The LPP had an extraction rate comparable to the SPP, showing that the particle size had no significant effect on the extraction rate. In summary, when using WPP for antioxidant extraction, higher TEY, TPY, and TPC can be achieved by increasing the extraction temperature, time, and solvent ratio. The DSA was independent of the extraction time and solvent ratio but decreased with the increase in extraction temperature. The two groups of peel particles, with average particle sizes of 0.60 and 0.38 mm, respectively, had no significantly different effects on the extraction of phenolics with varied extraction temperature, time, and solvent ratio. The highest TEY, TPY, and TPC obtained were 57.83%, 12.80%, and 22.06%, respectively. The DSA ranged from 5.37 to 6.35 g g-1. The results indicated that extraction of phenolics from peel particles, produced by grinding to less than 0.6mm with a large cutting head, at a temperature of 20°C for 6 min using a solvent ratio of 4:1 could be the most economical and sustainable approach for industrial-scale production. The chromatogram obtained from the HPLC, showing the peaks of major compounds in the peel extract, including gallic acid, ellagic acid, punicalagin , and punicalagin , is shown in Figure 2.5 a. The contents of the four major phenolic compounds produced by the five groups of extraction conditions are shown in Figure 2.5 b. The gallic acid content significantly improved, from 0.17 to 0.29 mg g-1 , with the increase in solvent ratio from 1:1 to 4:1. Except for the group with a 1:1 solvent ratio , the gallic acid contents obtained with the other groups with different solvent ratios varied from 0.27 to 0.35 mg g-1 and were not significantly different, regardless of the time and temperature. The ellagic acid content varied from 0.77 to 1.51 mg g-1, with no significant differences among groups G3, G4, and G5. The solvent ratio mostly influenced punicalagin. At the same extraction conditions, the punicalagin content increased from 2.13 to 4.48 mg g-1 when the solvent ratio increased from 1:1 to 8:1. In addition to the solvent ratio ,snap clamps ABS pvc pipe clip the extraction time and temperature affected the extraction of punicalagin , which can be seen from the increased punicalagin content from 7.51 mg g-1 to 9.17 mg g-1 .

The punicalagin purity ranged in order of G2 > G4 > G5 > G3 > G1, and the corresponding values were 88.99%, 88.27%, 87.73%, 87.64%, and 85.93%, respectively. Qu et al. compared the gallic acid, punicalagin, punicalagin , and ellagic acid concentrations of different pomegranate products. The results presented in this study showed significantly higher retention of punicalagin than the pomegranate peel extract using dried peel particles used by Qu et al. . The WPP extraction in this study also achieved slightly higher phenolic concentrations compared to Langers 100% pomegranate juice. To study the effects of drying, DPP was produced using HA drying and IR drying, and the peel compositions and phenolic extraction conditions were compared between DPP and WPP. The compositions of WPP and DPP on a dry basis are shown in Table 2.5 Composition of fresh and hot-air dried pomegranate peel. . The WPP had higher contents of protein, ash, and crude fat than the DPP. The loss of these contents was reduced by avoiding the drying process. On the other hand, the HA DPP maintained higher total dietary fiber at 25.44%, and the ratio of insoluble dietary fiber to soluble dietary fiber was 8.84. This was higher than the values for WPP, which maintained 17.19% TDF and an IDF/SDF ratio of 4.93. Morais et al. compared the compositions of raw, freeze-dried, and oven-dried papaya peels. They reported similar findings for the differences in fiber content, but the differences were not statistically significant. Figure 2.6 shows the TEY, TPY, DSA, and color characteristics of IR DPP, HA DPP, and WPP. The DPP resulted in significantly lower TEY, TPY, and TPC than the WPP. The DSA values were similar for both DPP and WPP at about 6.41 g g-1. In other words, extraction from WPP resulted in 10% more extract yield and 2.5% more TPY with similar DSA compared to DPP. Loizzo et al. investigated the phytochemical contents of extracts from fresh and processed peel and pulp. Compared to steamed, baked, and microwaved pulp, extraction with fresh pulp achieved up to 0.9% higher TEY and twice the TPC. Their results demonstrated that extraction with fresh peel or pulp could reduce the phytochemical loss that occurs during the drying process. Similarly, Mphahlele et al. compared the bio-active compounds in fresh peel and hot-air dried peel at 40°C, 50°C, and 60°C. As for color, extraction of WPP achieved significantly higher L* , a* , b* , and C* values.

The results demonstrated statistically higher retention of L* and a* values using WPP. According to Cadena et al. , changed color characteristics indicate the formation of caramel-colored pigments resulting from nonenzymatic processes, which are related to lower sensory acceptance. Therefore, extraction from WPP could be a more suitable method for the extraction of polyphenols for use in food product development and supplementation. PCA was applied to explore the interdependence among variables. Observations consisted of the average sub-sampling results from the 30 aforementioned extraction conditions at different extraction times, temperatures, and solvent ratios. Four vectors were estimated based on the eigenvectors of the correlation matrix of four variables: total extract yield , total phenolic yield , total phenolic content , and DPPH scavenging activity . The eigenvalues of F1 to F4 were 2.548, 0.899, 0.544, and 0.008, and the first three PCs accounted for 63.70%, 22.48%, and 13.61% of the sample variance, respectively, and represented 99.79% of the total variance in cumulation . Biplots of the observations and variables show the data distributions of F1-F2 and F1-F3. Confidence ellipses with 99% confidence intervals were used for each set of experiment groups, and no outliers were detected. PCA weighting scores of the four measured variables are listed in Table 2.6. For instance, TEY and TPC were positively correlated with the F1 axis, whereas TPY and DSA were negatively correlated. In addition, TEY and TPY were positively correlated with the F2 axis, while DSA was negatively correlated with the F3 axis. Figure 2.7 also shows the data distribution for F1-F2 and F1-F3. For instance, the data point with a higher F1-axis value had higher TPC, which was extracted at 60°C for 6 min using a solvent ratio of 8:1. This was following the experimental results, indicating that PCA can be applied for future condition prediction. Extraction of bio-active compounds from waste fruit peel is an efficient approach to improve food system sustainability and industry profitability.

This study developed a novel green process for antioxidant extraction from wet pomegranate peel and investigated the effects of extraction conditions on polyphenol yield and quality, including phenolic composition, DPPH scavenging activity, and color characteristics. PCA condensed the multivariable analysis into three factors, which explained 99.79% of the variance and could be suitable for future process development. Three parameters, including drying preparation, extraction temperature, and solvent ratio, significantly influenced the extraction rate. Considering water usage and energy consumption, WPP extraction at 20°C for 6 min with a solvent ratio of 4:1 is recommended as an economic and sustainable process, resulting in 10.53% total phenolic yield with 88.93% punicalagin purity. Overweight is raising concern worldwide due to its high prevalence and various adverse health outcomes. According to a report from World Health Organization, an adult with Body Mass Index between 25.0 to 30.0 is defined as overweight, and over 1.9 billion adults worldwide were overweight in 2016, accounting for 39% of the population . Being overweight can further induce obesity when BMI increased beyond 30.0. These two statuses are major risk factors of physical and mental illness. Wilson et al. conducted 44-year follow-up research on 5209 participants aged 30 to 62 years from the Framingham cohort . Results showed that being overweight was related to elevated cardiovascular risks, including hypertension , angina pectoris , and coronary heart disease . Calle and Kaaks reviewed obesity and obese-related epidemiological studies. An increased risk of cancers was noted from 1.2-2 folds, including colorectal, endometrial, kidney, and oesophageal cancer . BeLue et al. studied the relation between mental healthiness and overweight in youth aged 12 to years in different races and ethnicity . Their results revealed that overweight white and Hispanic youth possessed a higher percentage of self-reported depression, anxiety,greenhouse snap clamps and other mental and behavioral problems. Various causes contributed to being overweight. Among them, a calorie-dense and nutrient-poor diet is a major contributor along with a lack of exercise. Standard American Diet is a typical western diet that includes excess natural and added carbohydrates, fats, and sodium while lacking in consumption of fruits, vegetables, and whole grains . Improving the diet pattern for weight control is in need. Diet with the addition of phytochemicals, such as polyphenol, demonstrated positive health outcomes on weight management. Studies have suggested that polyphenol modulated the plasma and hepatic cholesterol in a few possible mechanisms, including inhibiting enzymes related to intestinal carbohydrate digestion and glucose absorption , inhibiting pancreatic lipase activity and fat absorption from the intestine , promoting β-oxidation of fatty acids , increasing bile excretion to eliminate the cholesterol , and regulating the gut microbiota towards a leaner composition .

Pomegranate peel is a common underused fruit by-product from the juicing process and consists of up to 53.01% of the fruit weight . The high molecular weight polyphenols in the pomegranate peel are the major high-value phytochemicals and have been proven associated with reduced risks of chronic diseases , including type 2 diabetes and cardiovascular diseases . Among all the polyphenols in pomegranate peel, gallic acid , ellagic acid , punicic acid, and punicalagin-α, -β are responsible for most health benefits . It was worth noting that punicalagin is unique in pomegranate peel and demonstrated the greatest antioxidant activities with abundant hydroxyl groups, which can trap peroxyl radicals to reduce oxidation . Therefore, pomegranate peel is a promising source for polyphenols. By far, nearly all the studies of health benefits in pomegranate peel utilized liquid extractable polyphenol. Limited research focused on the pomegranate peel as a whole. Labib and Hossin characterized the effects of pomegranate peel powders and extracts on obese hypercholesterolemic rats solely from anthropometric and serum lipid. Insights of hepatic lipid profile were missing and the regulating mechanisms were not investigated in their study . Moreover, research has shown that the polyphenol and fiber in the food matrix might have a synergistic effect to promote health . Therefore, the objectives of this research were to compare the hypolipidemic properties of PPP and PPE and investigate the regulating mechanisms by supplementing the high-fat diets with different percentages of PPP and PPE to male Syrian hamsters. Pomegranate peel of Wonderful variety was collected from a juicing plant located in Buttonwillow, California in October of 2017. The peel was processed based on Wu et al. . In summary, the peel was sliced and ground into particles less than 0.6 mm. Then extract was obtained by mixing the peel particles with 4 times of water at 20 ⁰C for 6 mins, then filtered before administration to the hamsters. The male Syrian hamster was used since it possessed similarities of hepatic cholesterol and bile acid metabolism with humans compared to other rodents . The compositions of peel powder and extract were listed in Table 2.5. The study was approved by the Animal Care and Use Committee, Western Regional Research Center, USDA, Albany, CA, USA. 45 male golden hamsters were acclimatized for 2 weeks. They were fed with Purina Rodent Laboratory Chow and individually raised in a 20−22 °C environment with relative humidity at 60 %, and 12 h alternating light/dark cycle. After that, 45 hamsters were randomly divided into five groups for each diet as indicated in. A high-fat diet with 20% fat energy intake was set as a control group. 5 and 10% of lyophilized PPP were supplemented into the HF diet ad libitum to evaluate the dose effects. In correspondence, 2.5 and 5% of lyophilized PPE addition were applied to investigate the effect of supplementation form. In this way, LP/LE group contained nearly 8.68 mg soluble phenolic compounds per kg body weight, and HP/HE group doubled the content. These dosages corresponded to approximately 70 mg and 140 mg per day in a 60 kg human according to the Km factor ratio of 5 and 37 for hamsters and humans , respectively .

Furthermore, previous work on apple and pear flowers has revealed considerable overlap in the identity of microbes associated with each host species . Such overlap, in addition to a reduction in diversity with increasing land cultivation, suggests a role for several key processes in shaping floral microbiomes in tree fruits. First, there is a high degree of shared usage of disease and pest management practices employed in pear and apple production systems, as both can suffer greatly from fire blight disease. Inputs applied in conventional and bIPM orchards, including antibiotics and fungicides , can act as strong environmental filters on potential floral colonists or serve as a source for inocula when applied as biologicals, as observed in organic orchards. Second, both apple and pear systems rely considerably on honeybees for pollination, which are known to leave a distinct imprint on floral microbiome diversity . Increased reliance on a single-pollinator species, combined with chemical and nonchemical inputs, are likely important contributors to patterns observed.Orchard management scheme was a key determinant of bacterial community similarity across sites; however, other predictors often explained high levels of variance in community structure across sites. In particular, geographic distance explained a significant amount of variance in both whole-community and taxon-related beta diversity of bacteria. In contrast, for fungi, geographic distance was a significant predictor of only abundance-related turnover. Beyond geographic distance, climatic conditions also contributed significantly to explained variance in the beta diversity or community turnover of fungal communities. In particular, VPD and temperature were negatively associated with fungal diversity, suggesting both microclimate variables affect either species-specific patterns of growth and/or competition. Moisture availability is also an important determinant of microbial growth on the surface of plant tissues , with free water and humidity often being necessary for conidial germination, germ tube growth,plant pot with drainage and potential penetration of plant tissues, including floral organs. This has been frequently observed in other flowering systems of commercial value, including blueberries , raspberries , strawberries , and cut roses .

Within these systems, infection of the gynoecium can be a primary route of disease development. Alternatively, infection of petals and other organs can facilitate secondary infections of fruits . Of the fungal genera examined in our study, Botrytis has been documented to successfully infect the mesocarp via stamen filaments . For the others of interest, it is unclear if there is a link between flower colonization and resulting development and pre- and post harvest diseases. More broadly, our results provide insight into local- and landscape-level drivers of floral microbiome diversity in an important tree fruit commodity, pear. Given the critical link between flowers, yield, and disease, identifying such drivers across both spatial and temporal scales could improve the understanding of links between management, host microbiome structure, and potentially disease resistance or susceptibility. With growing appreciation for the role of host microbiota in affecting resistance against disease , such information has potential to inform development of sustainable management practices in many different types of agroecosystems.We surveyed 15 orchards throughout the Wenatchee River Valley of central Washington in spring 2018. Within the United States, Washington State is the leading producer of deciduous tree fruit crops such as apples, pears, and cherries. These, as well as other commodities, are grown in variable intermountain river valleys and basins east of the Cascade Mountains. These production areas generally experience temperate, dry conditions, in addition to favorable access to irrigation water originating from streams and rivers fed by snowmelt . Given the diverse topography of this region, however, individual orchards range in elevation from 20 to 1,000 m above sea level . Key stages of fruit production, such as flower bloom, can thus experience considerable variation in microclimatic conditions among orchards, affecting bloom timing, fertilization, and fruit development . As flowers are a habitat for diverse microbiota , including a number of pathogenic species that cause pre- and post harvest diseases of tree fruits , microclimatic conditions could affect habitat quality, as well as colonization dynamics and the resulting structure of the floral microbiome. Our survey assesses microbe communities in orchards that used one of three management schemes, with five replicates per scheme, which include organically certified, conventional, and biological-based integrated pest management .

With each of these broad management types, growers were not restricted to a specific spray schedule, but each used a defined set of tools for pest and disease management . Conventional management followed a standard practice , while organic orchards were all managed following USDA-certified organic standards, which prohibits use of such synthetic chemicals. To control fire blight, organic producers often use Serenade Opti at full bloom, a bio-based fungicide and bactericide that leverages Bacillus subtilis endospores and its metabolic by-products as active ingredients . Serenade is not the only bio-based product leveraged by producers for control of fire blight in pear, however, and other products such as Blossom Protect can be used across organic, bIPM, and conventional schemes. Blossom Protect is derived from air-dried spores of Aureobasidium pullulans , an epiphytic or endophytic fungus associated with a wide range of plant species, including many tree fruits. For those orchards that employed the bIPM scheme, growers used a toolbox of cultural controls combined with pesticides with less documented negative impact on natural enemies and other beneficial organisms.Such products included lime sulfur, kaolin, spinosad, and biologicals applied at various stages of bloom . Orchards were sampled once at peak bloom, either on 30 April or 1 May of 2018. At each orchard, 10 trees were sampled, 5 near the edge of the orchard and 5 in the interior. We chose this approach because previous studies suggest that seminatural habitat in the surrounding landscape can both support and increase rates of visitation by native pollinators such as bees and flies . Moreover, pollinators can be important dispersal agents for microbes ; thus, our aim was to detect potential contributions of pollinator visitation to flower microbiome assembly in orchards. For each site and sampling event, 50 open flowers were collected using aseptic technique and pooled at the site level. Flowers with flat, fully reflexed petals that had been open for ;3 days were collected. Once collected, flowers were placed in a cooler, transferred to the lab, and then stored at 4°C until processing.Genomic DNA was extracted from samples using a ZymoBIOMICS DNA microprep kit following the manufacturer’s protocol. Extracted DNA was then used as the template for library preparation and amplicon sequencing following Comeau et al. , performed at the Centre for Comparative Genomics and Evolutionary Bioinformatics at Dalhousie University . There, amplicon fragments were PCR- amplified from DNA in duplicate, using separate template dilutions and high-fidelity Phusion polymerase . A single round of PCR was performed using “fusion primers” targeting either the 16S V4-V5 or ITS2 regions with multiplexing. PCR products were verified visually by running a high-throughput Invitrogen 96-well E-gel .

Any samples with failed PCRs were reamplified by optimizing PCR conditions to produce correct bands to complete a sample plate before continuing with sequencing. The PCRs from the same samples were pooled in one plate, cleaned, and then normalized using the high-throughput Invitrogen SequalPrep 96-well plate kit . Samples were then pooled to make one library and then quantified fluorometrically before sequencing. Amplicon samples were then run on an Illumina MiSeq using 2 300-bp paired-end V3 chemistry. Demultiplexed sequences were trimmed of trailing low-quality bases using the DADA2 pipeline  in R . Paired-end reads were then quality filtered, error corrected, and assembled into ASVs. Once assembled, chimeras were detected and removed, and taxonomic information was then assigned to each ASV using the Ribosomal Database Project naïve Bayesian classifier trained to either the RDP training set or UNITE general FASTA release for bacteria or fungi, respectively. ASVs that failed to classify to kingdom or identified as chloroplast or mitochondrial sequences were discarded. Further, potential contaminant ASVs were identified through inclusion of negative controls during sample and sequence processing and then removed using the “prevalence” method with the decontam package in R . This filtering resulted in samples sequenced at a mean depth of 43,057 sequences per sample for bacteria and 25,890 for fungi. Samples were then rarefied ,pot with drainage holes with all but one bacterial sample retained in the analyses that follow. Such a low cutoff for bacteria is a consequence of a large proportion of reads being identified as plastid DNA, which were removed from the data set. Despite this, we included bacterial data in our study because sampling curves indicate that we were able to identify the majority of bacterial taxa present in samples . Moreover, previous characterization of microbial communities associated with flowers has frequently observed low species richness .To assess the role of abiotic factors, high-resolution climatic metrics for each site were obtained from publicly accessible PRISM data in April 2018. PRISM data are collected at a spatial resolution of 2.5 arcmin . An arcmin is an angular measurement equal to 1/60 of a degree. PRISM data used included elevation , minimum and maximum temperature , minimum and maximum vapor pressure deficit , and precipitation . Vapor pressure deficit is the difference between the amount of moisture in the air and how much moisture the air can hold when saturated, where high VPD indicates drier conditions. As with land cover, the abiotic conditions where sites were located were variable, with elevation ranging from 1,152 to 1,526 m above sea level, April precipitation ranging from 4.2 to 5.3 cm, minimum temperatures ranging from 2.4 to 3.7°C, and maximum temperature ranging from 13.6 to 15.7°C. Statistical analyses. We used multivariate linear regression to assess effects of land cover, orchard management, and climate on the alpha diversity of pear flower microbiomes, using both the Shannondiversity and inverse Simpson index. We chose to include the latter metric to specifically isolate the evenness/dominance aspect of community structure from the taxonomic richness, which heavily contributes to the Shannon diversity metric. All analyses were conducted using R v3.6.1 . To reduce multicollinearity among predictors, we calculated variance inflation factors and used a threshold of 10 to eliminate variables with problematic covariance. This eliminated temperature, precipitation, and elevation from the alpha diversity models. We calculated multimodel average coefficients based on the 90% confidence interval of top models as well as the importance of each coefficient, which indicated the number of top models in which it appeared. We also assessed effects of landscape, climate, and farm management on the dominance of a few focal genera that are highly important for pre- and postharvest diseases of pear, including putative pathogens and beneficial taxa. These included fungal genera Aureobasidium, Botrytis, Cladosporium, Monilinia, Mycosphaerella, and Penicillium and beneficial bacteria, which included Bacillus, Pantoea, and Pseudomonas . One ASV , identified as an Erwinia sp., was detected at a single orchard in our survey. Given such limited detection, we were unable to perform an analysis of links between variables of interest and Erwinia presence and abundance. However, to examine associations between microbial genera and predictors described earlier, we used canonical correlation analysis , an extension of linear regression that finds linear relationships between combinations of explanatory and response variables which maximize the correlation. Separate models were run on fungi and bacteria of interest. Differences in species composition among sites could be affected by processes including substitution of taxa and variation in abundance of particular taxa, so we further evaluated the effects of farm management, land cover, and climate variables on abundance-related and taxon-related aspects of community turnover and the overall community dissimilarity . Beta diversity was partitioned into abundance-related and taxa-related components of Bray-Curtis dissimilarity using the bray.part function in the betapart R package . The influence of explanatory variables on these two components of community turnover between sites, as well as their cumulative overall Bray-Curtis dissimilarity, was investigated using restricted distance-based analysis and AIC model selection and executed using the capscale and ordiR2step functions in the vegan R package . The variance explained by factors included in the top AIC-selected models is included in the results.Fruit flavor is an elusive trait, influenced by many factors including genetics, environments and cultural practices .

Reverse pharmacokinetics can be used to guide potential target tissues/organs/molecules, and then further physiologically relevant pharmacological models are designed to discover bio-active compounds and reveal their corresponding mechanisms. It is worth noting that many compounds show low solubility, which limits their clinical efficiency and restricts their clinical use. Fortunately, there are multiple ways to enhance the bio-availability, such as cocrystallization and the formation of phospholipid complexes and nanoemulsions.Finally, based on the hypothesis that drugs targeting EMT have both antifibrotic and anticancer effects, many important mediators contributing to EMT have been discovered. Additionally, a great number of compounds suppress EMT in tumor and fibrosis by targeting these mediators. It is hoped that many new drugs are designed and developed in the future based on the aforementioned mediators to treat tumors and fibrosis.The first step in the aerobic nitrification process is the oxidation of ammonia to nitrite, mediated mainly by AOB or AOA in soil environments. The most numerous AOB isolated or detected by non-cultural methods in aerobic agricultural surface soils are consistently members of the Nitrosospira genus. Nitrosospira briensis C-128 is a chemolithoautotrophic ammoniaoxidizing betaproteobacterium isolated from a fertilized soil under cultivation for blueberry in Falmouth, Massachusetts, USA in 1971. The genome of Nitrosospira briensis C-128 is the third genome sequence from the genus Nitrosospira to be published and thus provides an important comparison among Nitrosospira. This report includes a summary of the genome sequence and selected features for Nitrosospira briensis C-128 and results are publically available in GenBank accession CP012371.Nitrosospira briensis was described by Winogradsky and & Winogradsky in 1933 as an ammonia-oxidizing bacterium isolated from soil.

The genus name, Nitrosospira, is derived from two Latin roots: nitrosus, meaning nitrous, and spira, indicating spiral. The species name briensis,black plastic plant pots refers to the original isolation location near Brie, France. The culture described by Winogradsky & Winogradsky was not maintained and reisolation of a replacement strain was reported by Watson in 1971. At approximately the same time, N. briensis strainC-128 was isolated by enrichment culturing from a surface soil sample collected from a fertilized blueberry patch in East Falmouth, Massachusetts in 1971 . In 1993, the genus Nitrosospira was emended to include the former genera of Nitrosovibrio and Nitrosolobus based on the high identities of the 16S rRNA gene sequences. Nitrosospira briensis was designated the type species for the genus with strain C- 76 as the type strain . The full-length 16S rRNA gene sequence of N. briensis C-128 is 99 % identical to the N. briensis strain C-76/ Nsp10 sequence . The culture of N. briensis strain C-128 was received in the Norton laboratory from F. Valois in 1995. Nitrosospira briensis C-128 is presently maintained in a culture collection at WHOI and may be obtained upon request from J.M. Norton. Classification and general features of Nitrosospira briensis C-128 are provided as Minimum Information about the Genome Sequence in Table 1. Electron micrographs of the pure culture organism are shown in Fig. 2 revealing the tight spirals visible with TEM negative staining and the convoluted surface of this Nitrosospira as revealed by SEM.Nitrosospira briensis C-128 was chosen for sequencing through the Community Science Program of the DOE Joint Genome Institute as an important representative of the AOB to improve the scope and quality of intra- and inter-generic comparisons in the Nitrosomonadales. The chemolithotrophic metabolism of the AOB, the pathways for production of nitrous oxide and urea metabolism were additional motivating interests in sequencing this genome. Sequencing, finishing, and annotation were accomplished by JGI. The genome sequence has been deposited in the Genome OnLine Database and is part of the NCBI Reference Sequence Collection.

A summary of the project information is found in Table 2.The genomic DNA of Nitrosospira briensis C-128 was sequenced at the DOE JGI using the Pacific Biosciences sequencing technology. All general aspects of sample handling, library construction and sequencing followed JGI isolate sequencing protocols. A PacBio SMRTbell™ library was constructed and sequenced on the PacBio RS platform, which generated 148,206 reads totaling 519.8Mbp. Raw reads were assembled using HGAP v. 2.2.0.p1 . The final draft assembly contained one contig in one scaffold, totaling 3.2 Mbp in size. The input read coverage was 176.1×. An earlier version of the genome was sequenced using the Illumina Hi-Seq 2000 platform. However, this earlier sequence assembly JHVX00000000.1 remained in 31 scaffolds with the nearly identical repeats of several key catabolic gene clusters remaining unresolved. Previously, genome closure for Nitrosospira was achieved only after extensive directed finishing to correctly assemble long nearly identical repeats of gene clusters encoding key catabolic modules including ammonia monooxygenase for the activation of substrate and hydroxylamine dehydrogense and hemecytochrome c proteins for the extraction of electrons and their delivery to the quinone pool in the membrane. The long read capability of the PacBio platform and our depth of coverage enabled sufficient discrimination of repeats to assemble across multiple nearly identical regions into a single contig representing the chromosome of the bacterium. For predicted genes outside of gaps and repeat regions the PacBio and the Illumina predicted genes were 100 % identical. Therefore, we did not combine the Illumina Hi-Seq data with the PacBio data for the complete genome sequence CP012371 reported here.Genes were identified using Prodigal , as part of the JGI’s Microbial annotation pipeline followed by a round of manual curation using GenePRIMP. The predicted CDSs were translated and used to search the NCBI nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. Transfer RNA genes were identified using the tRNAScanSE tool. Other non-coding RNAs were found using INFERNA. Further gene prediction and manual curation was performed within the Integrated Microbial Genomes platform developed at JGI.The genome of Nitrosospira briensis C-128 contains 3,210,113-bp in one chromosome with a GC content of 53.25 % and no plasmids .

The genome contains one complete ribosomal RNA operon similar to other AOB. Coding bases comprised 85.93 % of the total. We identified 3018 protein encoding genes, 55 RNA genes and 130 pseudogenes. For the identified genes, 74.23 % had a function prediction associated with them. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 % confirming species delineation. The genome statistics are summarized in Table 3 and genes associated with COG functional categories are summarized in Table 4.Alcohol consumption has been associated with an increased risk of developing colorectal cancer . One large meta-analysis reported an increased relative risk of 1.1 for developing CRC when consuming more than 2 alcoholic beverages per day . Other studies, including a large pooled analysis and meta-analysis , have shown a similar modest risk of developing CRC associated with alcohol consumption at approximately 2 drinks per day and higher risk associated with higher quantities of alcohol consumption. The specific type of alcoholic beverage consumed in the aforementioned studies was not associated with CRC risk. Total alcohol consumption has been shown to increase the risk of developing CRC in familial cases through an interaction with family history by several investigators, but the effects of wine have not been assessed . Controversy over this issue remains, as it has been reported that the risk of developing CRC may depend on the type of alcoholic beverage consumed. Beer intake has been shown to have a strong association with CRC in several studies . Interestingly, in a large population-based cohort study analyzing 28,000 individuals, alcohol intake was associated with an increased risk of rectal cancer; however, this risk was diminished in alcohol drinkers who consumed at least some wine versus those who did not drink any wine at all . In the same study,black plastic planting pots wine intake was associated with a non-significant trend toward decreased risk of developing colon cancer . Moderate wine consumption has been associated with decreased risk of total mortality, an effect attributed to decreased risk of death from cardiovascular causes and protection from cancer and other causes . Light to moderate wine drinkers have been observed to have a lower risk for death from cancer than those who did not drink wine— an effect not observed for consumers of beer and spirits . In a large U.S. mortality study, alcohol was noted to have a trend toward decreased CRC-specific mortality among women —particularly at light consumption levels . Familial CRC is characterized by multi-factorial inherited susceptibility to CRC and represents approximately 20% of CRC cases; another approximately 79% are considered to be sporadic cases. Based on evidence that there is a decreased risk of developing CRC for wine drinkers, that a decreased cancer-related mortality is associated with wine consumption, and that light to moderate alcohol use among female CRC cases results in a trend toward decreased mortality, we set out to determine if wine consumption was associated with favorable effects on tumor characteristics or survival among CRC cases.Using data from the University of California Irvine CRC gene-environment study , incident cases of invasive colorectal carcinoma during the period 1994–1996 were analyzed. Family history of cancer was ascertained via telephone interview.

Familial CRC cases were identified as those having at least 1 first-degree relative with CRC. Amsterdam criteria were used to define hereditary non-polyposis colon cancer families . HNPCC cases and 1 case with clinically diagnosed Familial Adenomatous Polyposis were excluded from the analysis . The remaining sporadic and familial CRC cases were included for analysis by wine consumption frequency group. Food consumption was self-reported via a validated 100-item National Cancer Institute -Block food-frequency questionnaire in which cases were asked to report their usual eating habits during the 1 yr prior to diagnosis of CRC . Frequency of wine , beer , and liquor consumption was recorded, and available responses ranged from “never” to “6+” servings a day. Total daily energy intake, total daily fiber intake, total daily dietary calcium intake, vegetable and fruit consumption, and body mass index were analyzed from FFQ data using the NCI-Block Analysis Program , version 4.0, as previously reported . All cases were dichotomized as either infrequent wine consumers or regular wine consumers . In the same manner, cases were classified as regular or infrequent consumers of beer and liquor. Clinical and demographic data from consented cases were obtained from the Cancer Surveillance Programs of Orange County, Imperial County, and San Diego County, California as described previously . Recorded data included demographic information , histology, tumor grade, stage at presentation, and survival status. Therapeutic information related to the first course of treatment was obtained including surgical treatment rendered at the primary site, treatment with radiation therapy, and use of chemotherapy. Data were abstracted from medical and laboratory records by trained tumor registrars according to Cancer Reporting in California: Vol. 1. Abstracting and Coding Procedures for Hospitals . Tumor site and histology were coded according to criteria specified by the World Health Organization in International Classification of Diseases for Oncology . Primary site code was searched as described previously using the Surveillance, Epidemiology, and End Results site code for colon and rectum . Appendiceal cancers were excluded. Histology codes included adenocarcinoma , mucinous adenocarcinoma , carcinoma , and not otherwise specified . Only invasive cases of cancer were included in the analysis. Staging was grouped into 3 broad categories that could be classified from clinical and pathologic records and defined according to SEER summary staging as localized disease, regional disease, and remote disease . Socioeconomic status quintiles were obtained from the SES variable available in the California Cancer Registry as described previously . This index variable utilized for SES includes a combination of 7 indicator variables for census block data including assessments of educational status, income, and housing information .In this observational study, earlier stage at presentation and improved OS were noted for familial CRC cases who were regular wine consumers prior to the time of diagnosis compared to those that were infrequent wine users. The observed survival benefit persisted after adjustment for age, gender, stage at presentation, SES, BMI, treatment status, and consumption of beer and liquor. In contrast, among sporadic CRC cases, no differences in stage at presentation or survival were noted for regular versus infrequent wine consumers. The observed survival differences based on reported wine consumption were not detected for beer or liquor consumption. Greater than 1/2 of the regular wine consumers in this study were moderate wine consumers .

To further scrutinize this unusual reverse EAG responses, we used gas chromatography with electroantennographic detection . In GC-EAD analyses, injected mixtures are separated by GC and subjected to antennal preparations under the same condition thus ruling out any possibility of mechanical interference and minor sample contamination. Here, methyl salicylate responded with regular EAG responses, i.e., with the first phase , which is referred to as rise of the receptor potential, and the second phase starting at the end of the stimulus, commonly referred to as the decline of the receptor potential . This is analogous to the depolarization, repolarization, and hyperpolarization of a nervous impulse. As opposed to methyl salicylate, eucalyptol consistently gave inverse EAD responses  thus corroborating what we observed in EAG analyses . Next, we recorded EAG responses when flies were challenged with odorants and an inhibitor. First, we compared the response of w1118 and Orco-Gal4/UAS-CqOR32 flies to -2-hexenal when it was delivered alone or in combination with eucalyptol. EAG responses from w1118 flies to 0.1% -2-hexenal alone or in combination with 10% eucalyptol did not differ significantly . By contrast, EAG responses from Orco-Gal4/UAS-CqOR32 flies to 0.1% -2-hexenal plus 10% eucalyptol were significantly lower than those elicited by 0.1% -2-hexenal alone . We then examined the dose-dependent effect of this inhibition by using Orco-Gal4/UAS-CqOR32 flies. Robust responses to 0.1% methyl salicylate were reduced in a dose-dependent manner with the addition of eucalyptol but remained unchanged at the end of the tests. Likewise, EAG responses to 0.01% -2-hexenal were reduced when coapplied with eucalyptol . Of note, -2-hexenal does not activate CquiOR32 . Such inhibition presumably results from CquiOR32 indirectly inhibiting responses of the fly endogenous receptors to -2-hexenal. In these continuous experiments, a small difference between EAG responses before and after costimulus tests may be due to loss of this volatile semiochemical from the cartridge rather than adaptation. Similar inhibition was observed when 2-heptanone was applied alone or coapplied with eucalyptol . Taken together, these results further suggest that intrareceptor inhibition occurs in vivo as indicated by the inhibitory effect of eucalyptol on methyl salicylate responses. Additionally,drainage planter pot the effect of eucalyptol on the response to -2-hexenal suggests that intraneuronal inhibition occurred.

A few lines of evidence support this hypothesis. First and foremost, eucalyptol does not cause inhibition in control flies and -2-hexenal does not activate CquiOR32 . The simplest explanation is that, in Orco-Gal4/UAS-CqOR32 flies, all endogenous receptors are coexpressedwith CquiOR32. Thus, CquiOR32 response to eucalyptol interferes with the response of DmelOR7a to -2-hexenal. In short, inhibitor and agonist are likely to be acting on different receptors in the same neurons, thus an intraneuron inhibition. To further test the notion of intraneuronal inhibition, we turned to single sensillum recordings .The best ligand for ab4A, the neuron in ab4 sensilla with a large spike amplitude, is -2-hexenal , although ab4A is also very sensitive to other ligands, including hexanal . Contrary to ab4B, ab4A houses only one OR, namely, DmelOr7a . Because expression of CquiOR32 was driven by DmelOrco, ab4A neurons in our transgenic flies house both DmelOr7a and CquiOR32. Coexpression was confirmed by a significantly stronger response to methyl salicylate recorded from Orco-Gal4/UAS-CquiOR32 than from WT flies , while retaining response to hexanal . It is known that methyl salicylate is the best ligand for DmelOr10a in ab1D but elicits only very low response in ab4A . The low response of WT flies to methyl salicylate did not differ significantly when the odorant was delivered alone or codelivered with eucalyptol . By contrast, responses recorded from Orco-Gal4/UAS-CquiOR32 flies were significantly lower when the two stimuli were delivered simultaneously from two different cartridges . Next, we tested whether CquiOR32 response to eucalyptol would affect DmelOR7a response to a cognate ligand, hexanal. Responses of WT flies to hexanal did not differ significantly when comparing hexanal alone with hexanal plus eucalyptol . Recordings from ab4 sensilla in the Orco-Gal4/UAS-CquiOR32 flies showed a slight, albeit not significant, increase in response to hexanal. This is unlikely to be due to hexanal activation of CquiOR32 . When hexanal and eucalyptol were delivered simultaneously firing of DmelOR7a was completely abolished . We also recorded from ab7 sensilla, which expresses DmelOR98a, in ab7A and for which butyl acetate is one of the best ligands . Eucalyptol elicited inhibitory response in ab7A neurons of Orco-Gal4/UASCquiOR32 flies . In the transgenic flies both methyl salicylate and butyl acetate generated excitatory responses , which were inhibited by eucalyptol . Because methyl salicylate and eucalyptol elicit inward and reverse currents in CquiOR32, this in vivo inhibition is not surprising.

However, the consistent observation that eucalyptol inhibits the response of an endogenous receptor to a cognate ligand supports the notion that intraneuronal inhibition occurs when receptors are colocated in a neuron. Specifically, the inhibitory responses of CquiOR32 interferes with the activation of a collocated receptor by a cognate ligand. For example, activation of DmelOR7a in ab4A neuron by hexanal and activation of DmelOR98a in ab7A neuron by butyl acetate were both inhibited by eucalyptol upon interaction with CquiOR32. Contrary to the fruit fly, which expresses only one receptor per neuron , mosquitoes can coexpress multiple ORs in the same neuron .CquiOR32 has an orthologue in the genome of the yellow fever mosquito, AaegOR71 , with 55.5% identity. We sequenced 20 clones and obtained 19 AaegOR71 sequences. Five clones showed sequences identical to the sequence in VectorBase and were, therefore, considered the WT. We expressedAaegOR71-WT in the Xenopus oocyte recording system and challenged the oocytes with compounds that elicited inward and inhibitory currents in CquiOR32. Cyclohexanone elicited inward currents, but the compounds generating the largest inward currents were 4,5-dimethylthiazole and 2-methyl-2-thiazoline ; no response was observed with methyl salicylate. Although eucalyptol and fenchone did not elicit measurable inhibitory currents, these two compounds reduced AaegOR71 responses to cyclohexanone, DMT, and 2MT . Four clones differed from WT in 7 amino acid residues, and 3 clones differed from WT in 11 amino acid residues. They both showed weak responses to odorants when tested in the Xenopus oocyte recording system. The other 7 clones differed from the WTin 6–12 amino acid residues. AaegOR71-V5 , AaegOR71-V14 , and AaegOR71-V15 differed in 12, 9, and 11 amino acid residues, respectively, and none of them responded to odorants. AaegOR71-V8 differed in 10 amino acid residues and showed very weak response only to the Orco agonist VUAA-1. AaegOR71-V4 , AaegOR71-V9 , AaegOR71- V17 differed in 8, 10, and 6 amino acid residues but gave weak to moderate responses to odorants. Next, we tested whether intrareceptor inhibition might be manifested in vivo in the antennae of the yellow fever mosquito. With 350 contacts, 69 recordings were made from SST-2 sensilla.

SSR showed that cyclohexanone, 2-methyl-2-thiazoline, and 2,4-dimethylthiazole elicited dose-dependent excitatory responses in neuron-A in SST-2, whereas eucalyptol and fenchone showed inhibitory responses . When costimulated with 2-methyl-2-thiazoline and eucalyptol, the response to the odorant decreased markedly . We then analyzed the effect of inhibitors on the responses to the three odorants that caused excitatory responses. Both eucalyptol and fenchone inhibited the responses of ORN-A in SST-2 to cyclohexanone , 2-methyl-2-thiazoline , and 4,5-dimethylthiazole in a dose-dependent manner.In 1970, Philip Bjork described a small fossil bear from the Pliocene Glenn’s Ferry Formation of southwestern Idaho. Based on a single m1 as the holotype, he was understandably perplexed and named it Ursus abstrusus. Additional material has not been forthcoming since its initial description and this bear has remained an enigma. Hence the discovery in the 1990s of a similar bear from more complete fossils in the Pliocene of the Canadian High Arctic throws much needed light onto the mystery . In addition to resolving the riddle of Ursus abstrusus, with a moderately complete skull and lower jaws with associated post cranials,plant pot with drainage the new materials present a rare opportunity to fill a large gap in our knowledge of North American High Arctic at a time in the early Pliocene when mean annual temperatures in the High Arctic were ~22 °C warmer than the present polar temperatures. Such a warm climate supported an extensive boreal-type forest biome, radically different from today’s arid polar tundr. Thus the evidence of this primitive bear in an extinct polar forest offers valuable information about the diet and habitat of this basal ursine. Te fossil records of basal ursines has improved with recent discoveries of three relatively complete specimens of basal ursines from China – a very advanced Ursavus and a very primitive Protarctos . We are now in a position to more tightly bracket the North American Pliocene bears as well as providing a wealth of information about cranial anatomy of basal ursines previously unavailable. Te present description of P. abstrusus and a phylogenetic analysis combining molecular and morphological data of most fossil and living ursines for the first time allows a much more detailed view of the history of bears at the critical juncture of their initial diversifcation. In addition, the presence of dental caries provides insight into the evolutionary history of diet of ursines.Protarctos abstrusus is a basal ursine the size of a small Asian black bear. It has a fat forehead covering an uninfated frontal sinus; very high sagittal crest that projects backward to overhang the occipital condyle ; P4 with a small, distinct protocone situated at the level of carnassial notch; M2 talon modestly developed but not very elongated ; no pre-metaconid on m1, smooth posterior surface of m1 trigonid without zigzagpattern, presence of a distinct pre-entoconid; m2 shorter than m1 . It is about the same size as P. boeckhi and difers from it in the relatively smaller p4, presence of a tiny cuspule on lingual side of posterior crest in p4, and presence of a pre-entoconid on m1. P. abstrusus is also similar in size to P. yinanensis and can be distinguished from the latter in a fattened forehead, posteriorly projected sagittal crest, p4 posterior accessory cuspule on lingual side of posterior crest, an m1 pre-entoconid, and less elongated M1 and M2. P. abstrusus difers from P. ruscinensis by its lack of unique features of the latter such as a deep angular process, reduction of P4 protocone, and a single entoconid on m1.There is much disagreement over the generic taxonomy of ursines. Most mammalogists and some paleontologists include all living black bears , brown bears, and polar bears in the genus Ursus but allow separate generic status for the sloth bear, Melursus, and sun bear, Helarctos, although some include all of above in Ursus and others use Talarctos for the polar bear. With a deep time perspective, vertebrate paleontologists either adopt some subgeneric names, such as Ursus for sloth bear, Ursus for Asian black bear, Ursus for American black bear, Ursus for some extinct bears or elevate some of them to generic status. In his remarks about carnivoran classifcation, Kretzoi erected a new genus, Protarctos, for Ursus boeckhi Schlosser, 1899. Kretzoi’s name has been adopted either at full generic rank or as a subgenus, although many authors still prefer a more inclusive usage of Ursus. In our cladistic framework in this study, some generic reassignment becomes necessary to maintain monophyly, especially in light of the general preference to giving sloth and sun bears distinct generic status.Te Beaver Pond site, 78° 33′N 82° 22′W, is a >20m succession of fne to coarse cross-bedded fuvial sands conformably overlain by cobble gravels interpreted to be glacial outwash and capped by 2m of till on the northeastern edge of an interfuvial plateau southeast of Strathcona Fiord on Ellesmere Island, Nunavut . A peat deposit near the base of the sequence, up to 2.4 m thick, produced exceptionally well-preserved plant, invertebrate and vertebrate remains , and is disconformably overlaying light-colored, tilted Eocene sediments. Abundant beaver-cut branches and cut saplings of larch trees suggest that the peat growth may have been promoted by beaver activity. Further supporting this view are the skeletal remains of multiple beaver individuals, and two clusters of beaver-cut branches found within the peat unit, at least one of which was interpreted to be the core of a dam. Using terrestrial cosmogenic nuclide burial dating, four samples of quartz-rich coarse sand from above the peat unit yielded a weighted mean date of >3.4+0.6/−0.4Ma, suggesting the peat accumulation was formed during a mid-Pliocene warm phase.At 78°N, the Beaver Pond site on Ellesmere Island is presently extremely cold and arid, with ice sheets, permafrost, and sparse vegetation.

Laboratory bio-assays indicate that reduced risk pesticides can, in some cases, still be toxic to natural enemies and thus an assessment of the toxicity of field aged residues of these products is key to understanding how well laboratory bio-assays translate to a field setting. To encourage a reduction of organophosphate use, the Environmental Protection Agency Office of Pesticide Programs’ called for incentives to promote the development and use of alternative reduced-risk pesticides. Subsequently, the EPA announced the Reduced-Risk Pesticide Initiative, which created incentives to promote registration of pesticides under the following reduced-risk criteria: reducing human health risks and reducing risks to non-target organisms such as birds, beneficial insects, and aquatic organisms . One such insecticide developed under the new criteria is chlorantraniliprole, which has frequently been shown to have little to no effect on several natural enemy traits, including survivor ship, predation rates, parasitoid emergence, or parasitism rates . For example, it was found to be compatible with beneficial insects such as Copidosoma bakeri Howard via direct contact, Harpalus pennsylvanicus DeGeer via treated food, and Tiphia vernalis Rohwer and Bombus impatiens Cresson via residual exposure . However, for two species of green lacewing, Chrysoperla carneaand C. johnsoni Henry, Wells and Pupedis , chlorantraniliprole caused 100% mortality . Lambda-cyhalothrin is another reduced-risk insecticide, but, unlike chlorantraniliprole, it has demonstrated lethal effects on several natural enemies. Lambda-cyhalothrin is lethal to larvae of C. carnea and C. johnsoni . Additionally, it is highly toxic to the parasitoid, Diadegma insulare , and resulted in a change in host preference . At the full field rate and, it caused high mortality in adults of the predatory mite, Galendromus occidentalisand for larvae that hatched from the eggs of treated females . Coccinellid populations topically exposed to lambda-cyhalothrin had significant decreases in suvivorship,25 liter pot including populations of Coleomegilla maculata , Cycloneda sanguinea , HarmoniaRecently, both lambda-cyhalothrin and chlorantraniliprole were formulated into a new combination foliar insecticide .

This combination was developed to provide broad spectrum control of both sucking and chewing insects, including lepidopteran, coleopteran, and hemipteran pests. Additionally, because the compound coats and penetrates the leaf tissue, it affects insects via multiple routes of exposure . Hence, the combination may target feeding and mobile life stages as wells as eggs. A range of other combination insecticides have been developed for use in agricultural crops, however, there is no evidence that they preclude resistance . The toxicity of insecticides to H. convergens is important for biological control efforts throughout the western United States, where it is a well-known generalist aphid predator . It is a particularly important natural enemy in highvalue tree crops, where both chlorantraniliprole and lambda cyhalothrin are used to control codling moth . In this study, we evaluated the acute toxicity to H. convergens of aged residues of a combination insecticide, chlorantraniliprole plus lambda-cyhalothrin. The objectives of this study were to 1) assess acute toxicity of the combination insecticide residues on two life stages of H. convergens , 2) determine how acute toxicity of residues is influenced by age, and 3) evaluate the differences in acute toxicity between residues aged in glass arenas in the laboratory bio-assay versus residues aged on foliage in the field.Aged residues of the combination insecticide, chlorantraniliprole plus lambda-cyhalothrin , were tested in comparison to a distilled water control. The combination insecticide was formulated as 0.835 lb of chlorantraniliprole and 0.417 lb of lambda-cyhalothrin per gallon . The solutions used for both laboratory and field aged residues were the equivalent of 0.73 l per ha . For the laboratory aged residues, the insecticide solution was prepared as 16.89 mg of formulated product in 50 ml of distilled water, and, for the field aged residues, the solution was prepared as 35.8 g of formulated product per 106 l of water. Four variables were manipulated 1) treatment , 2) life stage of H. convergens , 3) residue age, and 4) setting . A minimum of 28 replicates was used in all bio-assays. For all bio-assays, test insects were placed individually in 15 x 45 mm glass vial arenas, with cotton wool placed over vial openings to allow for ventilation.

Insects were kept at 22 ⁰C, 60-70% RH, and 16:8 h photoperiod. Bio-assays lasted for a period of 48 h, after which acute toxicity was recorded. Acute toxicity was estimated from the number of live and dead or moribund insects , where moribund insects were those that were unable to right themselves. For adult bio-assays, equal numbers of each gender were used and acute toxicity was recorded separately for each gender. The effects of laboratory and field aging were evaluated for residues 0, 1, 2, 4, 8, 16, and 38 d old. To test the toxicity of laboratory-aged residues, individual glass vials were treated by adding 4 ml of insecticide solution and turning 360 degrees in order to coat the entire inside surface before the solution was poured out. For residues aged 0 d, vials were inverted on a rack and allowed to dry for 4 h until they were used in the bio-assays. For all other residue ages, vials were inverted, suspended on a rack, allowed to dry in a fume hood for a period of 24 h, and then placed in an incubator maintained at 22 ⁰C, 60-70% RH, and 16:8 h photo period under fluorescent lights until used for the bio-assays. For field-aged residues, individual walnut trees were sprayed in a commercial walnut orchard in Tracy, CA. Eight walnut trees were treated with the insecticide and 7 trees were treated with water on June 19, 2013. Foliar sprays were applied with an orchard sprayer operating at 250 psi with a finished spray volume of approximately 2338.5 l per ha. For each sample date after spray application four leaves were collected from the lower canopy of each tree in each cardinal direction. In the laboratory, 4 cm x 5 cm sections were cut from each of the leaves and arranged as liners in individual glass vials such that the inside surface of each vial was covered by the lower surface of the leaf sections. Cotton wool plugs were placed at the bottom of each vial to secure the leaf sections in place. For both the laboratory and field aged residues, approximately 10 untreated adult A. pisum were then added to each glass vial as a food source, and a single untreated H. convergenswas introduced and allowed to crawl on the treated surface for a period of 48 h. The statistical program R was used for the analysis. Generalized linear models with binomial errors, or quasibinomial errors in cases where there was over dispersion, were used to analyze the effects of treatment , life stage , residue age , and setting on the acute mortality of H. convergens. For all GLMs, model reduction and log likelihood ratio tests were used to assess the statistical significance of each factor and their interactions on acute mortality at α = 0.05.

The uncorrected acute mortality data were analyzed, starting with a full model that included all four factors and interactions. The data set was finally subdivided into four separate models with no significant interaction between factors to compare the relative acute toxicity of treatment and age: 1) adults exposed to field-aged residues, 2) larvae exposed to field-aged residues, 3) adults exposed to laboratory-aged residues, and 4) larvae exposed to laboratory-aged residues. Additionally, we tested the effects of gender on adult mortality. In a separate analysis, the data was corrected to account for variability among control groups , and then used to examine comparative effects of life stage and setting. Due to significant interactions, the corrected data set was subdivided when necessary. Additionally, the decay in insecticide impact over time was fitted to a first-order degradation curve Mt = M0e – at where Mt is the corrected acute mortality of H. convergens exposed to residues of age t , M0 is the corrected acute mortality of H. convergens exposed to residues of age 0, and a is a rate constant . A linearized version of the degradation curve, a plot of ln on residue age,raspberry cultivation pot was used to fit a linear regression model and to estimate the rate constant a from the slope. From this we estimated the residue age that represents a 50% loss of the acute mortality response of H. convergens to the combination pesticide from its initial effect on day 0 from t1/2 = /a.There were substantial differences in the acute mortality responses of H. convergens to aging of field residues of the combination insecticide , but not of laboratory residues. Based on the decay rate of the responses over time, we were able to estimate the effects of differently aged residues on H. convergens mortality, and to categorize the residue ages according to the criteria used for toxicity classification by the International Organization for Biological Control . Field-aged residues were moderately harmful to adults for up to 1 day, but residues were harmless after 18 days from the initial application. Similarly, field-aged residues were estimated to be moderately harmful to larvae for 9 days, and were still slightly harmful after 51 days. In contrast, laboratory-aged residues were estimated to be moderately harmful to adults for a period of 29 days, and harmful to larvae regardless of residue age. Laboratory-aged residues produced higher mortality rate responses than field-aged residues, and the responses of larvae were greater than those of adults. High mortality rates from residual exposure to the combination insecticide were most likely due to the lambda-cyhalothrin component, which has been shown to be toxic to several natural enemies . For example, Neochrysocharis formosaand Ganaspidium nigrimanusexperienced high mortality rates when exposed to lambda-cyhalothrin residues . C. carnea and C. johnsoni adults and larvae experienced 100% mortality when treated with the maximum label rate .

Likewise, lambda-cyhalothrin exposure resulted in 100% mortality for D. brevis adults and nymphs . When exposed to a treated leaf surface, the parasitoid D. insulare and the predator C. maculata each had mortality rates > 80% . Exposure of H. convergens to fresh lambdacyhalothrin residues at the maximum field rate resulted in mortality rates > 90% for adults and larvae , and topically exposed pupae and eggs had mortality rates > 80% . Although the concentration of lambda-cyhalothrin in the maximum field rate dosage used in Chapter 2 was much greater than its concentration in the combination insecticide , the mortality rate response of H. convergens to the combination insecticide remained high for 0-1 d of the field-aged residues and for all ages of the laboratory residues. In contrast to the lambda-cyhalothrin component, it is unlikely that the chlorantraniliprole component of the combination insecticide accounted for the high mortality rates of H. convergens. Chlorantraniliprole was harmless to H. convergens adults and larvae via residual, oral, and topical exposure . Moreover, its primary mode of action is via ingestion, and it is unlikely that adults or larvae of H. convergens received oral exposure in our bio-assays with either field-aged or laboratory-aged residues. Chlorantraniliprole has also been demonstrated to be compatible with several natural enemies . For example, residual exposure was harmless to Orius armatusnymphs and adults . It was also harmless to multiple parasitoid species, including Aphelinus mali Haldeman , Diadegma semiclausum Hellen , and Dolichogenidea tasmanica Cameron . Even in a maximum exposure scenario, where the predator Macrolophus pygmaeuswas treated orally, residually, and topically, chlorantraniliprole had no effect on mortality . In a similar maximum exposure treatment, it had no effect on the mortality of G. occidentalis adults, and an LD50 could not be established due to its low toxicity . Given the low acute toxicity of chlorantraniliprole, the half-life response of H. convergens to the combination insecticide was probably unaffected by its rate of degradation under field conditions or by the difference in substrates used for laboratory and field-aged residues. Chlorantraniliprole was harmless to H. convergens adults and larvae exposed to residues on glass , and to Trichogramma pretiosum Riley as residues on filter paper or cotton leaves .

Primary among these questions is: what fitness benefit does transmission into seeds provide to microbes and their host plants? Such a question gets at the eco-evolutionary dynamics in these microbial meta communities, which can have long-term consequences for both microbes and plants. Because microbial communities behave and evolve at shorter time-scales than macro-organisms , it is feasible to design simple experiments testing how microbes evolve in response to plant defenses, nutrient availability, and micromorphology. Such eco-evolutionary studies may have applications in understanding microbial community shifts with crop domestication . Additionally, both microbes and seeds have dormant stages, which can impact meta community dynamics through trade offs with dispersal and delayed responses to environmental conditions . The role of dormancy in seed and plant microbial meta community assembly has yet to be explored, so there is much room to study how dormancy impacts these systems over longer temporal scales. Finally, a hot topic in plant microbiome research is how to modify plant microbial communities for climate resilience and other beneficial traits . However, the impacts of climate change-associated disturbances on plant microbiomes have been limited to pattern-based studies in leaves and roots . As such, more work can be done on how disturbances alter seed microbiome assembly processes and outcomes.Classical biological control aims to control an invasive non-native species via the deliberate introduction of its specialized natural enemy. The use of classical biological control became popular after the dramatic success of the control program for cottony cushion scale, Icerya purchasi , a major citrus pest, through the introduction of the ladybird beetle, Rodolia cardinalis , to California from Australia in 1888 .

More recently, classical biological control continues to be used to suppress increasing numbers of invasive species worldwide. In the United States,dutch bucket for tomatoes it has been estimated that, while invasive insect species are only a small percentage of total arthropod species , they represent approximately 35% of 700 important insect pests . Thousands of classical biological control introductions have been made worldwide, and it has been estimated that, in 17% of cases, there has been effective control, to the extent that the targeted invader is no longer considered a pest. In 43% of cases, introductions have led to at least partial control, thereby reducing ecological damage and the need for pesticide use. However, 40% of introductions were found to have negligible impact on the target pest . Thus, though complete success is possible, it is not characteristic of most classical biological control programs. More commonly, it results in partial control which positively contributes to pest management. This method of biological control suppresses pest populations by releasing commercially produced natural enemies. This is particularly useful when natural enemies are not present or are scarce, such as in greenhouses or large monocultures. Within augmentative biological control, there are different methods for releasing insects. For instance, inoculative releases introduce small numbers of natural enemies, allowing them to establish in a crop, reproduce, and provide season-long control. Inundative releases, on the other hand, involve a mass introduction of natural enemies, with the expectation that they will provide an immediate reduction in pest densities. Yet the effect will be short lived, because they do not reproduce or establish . For example, mass releases of Trichogramma dendrolimihave proved to be effective for control of two major pests, Adoxophyes orana and Grapholitha molesta . When released in apple orchards, egg parasitism ranged from 81-99%. In this case, mass reared T. dendrolimi were labeled with a radioisotope to distinguish them from naturally occurring populations.

The released T. dendrolimi were responsible for 74% of the egg parasitism, while 26% of the parasitized eggs were attacked only by wild T. dendrolimi . This indicates that, not only was augmentation alone significant, but it may compliment scarce populations of natural enemies that are already present in the field. When cropping systems are altered to enhance populations of natural enemies, this is known as conservation biological control. In some cases, this can involve providing natural enemies with a suitable plant surface to forage on, as some crop cultivars can be incompatible with natural enemies. For instance, high densities of trichomes on tomatoes increased entanglement of lacewing larvae . Also waxy blooms on cabbage plants can reduce the ability of lacewing larvae to move effectively, reducing predation rates on the diamondback moth Plutella xylostella. Providing nutritional supplements, such as floral resources or food sprays, is another way to conserve populations of natural enemies. In New Zealand apple orchards, under-planting apple trees with floral resources increased parasitism rates of Epiphyas postvittana. In cotton, reproduction of lacewings was enhanced by spraying a mixture of hydrolyzed protein, water, and sugar . While adding food sources and suitable habitat can enhance natural enemies, it is equally important to alter management practices that decrease natural enemies, namely, pesticides. Soon after the introduction of synthetic insecticides in the 1950s, researchers began to link secondary pest outbreaks and pest resurgence to the destruction of natural enemies . Since, then it has become abundantly clear that pesticides can affect natural enemies in numerous ways, inducing changes in foraging behavior, predation rates, survivor ship, fertility, fecundity, and development rates .Ladybird beetles, or coccinellids, are important predators of many pest species, including whiteflies, aphids, mealybugs, scales, and mites. In particular, aphidophagous ladybird beetles are prominent generalist predators . As mentioned above, one of the most well-known examples of the use of coccinellids in classical biological control was the importation of the vedalia beetle, Rodolia cardinalis , to control the cottony-cushion scale on citrus in California. Immediately after this success, many classical biological control programs began to focus on Coccinellidae, leading to the “ladybird fantasy” period .

One coccinellid commonly used in biological control programs in the United States is the generalist predator Hippodamia convergens. It is frequently used in augmentative biological control because it is easily collected and stored. In California, they are collected from overwintering sites in the Sierra Nevada and sold commercially, yet still maintain their ability to prey on pests relative those not collected and stored for commercial use . Due to rapid dispersal in a field setting, it is thought that mass releases of commercial H. convergens is ineffective . For instance, for aphid control in roses, the effective rate of H. convergens release was two orders of magnitude greater than recommended by commercial insectaries, and was no more cost effective than an application of the systemic pesticide imidacloprid . On the other hand, when placed in a more contained environment, such as a greenhouse, H. convergens has the ability to reduce pest populations . Additionally, H. convergens may be incorporated into conservation biological control programs. In western North America, it is an important natural enemy in high-value tree crops . However, some reduced-risk pesticides used within this system have been found to be toxic to H. convergens . Understanding how pesticides impact populations of natural enemies is key to integrated pest management and the conservation of natural enemies. For decades, the use of organophosphate pesticides has disrupted the activity of natural enemies. With the passage of the Food Quality Protection Act in the United States in 1996, this class of conventional pesticides became the primary focus of a registration review. With increased restrictions on use of organophosphates, growers began to use alternative pesticides for the control of pest populations. From 1990 to 2007, the use of organophosphates declined by approximately 60%, from 85 million pounds to 33 million pounds, and decreased from 70% of total insecticide use to 36% . In 1992, via the Federal Register, the Environmental Protection Agency Office of Pesticide Programs called for incentives to promote development and use of reduced-risk pesticides. The following year,blueberry grow pot the same office announced the Reduced-Risk Pesticide Initiative. The goal of this program was to promote the development and use of pesticide products that would pose a reduced risk to human and environmental health. Additionally, the EPA created incentives to promote registration of these pesticides under the new reduced-risk criteria. These criteria included reducing human health risks by reducing toxicity by a factor of 10-100 times relative to organophosphate insecticides. Of particular concern was reducing health hazards to pesticide applicators and field laborers, which is another reason the EPA actively promoted the replacement of organophosphates. In addition to human health, the criteria specified a reduction in risk to non-target organisms such as birds, beneficial insects, and aquatic organisms . Though the Reduced-Risk Initiative criteria aimed to reduce risks to human and environmental health, reduced risk does not guarantee there are no harmful effects to other non-target organisms, such as natural enemies. Chlorantraniliprole belongs to a class of chemicals known as anthranilic diamides. It acts on insect ryanodine receptors, and is most effective when applied to plant material and ingested. One formulation of this chemical is Rynaxypyr, the active ingredient in the pesticide Altacor. Altacor is designed to target various lepidopteran pests, such as leafrollers, crown borers, leafminers, and codling moth. It is approved for use in fruiting shrubs, vines, and tree crops, including banana, citrus, and pome fruit . Thus far, chlorantraniliprole appears to have little to no toxicity for most natural enemies. For example, it has shown demonstrated to have no toxic effects on the dogbane beetle Chrysochus auratus, , a beneficial insect that feeds almost exclusively on problematic weeds in blueberry crops .

According to the IOBC toxicity classification, chlorantraniliprole was ranked as slightly harmful to Orius armatus , which controls western flower thrips in greenhouse grown peppers . Similarly, it was found to be compatible with beneficial insects such as the Bombus impatiens , Copidosoma bakeri , an endoparasitoid, the predatory ground beetle Harpalus pennsylvanicus , and the ectoparasitoid, Tiphia vernalis. When tested for behavioral effects on the generalist predator Macrolophus pygmaeus , exposure to chlorantraniliprole reduced feeding, but had no significant effect on predation rates . Furthermore, there were no significant effects on survival, parasitism rates, or emergence of seven different species of parasitic wasps, including two sensitive indicator species, Aphidius rhopalosiphiand T. dendrolimi . When treated with chlorantraniliprole, adult and immature Deraeocoris brevissurvived at rates comparable to controls . Yet, contrary to the aforementioned studies, chlorantraniliprole caused 100% mortality in two species of green lacewing, Chrysoperla carnea and Chrysoperla johnsoni. Cyantraniliprole is also an anthranilic diamide. Another version of this active ingredient is known as Cyazypyr. Under the trade name Exirel, it is approved for use in several crops, including bushberries, citrus, pome, stone fruit, and tree nuts. With respect to high value tree crops in western North America, it is approved for use in Washington and Oregon, but not in California. This pesticide targets chewing and piercing sucking insects, primarily from the orders Lepidoptera and Hemiptera. Both Altacor and Exirel pose little human health risk. However, unlike Altacor, Exirel has application restrictions due to its risk to insect pollinators . Cyantraniliprole has been demonstrated to have no significant impact on the mortality of Tamarixia triozaewhen it is exposed to residue on either a glass or leaf surface . However, 25% of T. triozae died 24 h after ingestion of treated honey. For the predator mite, Galendromus occidentalis , cyantraniliprole caused no significant changes in mortality, egg hatch, or larval survivor ship, but there were reductions in prey consumption and fecundity . The treated larvae of two lacewing species, C. carnea and C. johnsoni, did not experience significant mortality or differences in sex ratio, yet exposure was highly toxic to adults . In nymphs of the predatory mirid, D. brevis, 23% mortality was observed when treated with the maximum recommended field rate, but there was no significant impact on mortality for treated adults . Additionally, treated nymphs had no significant difference in development time, but, when they emerged as adults, the sex ratio had a significant female bias . When applied as a systemic treatment in peppers , cyantraniliprole was found to have no impact on Orius insidiosuspopulations, but it also had no impact on populations of the target pest . Copper hydroxide and mancozeb are two active ingredients that may be mixed in a single pesticide solution and applied as a spray to control plant pathogens.

Studying the spatial distribution of cabbage aphids, Brevicoryne brassicae L. in commercial canola field sites, Severtson et al. also found significantly higher counts of this important pest within 20–30 m from field edges compared to further inwards into canola fields. Based on logistic regression, the population density of cabbage aphids was found to be negatively correlated with the distance from field edges in dryland canola host plants. Besides aphids, cabbage seed weevils, Ceutorhynchus assimilis Paykull , displayed a similar spatiotemporal pattern of distribution in winter oilseed rape . A study describing the distribution of Andean potato weevils, Premnotrypes spp. , showed heavier infestation of potato tubers along field edges . Edge-biased distribution was also reported regarding wheat stem sawflies, Cephus cinctus Norton , in dryland wheat fields .In the context of stored products, warehouse walls can be considered as physical or environmental edges. Insects associated with stored products have been shown to aggregate along warehouse walls and near physical edges. A study of the spatial distribution of red flour beetles, Tribolium castaneum Herbst , in stored wheat warehouse showed consistent aggregations along warehouse walls . This wall-biased distribution has also been observed regarding other stored product pests, such as Trogoderma variabile Ballion . Similarly, a study of the distribution of insect pests in a botanical warehouse in Florida found higher abundance of both moths and beetles [Cadra cautella Walker , Lasioderma serricorne Fabricius , Oryzaephilus mercator Fauvel , Typhaea stercorea L. , and Indianmeal moths, Plodia interpunctella Hübner ] along the walls and corners of the warehouse . In an experimental study with pheromone traps placed in 1-m intervals along a vertical gradient from the floor level to the ceiling in a 6-m tall warehouse,nft growing system most Indian meal moths were caught predominantly either near the ground level or near the ceiling , thus showing a vertical edge-biased distribution.

Interestingly, the same study showed that the moths’ preference for vertical edges could be eliminated through addition of landing surfaces to pheromone traps or by placing traps near walls. Thus, the study by Nansen et al. showed important ways to enhance moth trap captures through a combination of manipulation and targeted placements of traps near walls, and both improvements hinged on the importance of recognizing edge bias of moth captures.Several small-scale laboratory studies have indicated the occurrence of edge-biased distributions of insects. As an example, female almond moths, C. cautella, were released into a 120-cm-square arena with uniform layers of intact or cracked peanuts, and the spatial distribution of eggs laid by these female was recorded after 48 h . The results indicated that when peanuts filled the entire arena, female almond moths significantly aggregated their oviposition along arena edges. Moreover, when only the central 25% of the arena was filled with peanuts, the majority of the eggs were found along the edges of the peanut patches instead of the edge of the arena. Similarly, the infestation pattern of the red flour beetles, T. castaneum, also showed insect aggregations along arena edges .Given the prevalence of edge-biased distributions of insects in agricultural systems, it seems of considerable importance to unravel the driving mechanisms of the phenomenon. One of the common approaches used in the study of edge-biased distributions is the development of models that can simulate the edged-biased pattern of insect distributions. Although these models are theoretical and based on assumptions that are difficult to validate, they have been used widely on a conceptual basis and also to produce meaningful predictions of insect distributions.In Eq. , the factor D is known as the diffusion coefficient, which can be estimated through the mean square difference of displacement of insects over time . Predicted dispersal distributions based on Eq. 1 are presented in Fig. 2, and it is seen that they follow a normal distribution with population density being highest at the center of dispersal and gradually decreasing over distance.

Based on simple diffusion, an animal is predicted to have highest abundance near edges due to spillover , as individuals transition from one habitat into other and unlikely move far into the new habitat . A series of mark release and recapture experiments with multiple insect pest species [Phyllotreta cruciferae Goeze , Phyllotreta striolata Fabricius , and Trirhabda sericotrachyla Blake ] displayed distribution patterns characterized by highest population density at the point of release and gradual decrease over distance away from the original point of release . In addition, Severtson et al. conducted an experimental release study with alate cabbage aphids released into centers of small plots of canola and found that the distribution of cabbage aphids also followed a diffusive pattern. These experiments, as well as the predicted frequency distributed depicted in Fig. 2, assume dispersal from a single point. In reality, the actual insect distribution in agricultural systems would more likely involve multiple points of dispersal which, depending on their relative distances to each other and relative positions to field edges, can result in different distribution patterns. If centers of dispersal are located outside an agricultural system, simple diffusion models will predict that the colonization of insects will lead to higher population densities along field edges as compared to inwards into an agricultural system. However, if dispersal centers are located within an agricultural field, the bell-shaped curve distribution of insects will result in lower population density along field edges and higher population density in the interior. Such a counter-edge effect distribution pattern has been noted in nymphs of potato psyllid, Bactericera cockerelli Sulc , in commercial fields of potato .Despite support for the simple diffusion model, this model does not explain the initial aggregation point and therefore what is driving the establishment of insect populations near edges. In addition, Liebhold and Tobin argue that the relevance of simple diffusion models to predict spatial distributions of insects is limited to small spatial scales and fails to account for greater rate of diffusion at large spatial scales. In addition, largescale insect distributions show a certain degree of aggregation and patchiness that varies over time . To account for the patchiness of insect distributions and the faster speed of insect dispersal at a large spatial scale, Liebhold and Tobin propose stratified diffusion model to consider the effects of stochastic events, such as accidental spread of insects due to human activities and prevailing wind .

That means there will be groups of insect colonies leaping ahead of the main population front line. Each of these new groups become new centers of dispersal. Although stratified diffusion model has been shown to improve predictions of insect distributions compared to simple diffusion models, they are also known to have limitations. Stratified diffusion models,vertical hydroponic nft system just like simple diffusion models, rely on the concept of insect population density over distance as a time-dependent function. As time elapses, insects will eventually spread randomly and evenly across crop fields with little population density variance, failing to account for the aggregation and patchiness in insect distribution in many agricultural systems in the long term.To overcome the limitations of simple and stratified diffusion models, there is a need to revisit the major assumptions of these two models. Both models rely on the assumption that insect movement and dispersal, to a large extent, are intrinsic to their biological processes, such as their natural mobility and population growth rate. Thus, the complex influences of external environment have been simplified. Although stratified diffusion model does factor in the effects of stochastic events on insect distribution, these events often occur at irregular frequencies and within very short duration of time. After these short events, pockets of insects are still expected to spread via simple diffusion mechanism. Therefore, in relation to edge effect, the interest of modeling would be to directly address the question: How far does an edge environment affect the spatial distribution of insects in agricultural systems? The theoretical response to such a question entails three possibilities: Edges have no effect, repelling effect, and aggregating effect on insect spatial distribution. Several influential edge models have been developed to reflect the above mentioned possibilities of edge influence, including null-edge, attractive-edge, and reflective-edge models by Olson and Andow ; absorptive-edge model by Fagan et al. ; and the edge resource model . Therefore, nulledge model is essentially a simple diffusion model, which predicts a bell-shaped distribution of insects within an agricultural system . Unlike null-edge model, reflective-edge model considers edges as unfavorable environments that directly bounce insects back into the interior by altering their direction of movement . Meanwhile, absorptive-edge model assumes that the environment outside an edge is lethal for insects, resulting in declining population density towards the edge. Similarly, attractive-edge model assumes the ability of an edge to pull insects and/or trap them, leading to their aggregation along the edge . Although both absorptive-edge and attractive-edge models produce mathematical simulations for the aggregation of insects along edges, their difference lies in whether or not insects are lost to the adjacent habitat. In absorptive-edge model, once insects cross the edge boundary to the lethal habitat, they are lost from the original habitat. Meanwhile, in attractive-edge model, insects crossing the boundary to less favorable habitat can return to the original and more favorable habitat, leading to their accumulation along edges.

Ries and Sisk argued that accumulation of species at habitat edges is widely accepted to be driven by three mechanisms: spillover, edges as enhanced habitats, and complementary resource distributions. Moreover, they argued that a conceptual model based on resource availability and quality of bordering habitats can be used to predict the likelihood of edge-biased distributions. Of all the influential edge models, the attractive-edge model and the edge resource model most closely resemble the discussed edge biased distribution of insects, providing conceptual basis for the understanding of edge-biased distributions. The strength of attractive-edge modeling approach, as compared to simple diffusion modeling approaches, is its consideration of the constraints imposed by edge environment on insect spatial distribution. These constraints most likely stem from the inherent features of the edge environment , which are relatively stable. Therefore, the attractive-edge model can potentially provide the explanation of edge-biased distribution of insects in the long term as seen from certain case studies of edge effect.In light of an attractive edge as a potential explanation for the occurrence of edge-biased insect distributions in agricultural systems, the following question needs to be discussed: What set of conditions would make an agricultural edge attractive? Before further discussion of this question, it is worth mentioning that the term “attractive edge,” as described by Olson and Andow , should be broadly understood as an edge environment that leads to higher insect density than further inwards into agricultural systems. Therefore, an attractive edge does not necessarily act as favorable environment that attracts insects, but it can also or simply act as a trapping environment that reduces insects’ dispersal.Within the large body of literature on factors affecting insect movement, wind has been investigated extensively. Small-bodied, weak flying, or airborne insect pests often rely on air flows for their dispersal and colonization of crop fields . Studies of small-bodied flies and bark beetles showed less likelihood of dispersal under strong winds. However, in a study of fruit flies [Ceratitis capitata Wiedemann ] dispersal into an area of 3600 ha which was treated with chemosterilant bait stations, Navarro-Llopis et al. concluded that the fruit flies showed an edge effect but traveled over 1 km into the treated area. Wind patterns are relevant to a discussion about edge-biased insect distributions in agricultural landscapes, because the presence of hedgerows and artificial windbreaks along field edges has been shown to create a triangular region right behind it known as the “quiet zone” whose length extends to around twice the height of the barriers . This region is characterized by very weak or no winds . Right next to the quiet zone is the “wake zone” where wind speed starts to increase to its original value . Accordingly, Lewis conducted a series of studies to quantify the distribution of insects in relation to distance from artificial windbreaks in fields. The studies found that there were several fold higher densities of gall midges , moth flies , and seven times more fruit flies and day-flying thrips on the leeward side at a distance equivalent to one wind break height away from the windbreak as compared to unsheltered fields. A similar windbreak-skewed distribution was observed in the lettuce root aphid, Pemphigus bursarius L. .

Interestingly, Nrf2 and SIRT1 can positively coregulate each other. For example, treatments of either renal tubular cells or glomerular mesangial cells with resveratrol parallelly increased Nrf2 and SIRT1 expression. Knockdown of Nrf2 with siRNA decreases the expression levels of SIRT1, and vice versa. +erefore, resveratrol can sequentially or separately upregulate SIRT1 and Nrf2, while down regulation of Keap1 expression, resulting in increased expression of phase 2 antioxidant enzymes, which in turn protect the skin from UV irradiation- and oxidative stress-induced damage. Finally, one study showed that inhibition of phosphatidylinositol-3-kinase prevented the activation of Nrf2 induced by pterostilbene, a resveratrol analog, suggesting that resveratrol can also activate Nrf2 via activation of phosphatidylinositol- 3-kinase.For example, pretreatment of keratinocytes with resveratrol almost completely prevents the activation of NFκB induced by UVB irradiation, suggesting that resveratrol-induced inhibition of NFκB activation could contribute to its anti-UV irradiation properties. Resveratrol-induced upregulation of heat-shock protein 27 and down regulation of caspase 3 could also contribute to its anti-UV irradiation property. +us, resveratrol protects skin against UV irradiation and oxidative stress via multiple mechanisms.Both in vitro and in vivo studies have shown that resveratrol also inhibits proliferation, while stimulating apoptosis of cancer cells via several mechanisms. First,blueberry grow pot resveratrol induces apoptosis and phosphorylation of MAPK/ERK and MAPK/p38 in addition to increasing expression levels of caspase 3 and p53, while conversely, inhibition of p38 abolished its apoptotic effects.

It appears that resveratrol-induced phosphorylation of p53 and apoptosis is mediated by c-Jun NH2-terminal kinases because knockdown of c-Jun NH2-terminal kinase genes prevented both phosphorylation of p53 and apoptosis induced by resveratrol. +erefore, resveratrol-induced activation of the MAPK/p38 signaling pathway likely accounts, at least in part, for its anticancer effects. Regarding antiproliferation of cancer cells, resveratrol inhibits expression of MEK1-P and ERK1/2-P, leading to reductions in cyclin D1 and cyclin-dependent kinase 6 expression, resulting in cell cycle at rest. Moreover, resveratrol also decreased c-Jun levels and reduced DNA-binding and transcriptional activity of activator protein-1, which is required for initiation of DNA synthesis. Other studies showed that inhibition of NF-κB, cyclooxygenase 2, phosphatidylinositol-3-kinase, and P450 isoenzyme CYP1A1 and induction of caspases 3 and 9 also could contribute to anticancer effects of resveratrol. +us, resveratrol induced reductions in expression levels of MEK1-P and ERK1/2-P and decreased activator protein-1 activity could contribute to its inhibition of cancer cell proliferation.+e anti-inflammatory effects of resveratrol have been demonstrated in various in vivo and in vitro models, but the mechanisms of the actions of resveratrol are often unclear, depending on the inflammatory models employed in the studies. One possible mechanism is inhibition of NF-κB signaling pathways. Activation of NF-κB can upregulate transcription of cytokines while IκB inhibits NF-κB activity. Hence, degradation of phosphorylated IκB would increase NF-κB activity. Resveratrol-containing mixture inhibited IκB phosphorylation and decreased NF- κB, resulting in reductions in cytokine production in keratinocytes stimulated by TNF-α. Another study suggests that inhibition of cytokine production by resveratrol seems linked to upregulation of miR-17 expression in keratinocytes stimulated with lipopolysaccharide because inhibition of miR-17 overcame the inhibitory effects of resveratrol on inflammation.

But one study showed that resveratrol increases IL-8 production in keratinocytes stimulated with a combination of TNF-α and IFNc via upregulation of aryl hydrocarbon receptor expression. Inhibition of allergic contact dermatitis by resveratrol could be attributable to the down regulation of interferon regulatory factor 1/ STAT1 signaling pathway and inhibition of phosphorylation of MAPK/p38 and/or phospholipase Cc. Moreover, resveratrol inhibited proliferation and differentiation of CD+ T cells and proliferation of +17 T cells via upregulation of phosphorylated MAPK and downregulation of phosphorylated mammalian target of rapamycin in Jurkat cells. Furthermore, resveratrol-induced inhibition of TNF- α-induced cytokine production in fibroblasts is via activation of SIRT1 because knockdown of SIRT1 abolishes the inhibitory effect resveratrol on inflammation.Cutaneous wound healing is a complex process that can be accelerated by resveratrol via stimulation of neovascularization, keratinocyte differentiation, permeability barrier maturation, and antimicrobial activity. One study showed that resveratrol accelerates cutaneous wound healing and vascularization in aged rats through upregulation of SIRT1 and adenosine monophosphate-activated protein kinase pathway. +e role of SIRT1 signaling in vascularization has also been demonstrated in cutaneous wounds of diabetic mice. Topical applications of resveratrol to the wounded area of diabetic mice stimulated proliferation and inhibited apoptosis of endothelial cells, leading to accelerated wound healing, while either SIRT1 inhibitor or knockout of SIRT1 abolished the benefits of resveratrol in wound healing. SIRT1-mediated benefits of resveratrol in diabetic wound healing can also be attributable to protection of endothelial cells from oxidative stress. In addition, studies in mice indicate that resveratrol accelerates cutaneous wound healing by upregulation of vascular endothelial growth factor mediated by activation of at least two antioxidant enzymes. Because wound infections are the major cause of delayed wound healing, the antimicrobial properties of resveratrol could be another mechanism whereby wound healing is accelerated.

Lastly, the ultimate goal of cutaneous wound healing is the formation of intact permeability barrier, which requires both lipid production and keratinocyte differentiation. +us, resveratrol could also accelerate cutaneous wound healing through its well-known ability to stimulate keratinocyte differentiation and lipid production. Collectively, the resveratrol-induced acceleration of cutaneous wound healing can be attributable to activation of SIRT1 and AMPK signaling, antioxidative stress, and enhanced formation of epidermal permeability barrier.+e mechanisms whereby resveratrol induces apoptosis and inhibition of fibroblasts include inhibition of hypoxia-inducible factor 1, in which activation stimulates fibroblast proliferation while inhibiting apoptosis, downregulation of transforming growth factor β1, miR-17, as well as expression levels of mRNA for collagen 1 and procollagen 3, whereas resveratrolinduced upregulation of antimicrobial peptides is via enhancing expression of sphingosine-1-phosphate, leading to activation of N-FκB-C/EBPα signaling pathway. Resveratrol inhibits melanogenesis by at least four different mechanisms: in human melanocyte cultures, resveratrol inhibited tyrosinase synthesis and activity along with accelerated transport of newly synthesized tyrosinase to proteasomal complex, without dramatic alterations in mRNA levels of either melanocytic microphthalmia-associated transcription factor or tyrosinase; in melan-A cells, inhibition of melanogenesis by resveratrol is via induction of autophagy, leading to reduction in α melanocyte-stimulating hormone levels. +e latter stimulates melanin production and release via activation of melanocortin-1 receptor. Deletion of autophagy-related genes could prevent resveratrol-induced reduction in melanogenesis; in human melanocyte cultures, resveratrol activated c-Jun N-terminal kinase,hydroponic bucket resulting downregulation of MITF expression; and anti-inflammatory effects of resveratrol can be an additional mechanism contributing to decreasing pigmentation. +e antioxidant properties of resveratrol largely account for its antiaging effects.Nutritional overload induced by high dietary intake of fats and sugars is one of the main causes of obesity. Increased consumption of fructose has been associated with the prevalence of metabolic syndrome and obesity. MetS is a group of conditions that elevate risk of cardiovascular disease, stroke, and diabetes type 2, and include glucose intolerance, hypertension, and hyperlipidemia, and only recently neurological dysfunction have become part of the scenario. Fructose is a functional/constitutional isomer of glucose naturally found in fruits and honey, and high fructose consumption is getting recognition as a major cause of MetS . Fructose is a natural sugar that when consumed as part of fruits, vegetables and honey has healthy benefits. For example, blueberry powder dietary supplementation, which contains a high concentration of fructose, counteracts several of the deleterious effects of brain trauma. Since fructose has a chemical structure similar to glucose, and does not directly stimulate insulin secretion , the presence of this compound in the diet produces a lower increase in blood glucose when compared to the amount of other carbohydrates. Furthermore, the presence of water, fiber and antioxidants in the fruit causes fructose to be absorbed more slowly and thus tolerable to the body. On the other hand, fructose when ingested in high concentration for a prolonged time as an additive to meals has a myriad of unhealthy consequences within the spectrum of MetS, such as obesity, systemic inflammation, and behavioral dysfunction. In addition, the long term consumption of high fructose can result in development of nonalcoholic fatty liver disease, a manifestation of MetS which is common in Western industrialized countries. An increasing line of clinical and experimental evidence indicates that high fructose consumption correlates with rising rates of neurologic disorders, such that the study of the mechanisms involved on the impact of fructose on the brain is becoming an area of intense research. Research so far indicates that fructose can affect the brain directly and/ or indirectly by involving peripheral metabolism. This review will mainly discuss how fructose affects the brain via systemic physiology, as the direct effects of fructose on brain cells have been thoroughly reviewed somewhere else. Most fructose is metabolized in the liver after being absorbed by the intestine to the bloodstream. Given the action of liver on detoxification, synthesis of lipids and proteins essential for brain homeostasis, liver dysfunction can have devastating consequences for the brain.

We are starting to understand that liver disorders such as hepatic encephalopathy have serious neurological consequences that have been out of sight of mainstream studies. It is becoming to be understood that byproducts of fructose metabolism in the liver such as triglycerides and other lipid forms may influence brain function. Before agriculture was developed around 10,000 years ago, hunting, gathering, and fishing were the main strategies to procure food. Food was scarce and unpredictable to obtain such that accumulation of calories in the form of adipose tissue was an important strategy to survive times of scarcity. In this context, consumption of foods high in caloric content provided to our ancestors a secure way to cope with times of rainy days. Although it is difficult to establish how much sugar our prehistoric ancestors consumed, it is plausibly that wild fruits and honey were accessible to our ancestors, particularly to those who lived in regions of warm climate and forest such as in the African continent. Nowadays, regions in Tanzania are considered living remnant of full time hunter-gatherers, in which contemporary inhabitants live on what they find: game, plants, honey and fruits rich in fructose. It is important to consider that food procurement demanded high levels of physical activity for our ancestors, and this activity seems to have provided the caloric balance necessary to maintain overall health. The advent of agriculture approximately 10,000 years ago provided a more secure supply of foods, including fruits rich in fructose. The industrial revolution of the nineteen century represents a dramatic game changer for dietary practices as it enabled massive production of processed foods containing high levels of sugary components. In particular, high-fructose corn syrup , main form of currently consumed fructose in the U.S., was launched to market in 1970 based on enhanced sweetness and low price. Depending on the type of HFCS, fructose occupies between 42% and 55% of its composition. Today, fructose is widely consumed in many types of processed foods and fructose appears as an important factor in metabolic and neurological disorders. It has been shown that fructose exerts an impact on metabolic genes related to several metabolic disorders. It is noteworthy that the genomic makeup of living individuals is the product of dietary habits occurring thousands of years ago, as mutations occur in the range of many thousands of years. Therefore, increases in fructose consumption pose a big challenge to our conservative genes, and current habits can tip homeostatic balance towards disease stages. These limitations are even more alarming when considering that sudden increases in sugar consumption post-industrialization have been accompanied by a dramatic decrease in exercise. Although isolated fructose is poorly absorbed by the intestine, over-consumption of fructose results in unhealthy metabolic phenotypes including increased intrahepatic fat content, decreased insulin sensitivity, dyslipidemia and adiposity. In spite of the slow absorption rate of fructose by part of the intestine, excessive dietary fructose can remain in the gut for extensive time as fructose can reach up to a concentration of 2–3 mM before being utilized. The fructose in the gut is transported into the enterocyte through the specific fructose transporter GLUT5, independently from ATP hydrolysis and sodium absorption. Once inside the enterocyte, fructose is transported into the bloodstream via the GLUT2 transporter. It is noteworthy that excessive dietary fructose can overwhelm the absorptive capacity of the small intestine leading to incomplete absorption of fructose.

The activity and composition of the gut micro-biome is also affected by an individual’s attitudes, taste preference, and dietary habits that are likewise influenced by culture, the global food industry, and media. Furthermore, there is growing evidence that the human diet has undergone profound simplification since industrialization, which has occurred too recently on an evolutionary time scale for the human genome to adapt.This maladaption to the modern diet has been hypothesized to be the underlying evolutionary origin of “civilization diseases,” such as cardiovascular disease, in the 21st century.The gut micro-biome is remarkably stable and shares a high degree of functional capability across all human healthy individuals; however, intestinal bacterial communities are diverse and variable from person to person.For example, intraindividual variability of the fecal micro-biota is consistently lower than between-subject variability. Recent discoveries of greater similarities in gut micro-biota between monozygotic and dizygotic twin adults or between family members versus unrelated individuals highlight the powerful impact of shared environment, lifestyle, and diet as a whole on intestinal microbial configuration.Interestingly, in mice, genetics was shown to play less of a role than diet on the gut microbial community.Age and health are also associated with alterations to the intestinal micro-biota that might explain interindividual differences as well.In general, dietary effects on the intestinal micro-biota can occur on short and long time frames. An acute influx of energy and nutrients is assumed to induce bacterial blooms in a short time frame. As expected, short-term dietary modulation in a humanized gnotobiotic mouse model resulted in a significant shift within the micro-biome in a single day.A similar change in fecal micro-biome within a day of a dietary change was confirmed in a controlled-feeding study of 10 healthy volunteers.Likewise,nft hydroponic system in as short as 3 days, dramatic changes in the community composition of the gut micro-biome occurred with alterations in calorie content of the diet for several individuals.

Long-term, diet-driven structural and functional differences in the microbial community are apparent in populations from different geographic areas with very distinct dietary patterns. Studies employing culture-based and culture-independent methods found significant global differences in the fecal micro-biota from individuals in different cultures.For example, children from Burkino Faso practice a diet with high fiber and low animal protein and fat, consisting mainly of cereals, legumes, and vegetables. Italian children practice a typical Western-style diet characterized by high animal protein, simple sugars, starch, and fat with less vegetables and fiber than the diet in Burkina Faso. The microbial composition of children from Burkina Faso revealed higher levels of Prevotella and Xylanibacter , Treponema , and Butyrivibrio , which were absent in the Italian children.A similar observation was reported in a comparison of Bangladeshi and American children. Bangladeshi children, who consumed a diet similar to that of children from BurkinoFaso, exhibited a significantly greater bacterial diversity and distinct microbial community composition enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides in comparison with American children.Both children and adults from the United States have very different micro-biota from rural communities in Malawi and Venezuela. A typical U.S. diet that is rich in protein differs from the diets of Malawians and Venezuelan populations that are dominated by maize, cassava, and other plant-derived polysaccharides. The major change in macronutrient composition may contribute to the higher bacterial diversity of those in Malawi and Venezuela compared to adults living in U.S. metropolitan areas. Comparative studies between different geographic regions have been challenged with multiple dependent factors such as socioeconomic status, genetics, dietary habits, age, hygiene, food quality, pathogen exposure, history of antibiotic use, body composition , stress, physical activity, and other environmental conditions.

Despite ethnic and geographical variation, both comparative and controlled feeding studies conducted in the United States and Africa 63 revealed similar patterns of the Bacteroides−Prevotella balance based on diet. Global macro-nutrient profiles are recognized to modulate the intestinal microbial community. In a study charactering human fecal samples from 98 individuals, Wu et al. found that saturated fat and animal protein decreased microbial diversity and enriched the abundance of Bacteroidetes and Actinobacteria, whereas a plant-based diet with high carbohydrates increased microbial diversity and was linked with Firmicutes and Proteobacteria abundance.In a recent study, gnotobiotic mice colonized with 10 human intestinal bacterial species were provided diets containing various percentages of protein , fat , polysaccharides , and sucrose.Intriguingly, the authors were able to explain over half of the variation in species abundance in the fecal micro-biome depending on the food ingested, even when the mice were fed more complex diets.Recent evidence suggests that extreme changes in carbohydrate intake will lead to a shift in the composition of human gut micro-biota. Although reports of the relative proportion of Bacteroidetes and Firmicutes with respect to carbohydrate intake are contradictory in several studies,certain genera and bacterial families are associated with levels of carbohydrate consumption. For example, in human obese subjects, a declining carbohydrate intake induced a marked progressive decrease of a butyrate-producing subgroup of Clostridial cluster XIVa as well as bifidobacteria.A reduced-carbohydrate, high-protein diet resulted in decreased proportions of butyrate and total shortchain fatty acid by reducing butyrate-producing bacteria such as the Roseburia/Eubacterium rectale group.Likewise, Bifidobacterium levels decreased in mice fed a low-carbohydrate, high-fat “Atkin’s style diet” compared with their counterparts consuming a high-carbohydrate, high-fiber, and low-fat diet.More detailed documentation of diet-induced specific changes on the gut microbial relative abundance was reviewed by Krajmalnik-Brown et al.

Although many inconsistent results have been observed regarding the impact of diet on phylumwide changes in gut micro-biota composition and energyharvesting capacity, many have suggested that the complex relationship might involve the severity of obesity, microbial adaptation to diet over time and perhaps an age−microbial interaction. Notably, the high-fat, low-fiber diet has also been recognized as a well-established model of obesity;thus, the impact of differences in caloric consumption and subsequent response from host metabolic perturbations through weight change needs to be considered. Studies on experimental animals need to control for body mass and composition, which will allow a better comparison of the gut micro-biota without the confounding effects of weight/ adiposity.Although it appears that the overall macronutrient profile affects general patterns of fecal micro-biota, understanding the responses of intestinal microbial communities to major dietary composition presents an additional set of challenges. For example, a carbohydrate-rich diet is often accompanied with elevated dietary fiber intake and a low percentage of protein and fat; hence, the microbial composition should respond to the complex profile of the dietary structure instead of the shifting of a single dietary component. If not specifically controlled, dietary factors will affect the gut micro-biome in both energy intake and relative proportion of macronutrients in the diet. Recently, interest in microbial response to major dietary composition has re-emerged in many reviews.In this section, we will explore the complex influence of dietary structure on the gut micro-biome including gluten-free diet, vegetarian/vegan diet, and food restriction.To determine the effect of a gluten-free diet on the gut micro-biome, a crossover study involving 10 healthy subjects consuming a conventional diet without any restriction,hydroponic nft system except for gluten-containing products, resulted in a reduction in bacterial populations that are generally regarded as beneficial for human health such as Bifidobacterium and Lactobacillus, as well as an increase in opportunistic pathogens such as Escherichia coli and total Enterobacteriaceae.The observed changes might be explained by the associated reduction in polysaccharide intake that may have prebiotic action for certain bacteria. Provision of a gluten-free but polysaccharide- and probiotic-rich food intake could avoid this situation and provide better support to balance gut micro-biota.81Several small-scale culturebased studies examined the effect of a vegetarian diet on the composition of the human gut micro-biota.However, results from these studies offer no clear consensus.A crossover study reported that a Western-style diet high in meat facilitates the growth of Bacteroides, Bifidobacterium, Peptostreptococcus, and Lactobacillus spp. compared to a vegetarian diet.Similarly, elevated Bacteroides spp. levels were observed in a 4 week highbeef diet.Dietary modulation of 12 healthy male subjects with either mixed Western, lacto-ovo vegetarian, or vegan diet in a 20 day crossover study revealed significantly lower fecal lactobacilli and enterococci in the vegetarian diet than in the other two diets. Hayashi et al. reported a predominance of bacteria from the Clostridium cluster XVIII, in addition to high levels of bacteria from Clostridium clusters IV and XIVa in the fecal micro-biome of a strict vegetarian woman.However, Liszt et al.and Kabeerdoss et al.report that the proportions of Clostridium clusters IV and XIVa are lower in vegetarians. The inconsistent findings from these studies might be due to the use of different experimental methods, the limited number of individuals in these studies, or poorly matched control groups.The stool pH was lower among 250 subjects on strict vegan or vegetarian diets with equal numbers of age- and gender-matched control subjects compared to individuals consuming ordinary omnivorous diets, and this likely inhibited the growth of E. coli and Enterobacteriaceae in vegetarian/vegan subjects.

Furthermore, it has been established that microbial− mammalian co-metabolites may be measured in urine that may provide information concerning intestinal microbial metabolic activities.90 Clear metabolic differences in urine associated with the vegetarian and omnivorous diets have been observed, with creatine, carnitine, acetylacarnitine, and trimethylamine-N-oxide being elevated in a highmeat diet and p-hydroxyphenylacetate increased in a vegetarian diet.A 40% calorie restriction in mice for 9 weeks revealed small changes in fecal anaerobic populations using fluorescent in situ hybridization and denaturing gradient gel electrophoresis .Similarly, using conventional anaerobic culture of rat feces,small changes in fecal anaerobic bacterial populations with no significant difference in the bacterial cellular fatty acid profile were observed after caloric restriction.Patients with rheumatoid arthritis who participated in an intermittent modified 8-day fasting therapy also exhibited no changes in the fecal bacterial counts of clostridia, bifidobacteria, Candida, E. coli, Enterococcus, or Lactobacillus. Interestingly, the Lactobacillus spp. and archaeon Methanobrevibacter smithii counts were elevated in anorexia patients compared with healthy controls, and this difference was associated with the increased efficiency in removal of excess H2 from the human GI tract. In hibernating ground squirrels, the relative proportion of Firmicutes was decreased relative to Verrucomicrobia and Bacteroidetes after several months of fasting.Follow-up studies need to address the impact of food restriction in both the short- and long-term scale and the global significance of these changes in the intestinal micro-biota.In normal healthy individuals, the large intestine receives contents that escape from the terminal ileum, which are subsequently mixed and retained for 20−140 h to provide an opportunity for microbes to ferment a range of undigested dietary substances. The transition time through the colon strongly influences the gut microbial community, which has been correlated with stool weight and excretion of bacterial dry matter. Although few data exist on the nutrients that enter the colon from the small intestine, generally, about 85−90% of dietary sugar and starch, 66−95% of protein, and almost all fat are absorbed before entering the large intestine depending on genetics and other dietary factors . It is well established that dietary intake of non-digestible material, in combination with host-derived peptides,bile acids,and mucin,influences microbial anaerobic fermentation activity and microbial population in the colon. Increasing evidence supports that shifts in the microbial composition occur in response to changes in the content of the diet. Such changes can be expected to result from differential effects of substrates on stimulating or inhibiting microbial growth. Perhaps one of the greatest challenges in nutrition is to interrogate the interaction between the complex food matrices that integrate a wide range of biologically active compounds. This raises the question of whether there are specific dietary ingredients that have stronger selective forces on microbial diversity and configuration of functional communities than others. Dietary fiber and complex carbohydrates consist of nonstarch polysaccharides, such as resistant starch and oligosaccharides, as well as edible indigestible plant components that are resistant to digestion by endogenous enzymes in the small intestine and become the primary source of microbial fermentation, particularly in the large intestine.The effect of dietary fiber has long been proposed to contribute to human health through prebiotic enhancement of certain beneficial microbes that produce butyrate,absorb bile acids,decrease colon pH,112 and promote GI motility via shortening of the mean transit time.However, not all dietary fibers have the same effect, which is dependent on their physicochemical characteristics.The prebiotic effect of indigestible polysaccharides on gut micro-biota has previously been broadly discussed.