea , known as blue elderberry due to a white-colored bloom on the exterior of the berry which makes it appear blue. In California, it grows wild in riparian ecosystems near rivers and streams 86 , but is also planted in hedgerows on farms to improve water, air, and soil quality, in addition to providing a habitat for birds, pollinators, and other beneficial insects. The plant can grow several meters tall and wide and flowers from May to August, with peak fruit ripening throughout July and August. While elderberry prefer moist soil and some hedgerows may receive some irrigation during the summer months, most are not irrigated once the hedgerow has been established, about 2-4 years . That is one of the benefits of using native and drought-tolerant plants, as they can better withstand the natural climate without excess resources. Elderberries have a long history of use by Native Americans and Europeans in foods, beverages, and herbal medicines. Research exploring links between elderberry consumption and health has increased dramatically, particularly in the past decade. Numerous in vitro and in vivo studies demonstrate that elderberries have potent antioxidant, antibacterial, and antiviral properties. Results of two randomized, double-blind, placebo-controlled clinical trials suggest that elderberry supplements reduce the duration and severity of cold symptoms. Roscheck et al. identified two non-anthocyanin flavonoids in elderberry extract that inhibited viral ability to infect host cells when bound. While most bio-activity of elderberries is assumed to result from the phenolic compounds like anthocyanins, the high-molecular weight fraction of concentrated elderberry juice was found to contain acidic polysaccharides that had potent effects against the human influenza virus. The health-promoting properties of elderberry have led to recent increases in its use in products such as supplements, syrups, gummies, and teas, as well as wine and jams.

During the COVID-19 pandemic, elderberry supplements gained wide attention because of potential anti-viral activities; however, there is no strong clinical evidence that elderberry could be beneficial in preventing or treating COVID-19. The market for elderberries is expected to continue to increase, as the sales of herbal dietary supplements was over $11 billion in 2020, a 17.3% increase from 2019. Elderberry was the top selling herbal supplement, with sales over $275 million, as consumers became more interested with supporting their immune systems 9 . In addition to the interest in elderberry as an ingredient in functional foods, elderberry can be an excellent source of natural coloring agents for food and beverage applications due to the high content of red and purple anthocyanins.Characterization of the chemical composition, functional properties, and impact of processing on the bioactive compounds in elderberry is largely limited to S. nigra ssp. nigra and, to a lesser extent, S. nigra ssp. canadensis. S. nigra ssp. nigra is commonly referred to as the European black elderberry, which has many established cultivars, such as “Haschberg” and “Samyl”, vertical aeroponic tower garden and it has an established market. The European elderberry is the most frequently used subspecies in commercial elderberry-based products and has been extensively studied for its composition, anthocyanin stability, and health benefits in European black elderberry-based products . S. nigra ssp. canadensis is commonly referred to as the American elderberry, a subspecies native to the eastern and central regions of North America. There are several cultivars of the American elderberry, including “Johns” and “Bob Gordon”. The American elderberry, which is utilized in small-batch products, has also been evaluated for its composition and health-promoting properties . The acreage grown of this subspecies has been increasing rapidly and there is a goal to grow over 2,000 acres by 2025, according to the Midwest Elderberry Cooperative. Currently, there is no information on the chemical composition of the fruit of the blue elderberry . With the recent increase in demand for elderberry, blue elderberry grown in hedgerows may be an additional and valuable source of bio-active phenolics and natural colorants. The objective of this study was to determine the moisture content, soluble solids, pH, titratable acidity, and establish the anthocyanin and phenolic profiles of blue elderberries grown in Northern California to support the use of this robust, native crop in commercial products.Hedgerows of S. nigra ssp. cerulea were identified on five farms near Davis, California in Spring 2018 with the assistance of an experienced agronomist at The Cloverleaf Farm . Farm, hedgerow, and harvest information is presented in Table 1. Blue elderberries were determined to be ripe when the berries in a cyme were deep purple, with or without the white bloom, and had no green berries present. Ripe elderberries were harvested by hand from all four quadrants of the elderberry shrub, totaling approximately 3 kg of elderberries. The berries were placed in clear plastic bags, stored on ice, and transported to the laboratory. A subsample was separated for moisture analysis, while the rest was de-stemmed and stored at -20 °C until analyzed.Elderberries were extracted by combining 5 g frozen berries with 25 mL MeOH:formic acid in a conical tube. The contents were homogenized, placed in a shaker without water at speed 7.5 for 20 min, then centrifuged at 3,000 rpm for 7 min. The supernatant was transferred to a 15 mL plastic tube and stored at -80 °C for no more than two weeks prior to analysis. Duplicate extracts were made from each shrub. TPC was determined using the Folin-Ciocalteu method. First, elderberry phenolic extract was diluted 1:4 with water. Each extract was analyzed in duplicate and averaged. In 10 mL glass tubes, 6 mL water was combined with 100 µL sample and 500 µL Folin-Ciocalteu reagent. After mixing and incubating for 8 min at room temperature, 1.5 mL 20% aqueous sodium carbonate was added. The tubes were mixed, covered with foil to avoid light exposure, placed in a water bath at 40 °C for 40 min, then cooled at room temperature for 15 min. The samples were read by a UV visible spectrophotometer at 765 nm and quantified using an external standard curve prepared with gallic acid . TPC is expressed as mg gallic acid equivalents per 100 g FW.Five grams of frozen berries were mixed with 25 mL of in a conical tube, which was then homogenized for 1 min at 7,000 rpm . The mixture was stored at 4 °C overnight, then in the morning, centrifuged at 4,000 rpm for 7 min. The supernatant was used directly for analysis. Three pooled samples were made for each hedgerow, each consisting of even amounts of berries from three distinct shrubs. Eachpooled sample was extracted once to give 3 biological replicates, and each extract was run in duplicate . The concentration of phenolic compounds in blue elderberry followed the method by Giardello et al. with some modifications. Briefly, samples were analyzed via reversed-phase liquid chromatography on an Agilent 1200 with a diode array detector and fluorescence detector . The column used was a PLRP-S 100A 3 µm 150 x 4.6 mm at 35 °C, and the injection volume was 10.0 µl. Mobile phase A was water with 1.5 % phosphoric acid, while mobile phase B was 80%/20% acetonitrile/ mobile phase A. The gradient used was 0 min 6% B, 73 to 83 min 31% B, 90 to 105 min 6% B. The DAD was used to monitor hydroxybenzoic acids at 280 nm, hydroxycinnamic acids at 320 nm, flavonols at 360 nm, and anthocyanins at 520 nm. The FLD was used to monitor flavan-3-ols, with excitation at 230 nm and emission at 321 nm. External calibration curves were prepared using chlorogenic acid for phenolic acids, rutin for flavonols, and cyanidin-3-glucoside for anthocyanins , at the following concentrations: 200, 150, 100, 75, 50, 25, 10, 5, and 2.5 mg/L. Catechin was used to quantify flavan-3-ols and standards were run at 150, 100, 75, 50, 25, 10, 5, 2.5, and 1 mg/L.

During the experiment conducted in the 2019 growing season, the kaempferol proportion increased in LR and ST treatments, but largest increase was measured when ST and LR were applied concurrently. Likewise, the higher the degree of exposure degree a greater kaempferol accumulation was observed during the 2017 growing season. The increase in kaempferol in total proportion of flavonols was accompanied with a concomitant decrease of quercetin and myricetin proportions. These results are corroborated with our previous work performed on Merlot and Cabernet Sauvignon., and by others on Cabernet Sauvignon, Nero d’Avola, Raboso Piave, and Sangiovese in Italy . We previously reported the proportion of kaempferol was a feasible tool for accounting the solar radiation received by berry due to the greater canopy porosity and this corresponded to the 1930 W·m−2 of global radiation accumulated at the research site in Experiment 3. On the other hand, the higher proportion of quercetin derivatives in detriment of myricetin derivatives found in LR vines has been related to down regulation of F3’5’H family genes . Previous work on red grapevine berries, indicated that IBMP content decreased with greater solar exposure due to the canopy management practices during berry ripening . In our work, the lowest IBMP content was measured in LRST berries. Our results indicated a negative and linear relationship between leaf to fruit ratio and IBMP content. Conversely, blueberry grow pot the relationship between kaempferol proportion and IBMP was not significant.

Therefore, our data suggested that the decrease of IBMP content was better explained by changes in the source-sink balance rather than differences in solar exposure. Likewise, Koch et al. provided evidence that solar exposure affected IBMP content to a greater extent when canopy porosity was enhanced before fruit set and not during berry ripening corroborating our results. The lower berry IBMP content was explained by a diminution of the accumulation rates rather than increased rates of degradation due to canopy management practices and restriction of applied water between fruit set and veraison in a warm climate.The total operating costs per hectare of a Cabernet Sauvignon vineyard in Napa County, CA U.S.A. is approximately US$ 40,382 . The labor operations costs of canopy management practices per hectare are 25% of the total costs. Our data indicated that although some berry traits were improved by the removal of shoots and leaves or the more common practice of doing them concurrently, their profitability is not ensured in warm climates. The unit cost to produce one unit of anthocyanin increased by about 10-fold with the additional canopy management practices. Therefore, the unfavorable leaf area to fruit ratios increased the cost of producing anthocyanins as previously reported by Cook et al. in Merlot grapevine grown in a warm climate. Likewise, the diminution of accumulation rates of IBMP were not as economically effective as once thought due to loss in yield and reduction in gross income per hectare for the grower. Finally, the breaking points determined through segmented regression analysis indicated that although increases in solar exposure led to significant IBMP content decreases , however, we were unable to elucidate this effect on anthocyanin content .

Since the effect of canopy management practices lead to higher solar exposure in hot climates that might be deleterious on grape quality, we aimed to elucidate the thresholds for maintaining anthocyanin content, while waiting for the target TSS required for fermentations and green aroma removal without compromising the yield. Although increasing canopy porosity through canopy management practices can be helpful for other purposes such as pest protection, this may not be the case of flavonoid compounds when a certain proportion of kaempferol is attained. Our data from these trials revealed different sensitivities to degradation within the flavonoid groups, flavonols being the only monitored compounds that were upregulated by solar radiation. Anthocyanin depletion was observed in all the trials with increasing solar radiation exposure . Under our experimental conditions, ST and LRST hastened fruit maturity; however, a clear improvement of the flavonoid compounds was not observed at harvest. On the other hand, all the canopy management practices studied decreased IBMP from mid-ripening to harvest. Therefore, although some berry traits were improved due to canopy management practices , this came with costs of labor and yield and gross income reduction that decreased flavonoid productivity per hectare; and these all should be assessed together when taking the decision to apply these treatments in hot climates.Grapes are profitable fruit crop that are widely grown in the state of California, with an increasing need to accomplish cultural tasks mechanically , 2020; Kurtural and Fidelibus, 2021. However, there are many factors that are currently challenging the productivity, quality, and sustainability in wine grape vineyards, one being the increasingly significant global warming trend affecting California and the whole world , where more frequent heat waves and continued warming of air temperature imposes great threats to vineyard yield, berry and wine composition .

Grape berry and wine quality are determined by the composition and concentration of secondary metabolites accumulated in berries. Flavonoids are the most abundant secondary metabolites and contribute to many quality determining traits, including color, mouthfeel, and aging potential of wine . There are generally three classes of flavonoids in wine grapes, including anthocyanins, flavonols, and proanthocyanidins. Anthocyanins are responsible for grape berry and wine color, and they are sensitive to external environmental conditions when clusters are exposed to solar radiation and heat, with overexposure resulting in anthocyanin degradation . On the other hand, flavonols tend to be positively related to solar radiation . Solar radiation, especially UV-B, can often up-regulate flavonols’ biosynthesis, resulting in more flavonols accumulated in berry skins. However, excessive solar radiation received and heat accumulated in California would accelerate the degradation of not only anthocyanins, but also flavonols, which will cause a decline in the antioxidant capacity of resultant wine and a possible reduction in wine aging potential . In viticulture, trellis system selection is a critical aspect grower needs to consider when establishing a vineyard. An ideal trellis can promote grapevines’ photosynthetic capacity through optimizing light interception by the grapevine canopy. Most importantly, a suitable trellis can optimize canopy microclimate by providing sufficient solar penetration into canopies since solar radiation is necessary to enhance the berry composition without excessive exposure of clusters to direct sunlight to avoid flavonoid degradation . There is evidence that grape clusters over-exposed to solar radiation are prone to occur with some of the widely used trellis systems. For example, vertical shoot position , a traditional and commonly used trellis system in viticulture production, has been found to produce canopies with high porosity which increases vulnerability of clusters to over-exposure , causing overly enhanced maturity and considerable degradation in berry anthocyanins . However, square plastic pot there is a lack of evaluations of the performance among various trellis systems in relation to the warming climate trends, and how their specific architectures contribute to variations in berry chemical profiles. In warm climates such as California, viticulture relies on irrigation for maintaining production, and previous work in the area showed that the application of different amounts of crop evapotranspiration can significantly modify polyphenolic and aromatic profiles in wine . Due to the increasingly frequent drought condition in many wine grape growing regions, recent studies have been focusing on the grapevine physiological and berry chemical responses towards specific levels of water deficits imposed by different ETc replacements, where water deficits are affective in manipulating grapevine water status, leaf gas exchange, components of yield, and berry composition: often, more water deficits applied to the grapevines would diminish photosynthetic capacities, but promote berry maturity . In some extremely drought conditions, however, severe water deficit might lower flavonoid concentration due to encouraged chemical degradation . Moreover, these effects resulted from different irrigation regimes can be modified by the canopy architecture as functions of trellis system since trellis systems can directly determine canopy sizes, hence resulting in different water demands from grapevines accordingly . On the other hand, over extraction of ground water to irrigate permanent crops have recently been questioned and legislation has been enacted in the state of California called the ‘Sustainable Groundwater Management Act’ . As a result, in some regions such as Napa Valley of California, grape growers will only be allowed to irrigate 120 mm per year. However, there is a lack of information on how the existing vineyards will cope with this water limitation in terms of irrigation scheduling. Therefore, the objectives of this study were to evaluate and compare 6 different trellis systems in combination with 3 irrigation strategies to understand the impact of trellis system and applied water amount on canopy architecture, grapevine physiology and berry composition. We hypothesized that traditional VSP systems would not be as efficient as the other trellis systems in terms of yield production and flavonoid accumulation, leading to greater berry flavonoid degradation and overall lower flavonoid concentrations.

The second subset of 20 berries was used for the determination of skin flavonoids from each individual treatment-replicate. Skins were manually removed from the subset of 20 berries and subsequently lyophilized . After lyophilization, dry skin weights were recorded and then, the dried skins were ground into fine powder with a mixing mill . 50 mg of the freeze-dried berry skin powder were collected, and the skin flavonoids were extracted with 1 mL of methanol:water:7M hydrochloric acid to simultaneously determine flavonol and anthocyanin concentration and profile as previously described by MartınezLüscher et al. . The extracts were stored overnight in a refrigerator at 4°C. In the next day, the extracts were centrifuged at 30,000 g for 15 minutes, and the supernatants were separated from the solids and transferred into HPLC vials after being filtered by PTFE membrane filters . Then, the samples were injected into HPLC for chromatographic analysis.Anthocyanin and flavonol concentrations in berry skin tissues were analyzed with a reversed-phase HPLC with the use of two mobile phases: 5.5% formic acid in water and 5.5% formic acid in acetonitrile. The specific method used for this study required a C18 reversed-phase HPLC column for the analysis . The flow rate of the mobile phase was 0.5 mL min- 1 and the flow gradient started with 91.5% A with 8.5% B, 87% A with 13% B at 25 min, 82% A with 18% B at 35 min, 62% A with 38% B at 70 min, 50% A with 50% B at 70.01 min, 30% A with 70% B at 75 min, 91.5% A with 8.5% B from 75.01 min to 90 min. The column temperature was maintained at 25°C on both left and right sides of the column. All chromatographic solvents were of high-performance liquid chromatography grade, including acetonitrile, methanol, hydrochloric acid, formic acid. These solvents were purchased from Thermo-Fisher Scientific . Detection of flavonols and anthocyanins was recorded by the diode array detector at 365 and 520 nm, respectively. Investigated anthocyanin derivatives included di-hydroxylated forms: cyanidin and peonidin, and trihydroxylated forms: delphinidin, petunidin, and malvidin; investigated flavonols included a mono-hydroxylated form: kaempferol, di-hydroxylated forms: quercetin and isorhamnetin, and tri-hydroxylated forms: myricetin, laricitin, and syrigintin. Post-run chromatographic analysis was conducted with Agilent OpenLAB software and identification of individual anthocyanins and flavonols was made by comparison of the commercial standard retention times found in the literature . Myricetin-3-O-glucuronide, myricetin 3-O-glucoside, quercetin 3-O-glucuronide, quercetin 3-O-galactoside, quercetin 3-O-glucoside, kaempferol 3-O-glucoside, isorhamnetin 3-Oglucoside, and syringetin 3-O-glucoside used for flavonol identification were purchased from Sigma-Aldrich . Flavonol molar abundant was calculated as the percentage of specific flavonol derivatives’ concentration over total flavonols’ concentration.The statistical analysis for the experiment was performed using MIXED procedure of SAS . All the datasets were first checked for normal distribution using a Shapiro-Wilkinson test before running the two-way MIXED procedure. A Tukey’s HSD post-hoc test was performed to analyze the degree of significance among the various measurements. The levels of significance ≤ 0.10 were the results that were considered for the Tukey’s post hoc tests. Season-long measurements of leaf gas exchange variables were analyzed for each year via three-way Analysis of Variance using the MIXED procedure of SAS using REPEATED option for measurement dates. A regression analyses was performed between variables of interest and, p values were acquired to present the significances of the linear fittings, as well as the regression coefficient .Both seasons were considerably arid as the experimental site only received 233.9 mm and 276.9 mm of precipitation from the previous dormant season until harvest in 2020 and 2021, respectively .

The glucose and insulin responses after mango intake were also moderated, compared to ingesting of an isocaloric amount of white bread. While the effects of mango intake on microvascular function were not as significant as the response from other whole foods, other measures of cardiovascular health, as well as glucoregulatory benefits, warrant further study.Epidemiological studies suggest that diets rich in carotenoids can be beneficial for vision, heart, bone health, cognitive performance, and cancer prevention. The current review focuses on the potential role of the xanthophyll carotenoids lutein and zeaxanthin in eye health, specifically their potential role in reducing risk of age-related macular degeneration . We review the absorption, distribution, and metabolism of L and Z, and the current dietary recommendations for these carotenoids, then speculate about their putative role in maternal and infant health. Lastly, we discuss the potential value of goji berry within the diet as a food with the highest known amount of Z. Carotenoids contribute to the bright red, orange, and yellow color in plants. These fat-soluble phytochemicals are classified into two categories: carotenes, dutch buckets system which include only hydrocarbons, and xanthophylls that also contain oxygen. While some dietary carotenoids serve as vitamin A precursors most of the approximately 100 carotenoids found in plants do not. Among the carotenoids devoid of vitamin A activity are L and Z, along with meso-zeaxanthin , a stereoisomeric metabolite of L.

Absorption involves enterocyte uptake by CD36, scavenger receptor class B type I , and Niemann-Pick C1-like transporter 1 at the apical membrane. Xanthophylls are then secreted through the basolateral membrane of the enterocyte, mainly by ATP binding cassette A1 and carried by lipoproteins to target tissues. SR-B1, SR-B2, and CD36 transport L and Z into the tissues. Steroidogenic acute regulatory domain protein 3 has been identified as a binding protein for L in the retina, and glutathione S-transferase pi isoform for Z. Lutein, Z, and meso-Z impart a distinctive yellow color to the fovea of primates – the specialized central area of the macular region of the retina that is rich in cone photoreceptors and optimized for high-acuity central color vision. The compounds have a maximal absorbance at a wavelength near 460 nm and are most concentrated in the inner and outer plexiform layers, which consists primarily of axonal connections between the retinal layers. Their combined density is greatest in the center of the macula and decreases with increasing retinal eccentricity. In the central fovea, the concentration of Z and meso-Z is higher than L at a ratio of 2.4:1. Lutein is most abundant in the peripheral macula, with a Z + meso-Z to L ratio of 1:2 when measured by highperformance liquid charomatography. However, a newer technique, confocal resonance Raman microscopy suggests that the Z + meso-Z to L ratio is as high as 9:1 at the central fovea. Protection from blue light is critical for eye health. Compared to longer wavelengths of visible light, short blue wavelengths are higher in energy and generate reactive oxygen species .

Zeaxanthin can provide stronger oxidant defense than L during photooxidation, while lutein has a greater capacity to absorb short wavelength light irradiation in lipid membranes.20 Compared to other carotenoids , L and Z are more effective in scavenging ROS and can also reduce phospholipid peroxidation. The photoreceptor-retinal pigment epithelium complex in the outer retina is particularly susceptible to ROS damage due to its high polyunsaturated lipid content . Quenching of singlet oxygen appeared best when L, Z, and meso-Z were mixed in equal ratios rather than separately when assessed in an eye tissue model, suggesting some synergy between the these macular pigments in their antioxidant properties. The most common method to quantify xanthophylls in the retina is to assess macular pigment optical density . This parameter is measured through techniques such as heterochromatic flicker photometry , a non-invasive psychophysical technique, fundus reflectometry, resonance Raman spectroscopy, or autofluorescence imaging. The MPOD index is associated with plasma levels of L and Z, and has been used to assess the risk for AMD. However, some studies report no correlation between MPOD and risk of AMD, which suggests that other ocular measures may be useful to obtain a more complete profile of AMD risk. In human donor eyes, the amount of L and Z was inversely associated with AMD. Supplementation of L, Z, and meso-Z have been shown to significantly increase MPOD in both healthy individuals and patients diagnosed with AMD. However, studies using foods rich in L and Z have produced inconsistent results, which may be due to the relatively modest amounts of these carotenoids in foods compared to supplements. Importantly, the plasma concentration of L and Z has been more strongly associated with MPOD than the correlation between MPOD and dietary intake. 

Age-related macular degeneration is the third leading cause of blindness worldwide after uncorrected refractive errors and cataracts. An estimated 288 million people worldwide are projected to suffer from AMD by 2040. In the United States, the prevalence of early-stage AMD was 9.1 million in 2010, and this number is projected to increase to 17.8 million by 2050. AMD is characterized by a gradual loss of eyesight from the central visual field.40 Although the exact etiology of AMD is not clear, common pathologic progress includes oxidative stress, lipofuscin toxicity, lipid accumulation, immune dysregulation, and choroidal hyperperfusion. Age-related processes such as a decrease in retinal neuronal elements, alterations in the size and shape of RPE cells, and thickening of Bruch’s membrane alsoparticipate in the pathology of AMD. Damage to mitochondria in RPE cells has also been suggested to play a role. Dry AMD, also termed non-exudative AMD, involves the formation of drusen, which are mainly lipid and protein deposits that accumulate between the RPE and Bruch’s membrane in the macula. In contrast, wet AMD, also termed exudative or neovascular AMD, is a consequence of abnormal blood vessel formation arising from the choroid, known as choroidal neovascularization . Clinically, AMD is classified as early or intermediate stage based on the size and number of drusen, as well as presence of pigmentary changes.46 The AMD is considered late or advanced stage in the presence of CNV, where fluid accumulation may result in damage to the neurosensory retina and fibrous scarring, or geographic atrophy , where loss of the RPE result in damage to overlying photoreceptors and underlying choriocapillaris causing irreversible vision loss. The main risk factors for AMD are aging and smoking, although some studies have shown no difference in MPOD between healthy older individuals and healthy young. Other risk factors may include race, obesity, previous cataract surgery, presence of cardiovascular disease, and hypertension. According to the U.S. National Institutes of Health, the prevalence of AMD is highest among Caucasians as compared to other races, and higher in females than in males. Genetic factors are also associated with AMD, with several high-risk single-nucleotide polymorphisms identified from genome wide association studies. The strongest risk variants include the Y402H variant of complement factor H gene as well as those in the age-related maculopathy susceptibility 2 locus. Whether the color of the iris or sunlight exposure are related to the risk of AMD is still being explored. Dietary interventions using L- and Z-rich foods have generated inconsistent results regarding the risk of AMD. In a cohort study that assessed dietary carotenoid consumption among individuals without AMD at baseline over more than 20 years, increased predicted plasma carotenoid score of L, Z, β-carotene, α-carotene and β-cryptoxanthin were associated with a lower risk of advanced, but not early or intermediate AMD. Similarly, dutch buckets a meta-analysis of six longitudinal cohort studies found that the dietary intake of L and Z significantly reduced the risk of GA by 26% and CNV by 32%, with no apparent impact on early stages. Another metaanalysis concluded that supplementation with L, Z, and meso-Z significantly increased MPOD levels in both AMD patients and healthy individuals in a dose-response manner.70 However, whether the improvement in MPOD could be sustained after L and Z supplementation is discontinued remains unclear. The Age-Related Eye Disease Study was a multi-center study that assessed the efficacy of a dietary anti-oxidant supplements on subjects who are 50 to 80 years old, with and without AMD or cataracts, for more than seven years. The initial study used a formula containing 15 mg of β-carotene, 500 mg of vitamin C, 400 IU of vitamin E, with or without 80 mg of zinc and 2 mg of copper.

Lutein and Z were not included because the scientific evidence to include these two carotenoids was not yet clear. Compared to the placebo group, participants consuming the antioxidants plus zinc and copper showed a 28% reduction in progression to advanced AMD after five years. Subsequently, the AREDS2 was conducted with a newer formulation that included vitamins C and E, either 10 mg of L plus 2 mg of Z, and either 350 mg of docosahexaenoic acid plus 650 mg of eicosapentaenoic acid , or both. Patients were also given either 25 or 80 mg of zinc, each with 2 mg of copper. Beta-carotene was eliminated from the supplement due to a potential increased risk of lung cancer among smokers, who were already at high risk for AMD. Primary analyses of the AREDS2 formula found no additional benefit in reducing progression to advanced AMD, in comparison to the original AREDS formula. However, in a secondary analysis of combined data from AREDS and AREDS2, the progression risk in those receiving L and Z was significantly lower than in other groups. Neither formulation reduced the progression from early to intermediate AMD. These clinical trials did not monitor the MPOD status over time, thus limiting our understanding of the link between L and Z intake, retinal accumulation, and AMD development or progression. To date, the AREDS2 formula remains the standard of care for management of patients with intermediate AMD.The accumulation of L and Z in the macula starts in utero in primates and plays a critical role in visual development and maturation later in life. Lutein and Z were detected as early as 20 weeks of gestation in macular tissue from human fetuses inspected at autopsy.15 Unlike fully matured human eyes, L is the dominant macular pigment in infants under the age of two regardless of eccentricities. The retina is less mature at birth compared to other eye structures, with complete differentiation requiring four to five years. The maturation of the macula is associated with a change in the L:Z ratio over the first four years of life, which correlates with the development of cone photoreceptors. Studies in premature infants illustrate the importance of these L and Z in visual development. In preterm human neonates, extremely low levels of serum L and Z are associated with an undetectable MPOD.79 When a carotenoid-fortified formula containing 211 µg/L of combined L and Z was given to preterm infants, plasma carotenoid levels became comparable to breastfed preterm infants, and were significantly higher than those fed formulas without L or Z fortification. In a small study that monitored the concentration of L and Z in various infant formulas and breast milk from different mothers, Z was not detected in any formula but was present in all breast milk samples, while L was consistently higher in breast milk. Serum L was also noted to be six-fold higher in breastfed infants compared to those fed with a formula devoid of L. Further studies are warranted to assess the prospective effects of L- and Z-fortified formula on MPOD and visual development in infants as they enter adulthood. Lutein and Z may also protect against oxidative damage in premature infants, especially those with retinopathy of prematurity . Premature infants with ROP usually have poor visual acuity, even after laser treatment or intravitreal injection of anti-vascular endothelial growth factor agents. In a model of oxygen-induced retinopathy, mouse pups given L showed less vessel leakage and lower avascular area compared to those given a L-free control. The authors suggested that the anti-oxidant properties of L may have contributed to these results, although ROS levels were not measured. Studies that investigate L and Z supplementation in ROP babies have produced inconsistent results.

For test management, the Raspberry Pi handles another thread responsible for converting the dataset into EEG signals that are acquired by the ADC. To avoid data overlapping in the process of writing—DAC—and reading—ADC—the samples, a synchronization method is used between the two threads. Synchronization involves multiple threads efficiently waiting for each other to finish tasks. Specifically, the ADC thread waits to read the data until the DAC finishes writing the data, and the DAC waits to write new data until the ADC finishes reading the previous one. The ADC thread stores the read samples in a buffer, from which the classification thread reads them. Figure 8 illustrates the block diagram of the algorithm of the system software. As for the hardware design of this work, a proof of concept EEG-based real-time identification system using Raspberry Pi is demonstrated that integrates all the components needed for the practical use of a real subject identification system. The execution of the thread parallelism has been performed without any problem, and all the threads are synchronized to achieve their tasks without any errors. The MSE is low with respect to the range of the data conveying high similarity between the original dataset and the data generated by the DAC, which demonstrates the reliability of the results obtained during the model evaluation stage. Finally, Raspberry Pi provides portability and allows the system to be integrated into a network; hence, grow strawberry in containers the information is accessible from anywhere. We plan to develop a system for EEG acquisition and integrate it with the current Raspberry Pi-based system. The development of an acquisition system will eliminate the use of converter DAC and the need for a pre-stored dataset.

The motivation for developing our device comes from the comparison of the different commercially available products. The devices found were developed only for acquisition purposes or for more complex applications and most of them are very costly. For this reason, we are motivated to develop our own end-to-end, low-cost, real-time device involving EEG acquisition from minimum necessary channels for EEG biometrics, preprocessing, feature extraction, and subject identification. In the future, to improve our device, we will perform a deeper analysis of the hardware by studying the power and time consumption and alternative technology for minimization of cost and size of the device. The civilian use of autonomous craft for scientific as well as commercial purposes has grown significantly in the last few years. A 2018 report from the National Oceanic and Atmospheric Administration detailed the use of un-crewed systems, UxS1 , for the agency. The number of types of un-crewed aerial vehicles employed by the agency doubled in a one year period and the number of total vehicles deployed increased by 38% for the same year. Use of other UxS by the agency show a similar trend. In the same report they detail the use of UxS from space to the ocean floor and nearly every environment in between. UxS are also used to monitor dangerous environments. A New York Times article from 2021 demonstrated the use of a novel autonomous surface vessel that collected video imagery from within the eye of Hurricane Sam. There are examples in the literature of the use of UAVs to monitor wildfires and indeed commercial products exist for that purpose. UxS are in use in commercial sectors as well. In agriculture, for example, many types of systems exist for crop health monitoring, water use monitoring, crop phenotyping, and even autonomous weeding for organic crop production. Othercommercial applications exist in film making, sports broadcasting, real estate sales, house cleaning, personal use, etc. UxS are even deployed on other planets.

NASA currently has an autonomous ground vehicle on Mars, the “Perseverance,” but also a UAV specifically designed for the thin atmosphere of the planet . Clearly the use of these systems is widespread and growing. At the same time the autonomy requirements for the systems are growing more challenging. The ASV cited in the New York Times article, for example, can be deployed on missions up to one year in duration and the Mars Rover mission duration is likely longer. The implication for these longer duration missions is that vehicles must have onboard path finding capabilities, automated data capture and sample analysis, failure detection algorithms, data storage, and communication abilities to name just a few. Processing power requirements for autonomous systems are increasing as well, driven by the need for computationally expensive operations such as onboard computer vision, LiDAR sensor processing, and for evaluating machine learning models for object detection, image classification, and natural language processing. Longer duration missions and navigating complex environments place additional demands on the onboard processors. Finally, interacting in multi-agent environments, that is, environments with multiple autonomous systems adds dramatically to the complexity of the control system. Designing a modern autonomous system involves significant engineering effort and requires expertise in multiple areas. Given the widespread interest and use of autonomous systems there exists a need for a vehicle-agnostic controller—or autopilot—to enable the research and development efforts for new vehicles and new vehicle types. This autopilot should be capable of real-time computation ; easily modifiable in order to adapt to different vehicle configurations; and open-sourced in order to be accessible to a wide audience of users and contributors.

Furthermore, the autopilot may form the real-time core of a larger, distributed control system that also includes a single board computer for non-real-time tasks and a tensor processing unit to enable onboard ML capabilities. This architecture allows a developer to take advantage of the advancements in computing for SBCs and TPUs as well as to solve the issue of handling real-time tasks and non-real-time tasks simultaneously. To enable a distributed control system the autopilot must integrate with the external modules using a standard interface and a lightweight, extensible binary communication protocol. This architecture offers unique capabilities for autonomous vehicles. There are several sub-problems that can be specifically addressed with this architecture. The first is the means to develop and integrate real-time algorithms such as state estimation and vehicle control onto the autopilot. The embedded firmware operates using the simplest structure possible, with a hardware timer to dictate sensor and control update intervals. This structure allows an algorithm or sensor measurement to be encapsulated into a single function and therefore replaced or modified with minimal disruption to the remainder of the firmware. The controller can be adapted to any type of vehicle with relative ease, for example, or to evaluate different state estimation algorithms by changing one function and recompiling the firmware. Second, the SBC enables new capabilities for autonomous vehicles. Typically, the SBC has a Linux operating system providing access to standard functionality such as file storage, internet access, camera integration, USB devices, and running WiFi access points. These capabilities allow storage of sensor and vehicle state information into files from the vehicle, run mission planning software, or connect to USB peripherals such as the TPU. The OS also opens up extensive capabilities provided by open source software. For example, scientific software such as SciPy, computer vision software , ML packages , or even convex optimization software are all readily available to download onto the SBC. These advanced computational packages enable capabilities such as optimal trajectory generation, hydroponic nft channel mapping of landmarks, and advanced vision sensors. Finally, the TPU is a specialized processor that is designed to speed up ML inferencing tasks. The increased use of machine vision has made the need for onboard ML capabilities an attractive feature for many types of autonomous systems. It enables fast object detection or image classification without placing a computational burden on the SBC. For example, object detection allows for identification of landmarks or obstacles.

The TPU integrates seamlessly with the SBC via a USB interface and as in the case of the SBC runs open source software if possible. In summary, the increasing demands on autonomous systems and the technological advances in SBCs, TPUs, and sensing technology, suggest that a modular, distributed control system that includes a dedicated real-time autopilot is needed for the development of new autonomous vehicle classes. Small, resource-constrained systems benefit the most from this architecture and motivate this work. Given the proliferation of autonomous systems it is somewhat surprising that real time controllers are not more ubiquitous, few of the ones that do exist use open source firmware, and fewer still have open source hardware. The most promising one is a vehicle-agnostic control system: the modular rapid prototyping system, R2P. The project hardware and software are both open source. The system is designed so that each sensor or actuator is a standalone module called a node. The authors have developed a publisher-subscriber middleware to connect the nodes, a protocol called RTCAN. A series of connected nodes form the robot architecture. One downside to this approach is that the developer is restricted to the modules that have been developed for the system, that is, the system doesn’t have the ability to communicate directly with off-the-shelf sensors, nor can they easily be created by the user. Furthermore, each module is separately controlled with its own microcontroller and has an RJ45 wired connector so a complex system rapidly becomes unwieldy with many small boards wired together. Another downside for optimal real-time performance is the use of a real-time operating system , specifically the ChibiOS/RT. This is a powerful, lightweight and widely-used RTOS with a hardware abstraction layer that allows for re-use of peripheral drivers across different hardware platforms. However, modifying the firmware of a given module for a custom algorithm may be difficult to debug for real-time performance. For example, the inertial measurement unit module has its own attitude estimation algorithm encoded in it. If a developer needs a different attitude estimation algorithm it may be challenging to implement it and still guarantee the latency needed for the application. Nevertheless this system allows robot developers a path to quickly build and test a prototype robot, particularly if autonomy isn’t required and size of the control system is not a factor. An open source autonomous vehicle platform is found in the literature, the F1/10 platform. Although the project labels itself as an autonomous cyber-physical system platform, it is a 1/10 scale race car, employing an NVIDIA Jetson TX2 SBC running the Robot Operating System middleware. While this is a powerful SBC and ROS is a widely adopted middleware for robots, it is not real-time. In fact, the recent launch of ROS2 in part is due to the need for lower latency operations—a closer approximation to real-time, although it isn’t strictly real-time as it continues to operate on the Linux OS. In any case, this project is dedicated to a specific racing platform and therefore not easily adapted for other purposes. Aerial vehicles provide the richest source for real-time controllers, some of which have been adapted to different classes of vehicles. Table 1.1, adapted from a recent survey of open source UAV hardware controllers list the ones active as recently as 2018. Most of the platforms listed that use the STM microcontroller are designed to operate with an RTOS as the middleware, with the autopilot firmware loaded over it. The exceptions to this is the Chimera, which uses the Paparazzi autopilot firmware which has both an RTOS based firmware as well as a ‘bare metal’ implementation2 . The most prevalent autopilot firmware packages are PX4, Ardupilot, and LibrePilot . The other devices in the table, FlyMaple, APM2.8, Erle-Brain and PXFmini are no longer available. Both PX4 and Ardupilot support non-aerial vehicles to some extent. However, modifying the firmware within the RTOS is notoriously challenging due to the complexity of the code base. It is particularly difficult to implement a new vehicle type but also challenging to guarantee that latency requirements are met when modifying the estimation or control algorithms. These firmware packages are better suited to projects where modifying any of the underlying algorithms isn’t desired. The topic of an RTOS versus a bare metal application merits further discussion and will be covered in a later chapter.There are many papers on self-driving cars that describe vehicle control systems but very few discuss ones suitable for resource-constrained vehicles. For example, demonstrates a distributed architecture of a full size autonomous racecar that requires computational resources far beyond those available to resource-constrained systems. One exception to that, however, comes from, which reviews four different architectures with a focus on how resource-constrained systems can inform design choices for full size vehicles.

Through our work, we demonstrated a way to map out the Berry curvature distribution over the Brillouin zone and provide a direct probe of the topological character of strongly spin-orbit-coupled materials. This stands in contrast with transport measurement of spin and charge which reflect the global momentum-space average of the Berry curvature. In this regards, CD-ARPES can be a useful experimental tool to investigate certain aspects of the phase in electron wave functions if one can disentangle different contributions in the CD-ARPES. This work was supported by Research Resettlement Fund for the new faculty of Seoul National University and the research program of Institute for Basic Science . S. R. P. acknowledges support from the National Research Foundation of Korea . The Advanced Light Source is supported by the Office of Basic Energy Sciences of the U.S. DOE under Contract No. DE-AC02-05CH11231.In the momentum space of atomically thin transition metal dichalcogenides , a pair of degenerate exciton states are present at the K and K’-valleys, producing a valley degree of freedom that is analogous to the electron spin. The electrons in the K and K’-valleys acquire a finite Berry phase when they traverse in a loop around the band extrema, with the phase equal in magnitude but opposite in sign at the K and K’-valleys, as required by the time-reversal symmetry. The Berry phase not only has close connections to the optical selection rules that allow optical generation and detection of the valley-polarized carriers by circularly polarized photons, dutch bucket for tomatoes but also plays a central role in novel electron dynamics and transport phenomena in TMD and graphene layers, such as the valley Hall effect.

In principle the Berry phase, together with other effects from inversion symmetry breaking, can have profound consequences for the wave function and energy spectrum of the excited states in two-dimensional materials. TMD monolayers are known to host strongly bound excitons with a remarkably large exciton binding energy due to enhanced Coulomb interactions in 2D. It was recently predicted that the Berry curvature of Bloch states can add an anomalous term to the group velocity of electrons and holes and creates an energy splitting between exciton states with opposite angular momentum. Fig. 1a shows a simplified exciton energy spectrum illustrating the exciton fine structure based on our ab initio GW-Bethe-Salpeter equation calculations. The 2p+ and 2p− exciton states are split in energy with opposite order for the K and K’ valleys due to the opposite chirality in the two valleys. Such novel exciton fine structure, which embodies important wave function properties arising from the Bloch band geometry, can strongly modify the intraexcitonic light-matter interactions. Experimental observation of this predicted exciton spectrum, however, has been challenging, because it requires new spectroscopic probe that can distinguish both the momentum valley and the exciton angular momentum. Here, we report the first observation of the Berry-phase effect in the exciton spectrum of MoSe2 monolayer using intraexciton optical Stark spectroscopy. We demonstrate that the degeneracy between the 2p±-exciton states is lifted by the Berry phase effect, and enabling a valley-dependent Autler-Townes doublet from strong intraexciton light-matter coupling.

We coherently drive the intraexciton transitions using circularly-polarized infrared radiation, which couples the 1s exciton to the 2p+ or 2p− states selectively through the pumpphoton polarization . The pump-induced changes in the 1s exciton transition are detected by circularly polarized probes, which selectively measure the K or K’-valley excitons. Independent control of pump and probe photon polarization enables us to distinguish the exciton fine structures in the K and K’-valleys. We determine an energy splitting of 14 meV between the 2p+ and 2p− exciton states within a single valley, and this energy splitting changes sign between K and K’-valleys. We determine the 1s-2p transition dipole moment to be 55±6 Debye. This leads to an optical Stark shift that is almost 40 times larger than the interband counterpart under the same pump detuning and driving optical field strength. Such strong and valley-dependent intraexciton transitions open-up new pathways for the coherent manipulation of quantum states in 2D semiconducting materials using infrared radiation. To investigate the fine structure of the excitonic p-manifold, we fabricated a high quality MoSe2 monolayer that is encapsulated in hexagonal boron nitride layers using mechanical exfoliation and stacking following Ref. 21. The sandwiched hBN-MoSe2-hBN heterostructure was then transferred to an alumina-coated silver surface . The device was kept in vacuum at 77K for all optical measurements. This Aexciton peak arises from the optical transition between the ground state and the lowest energy 1s exciton state in MoSe2 monolayer, which is well-separated from the higher-lying exciton states due to strong Coulomb interactions in TMD monolayers10,11,20,24. We use intraexciton optical Stark spectroscopy with helicity-defined pump and probe light to selectively access the 2p+ or 2p− exciton states in the K and K’-valleys.

Quantum-mechanical coupling between the infrared photon field and the 1s-2p+ electronic transition leads to an avoided-crossing behavior that modifies the 1s-exciton state systematically with the changing infrared photon energy, as illustrated in Fig. 1d. When the infrared photon energy is below the 1s-2p+ resonance, the non-resonant hybridization leads to a decreased energy for the 1s exciton state.Since the infrared pump photon energy is much lower than the transition energy of 1s exciton, our measurement scheme probes only the coherent optical Stark effects without non-coherent contribution from real carrier generation. The colors in Fig. 2a-c represent the pump-induced change of the probe reflectivity Δ R, which is directly proportional to the change of absorption. The positive Δ R, is proportional to the decrease of absorption. The horizontal and vertical axes show the probe energy and pump-probe time delay, respectively. Strong transient signals are present for pump-probe delay closed to zero and they become negligible at pump-probe delays larger than 500fs. These instantaneous signals confirm the optical responses arise from coherent optical Stark effects.The evolution of the 1s exciton absorption in monolayer MoSe2 under coherent infrared driving can be better visualized directly from the optical absorption spectra characterized by the imaginary part of optical susceptibility.It shows clearly that the 1s exciton transition exhibits avoided-crossing behavior in both valleys, which evolves gradually from energy blueshift to splitting and then to redshift as the pump photon energy is decreased. It shows that the 1s-2 p+ intraexciton transition energy differs by 14 meV for the K and K’ valleys. Due to the time-reversal symmetry between K and K’-valleys in MoSe2 monolayer, this observation also indicates that the 2p+ and 2p− exciton states are non-degenerate and has an energy difference of 14 meV in a single valley. We further plot the blue- and red-shifted 1s resonance as a function of the infrared pump photon energy in Fig. 3b. We find that the energy shifts induced by the intraexciton optical Stark effect are almost 40 times larger than its interband counterpart at the same pump intensity and resonance detuning. To better understand the experimental results, we performed ab initio GW-BSE calculations using the BerkeleyGW package to determine the exciton energy levels and optical selection rules of exciton and intraexciton transitions in monolayer MoSe2. In these calculations, blueberry grow pot environmental screening effects from the hexagonal boron nitride encapsulation layers are included from first-principles . The simulation confirms the energy level diagram of the 1s, 2p+, and 2p− excitons and the optical selection rules in K and K’- valleys in Fig. 1a. Our calculations find that the energies of the 1s and 2p− exciton states are separated by 117 meV, with 2p+ exciton states further separated by 7 meV in K-valley. The energetic order of 2p+ , and 2p− excitons states is opposite in the K’-valley, as a result of time-reversal symmetry. Although the 2p± excitons are dark in linear optics, they are optically active when coupled to the 1s exciton with circularly-polarized light . The 1s-2p− intraexciton transition, on the other hand, coupled exclusively to the right-handed circularly polarized light. The experimentally observed intraexciton dipole moment and valley-dependent exciton fine structure match reasonably well with the ab initio GW-BSE calculations. The combination of 2p±-exciton splitting and extremely strong intraexcitonic light-matter interaction allow us to observe valley-dependent Autler-Townes doublets at higher pump intensity in MoSe2 monolayer. Towards this goal, we fabricated a hBN-encapsulated MoSe2 heterostructure on a zinc-sulphide substrate, where the local field factor on the sample for the infrared pump light is more favorable than that for MoSe2 on alumina coated silver substrate . In this device the 1s-2p+ intraexciton transition energies for the K and K’-valleys are determined to be 150 meV and 138 meV, respectively .This Autler-Townes doublet leads to a valleydependent electromagnetically induced transparency in the 1s exciton transition, where the absorption at the 1s exciton resonance is reduced by more than 10-fold compared to the undriven exciton . Our findings offer a new and effective pathway to coherently manipulate the quantum states and excitonic excitations using infrared radiation coupled to the 1s-2p+ intraexciton transition.Sample Fabrication. The MoSe2 monolayer encapsulated in hBN flakes were prepared with a polyethylene terephthalate stamp by a dry transfer method21. Monolayer MoSe2 and hBN flakes were first exfoliated onto silicon substrate with a 90 nm oxide layer. We used PET stamp to pick-up the top hBN flake, monolayer MoSe2, and bottom hBN flake in sequence with accurate alignment based on an optical microscope. The hBN/MoSe2/hBN heterostructure was then stamped on a silver substrate coated with a 85 nm alumina layer or on a zinc sulphide substrate.

Polymer and samples were heated to 60oC for the pickup and 130oC for the stamping process. Finally, the PET was dissolved in dichloromethane for 12 hours at room temperature. The sample temperature was kept at 77 K in a liquidnitrogen cooled cryostat equipped with BaF2 window during optical measurements. Intraexciton Optical Stark Spectroscopy. Pump-probe spectroscopy study is based on a regenerative amplifier seed by a mode-locked oscillator . The regenerative amplifier delivers femoto second pulses at a repetition rate of 150 kHz and a pulse duration of 250 fs, which were split into two beams. One beam was used to pump an optical parametric amplifier and the other beam was focused onto a sapphire crystal to generate super continuum light for probe pulses. Femto second mid-infrared pump pulses with tunable photon energies were generated via difference frequency mixing of the idler pulses from the optical parametric amplifier and residual of fundamental output from regenerative amplifier in a 1 mm thick silver gallium sulphide crystal. The mid-infrared pulse duration is ~350 fs. The pump-probe time delay was controlled by a motorized delay stage. The helicity of pump and probe pulses was independently controlled using Fresnel rhomb and broadband quarter-wave plates, respectively. The experiment followed a reflection configuration with a normal incidence and collinear pump-probe geometry, where the absorption spectra are extracted from the reflectance contrast as described in the supporting information.This work was primarily supported by the Center for Computational Study of Excited State Phenomena in Energy Materials, which is funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05CH11231, as part of the Computational Materials Sciences Program which provided the experimental measurements and GW-BSE calculations. The sample fabrication and linear optical spectroscopy was supported by the US Army Research Office under MURI award W911NF-17-1-0312. The pump-probe setup was supported by the ARO MURI award W911NF- 15-1-0447. This research used resources of the National Energy Research Scientific Computing Center , a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and the Extreme Science and Engineering Discovery Environment , which is supported by National Science Foundation grant number ACI-1548562. S.T. acknowledges support from NSF DMR-1552220. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST , JST. E.C.R acknowledges support from the Department of Defense through the National Defense Science & Engineering Graduate Fellowship Program. C.-K.Y. and C.S.O. acknowledges useful discussion with Prof. Ajit Srivastava. Viruses are obligate intracellular pathogens that require living host cells to replicate and spread in the infected plant. During compatible interactions, viruses overcome the plant immune system and hijack host cellular processes to establish active infections .