Nature Ecrogrow

To estimate the extent of incorrectly-predicted pathways in the PMN databases, and to measure the overall accuracy of the computational predictions, both alone and in conjunction with manual curation, we evaluated the prediction of 120 randomlyselected pathways on both the released single-species databases in Pathway Tools and naïve prediction versions generated using only computational prediction . Biocurators evaluated the pathway assignments to the 126 organisms currently in PMN, and classified them as “Expected” , “Broader” , “Narrower” , or as NonPMN Pathways . In the naïve prediction databases, only 15% of selected pathways were predicted within the phylogenetic ranges expected from the literature, and 58% were NPPs. In the released PGDBs, however, 78% of evaluated pathways were predicted as expected . In addition to correcting the prediction for 94% of all NPPs of the surveyed pathways, incorporating curated information also reduced the percent of pathways predicted beyond their expected phylogenetic ranges from 13% to 4%. Thus, the applicationof phylogenetic information and manual curation drastically improves the quality of pathway prediction throughout PMN databases over the use of computational prediction alone. To determine whether different groups of plants can be differentiated solely by their metabolic capacity, we performed multiple correspondence analysis , a type of dimension reduction analysis that is similar to principal component analysis but can be used for categorical data . MCA was carried out using presence-absence matrices for pathways, reactions, and compounds . Reactions were considered present only if at least one enzyme in the species was annotated as catalyzing the reaction. Independently,25 liter pot the plants were categorized according to phylogenetic groups. Dimensions 1 and 3 of the pathway and compound MCA, and dimensions 1 and 2 of the reaction MCA, separated the species into several phylogenetic groups .

Phylogenetic groups that clearly cluster together and away from other groups include algae, non-flowering plants, Brassicaceae, and Poaceae . Dimension 1 separates the chlorophytes from land plants and dimension 3 separates certain angiosperm families such as the Brassicaceae and Poaceae well. No clear separation was observed among other eudicot groups. In addition, dimension 2 of the pathway and compound MCA mostly separated a small number of highly curated species from all the rest . Overall, the MCA clustering shows that some groups of plants can be readily differentiated based on their metabolic information in PMN, while other groups cannot, suggesting that further curation of species in these groups may be beneficial. We next asked which metabolic pathways drive the separation of the taxonomic groups on each dimension . Seventy percent of the variance in dimension 1 was described by 109 pathways, all of which were predicted to be either embryophyte-specific pathways or present in a larger proportion of embryophytes than chlorophytes. This mirrors the separation of the Chlorophyta cluster in dimension 1 of the MCA plot . Similarly, 70% of the variance along dimension 3 was captured by 150 pathways, of which 81 were associated more strongly with Poaceae and 69 were associated more strongly with Brassicaceae . The pathways that contributed 95% of the variance in dimension 1, which separates chlorophytes from embryophytes, were enriched for hormone metabolism . Hormone metabolism may have helped support the increased complexity of land plants compared to their algal ancestors . In contrast, pathways responsible for clustering along dimension 3 were enriched for specialized metabolism , which is more lineage-specific than other domains of metabolism and can help distinguish between clades of angiosperms . Thus, it appears that metabolic data in PMN can effectively differentiate groups of species not only by the presence or absence of specific pathways and reactions, but also by the types of metabolic processes which are related to their evolutionary divergence. One of the major advantages of PMN 15 is the ability to quantitatively and qualitatively analyze omics data in the context of global metabolism for the 126 species represented in the resource.

Here we demonstrate two applications of integrating omics data with PMN 15 to gain novel insights about plant metabolism. Pathway Tools’ Omics Dashboard allows users to visualize omics data across experimental timepoints and conditions across a broad range of cellular subsystems and at multiple scales of resolution . To demonstrate the utility of the Omics Dashboard within a metabolic context, we used a transcriptomic survey of two sorghum cultivars, RTx430 and BTx642, subjected to drought stress . RTx430 is tolerant to pre-flowering drought, whereas BTx642 is tolerant to post-flowering drought. To see if there was any difference in metabolic gene expression between the two cultivars in response to post-flowering drought, we examined differentially expressed genes in droughted plants compared to well-watered plants from the last week of watering to the first two weeks of post-flowering drought . We observed a consistent down-regulation of biosynthetic activity from root tissues in the post-flowering drought sensitive cultivar RTx430 compared to relatively stable expression in the post-flowering drought tolerant cultivar BTx642 . This observation is consistent with the authors’ findings that BTx642 demonstrated higher levels of redox balancing and likely experienced lower levels of reactive oxygen species stress, compared to RTx430, as a result of drought. By analyzing expression patterns of all metabolic genes, we observed a widespread metabolic down regulation in RTx430 root tissue, which was not reported previously . Drought-responsive DEGs were enriched in metabolic genes among both leaf and root tissues. However, contrary to the clear cultivar-specific trends shown in the root DEGs , there was no clear trend in expression patterns of metabolic genes in the leaves of either cultivar as a result of drought . To determine whether the consistent reduction of metabolic gene expression observed in RTx430 roots in response to drought was a global trend in the transcriptome or specific to metabolic genes, we compared relative expression levels of all non-metabolic root DEGs to all metabolic root DEGs in both cultivars during the same 3-week period.

While the average relative expression decreased each week among both metabolic and non-metabolic genes in RTx430, the down regulation was greater among metabolic genes at both time points . In contrast, BTx642 roots showed no difference in expression among both metabolic and non-metabolic genes in response to drought , suggesting a global metabolic homeostasis in sorghum drought tolerance. By comparing the patterns of expression among DEGs in root and leaf tissues, rather than solely the number of DEGs, analysis via the Omics Dashboards revealed that roots exhibited stronger genotype-specific responses to drought than leaves, which was not observed previously . In addition to offering a visual overview of metabolism via the Omics Dashboard, PMN’s analytical toolkit allows researchers to easily conduct enrichment analyses among a set of genes or compounds of interest. From within a SmartTable, users can view the pathways associated with a set of genes or compounds, and can then ask whether those genes or compounds are enriched for specific pathways. Broader metabolic classifications can also be added to the list of enriched pathways to better understand which area of metabolism are most enriched. For example, among the set of drought-responsive DEGs in RTx430 roots, we observed an enrichment in various domains of carbohydrate and amino acid biosynthesis and degradation, in addition to chitin degradation, consistent with the authors’ observation of drought-induced responsiveness of biotic defense genes . Thus, by combining PMN’s analytical capabilities with its broad set of metabolic data, users can find additional means of supporting existing hypotheses, uncovering novel insights, and finding new avenues for exploration in their own research. PMN 15 data can also be integrated with other cutting-edge datasets to investigate novel biological questions. As an example, we integrated A. thaliana root single-cell RNA-seq datasets from five independent studies to examine cell type specificity of metabolic domains and pathways . We define cell type-specific metabolic domains as those whose constituent genes show significantly higher expression levels in certain cell types compared to their average expression level in total cells. Different metabolic domains showed overlapping as well as distinct cell type specificity . First,25 liter pot epidermal and cortex cells were most metabolically active throughout the various domains of metabolism . This is consistent with previous observations that the major groups of metabolites detected in Arabidopsis roots, including glucosinolates, phenylpropanoids, and dipeptides, were highly abundant in the cortex . In contrast, maturing xylem showed relatively low metabolic activity as the major roles of these cells are structural support and water/soluble transport . Viewed from the level of metabolic domains, this analysis demonstrates a diverse range of metabolic activity across unique cell types in Arabidopsis roots. We next probed cell-type specificity of individual pathways. Among the 198 pathways associated with at least 10 genes, 40 pathways showed specificity in at least one cell type compared to their background gene expression levels represented by the average expression level of the pathway across all cell types . For example, in actively dividing cells, such as meristematic xylem cells, pathways involved in pyrimidine, histidine, arginine, and lysine biosynthesis showed high activity . These pathways are involved in essential metabolism, which are critical for maintaining cell division and growth. On the other hand, hormone biosynthesis pathways, such as cytokinin glucoside and gibberellin, showed high activity in the cortex. This is consistent with current understanding that the cortex is one of the predominant cell types that synthesizes these two hormones in the Arabidopsis root .

By elucidating cell type-level activity of metabolic pathways, we can begin to map metabolism at cellular and tissue levels, which will be instrumental in understanding how metabolism affects plant development and responses to the environment as well as enabling effective engineering strategies. Similar to cell-type specificity, the concept of pathway divergence at the individual cell level can also be explored using single-cell transcriptomics data. To probe this question, we asked whether isozymes catalyzing the same reaction are more likely to be expressed in different cells compared to enzymes catalyzing different reactions in the same pathway. Isozymes are defined as enzymes encoded by different genes catalyzing the same reaction, which are usually the result of gene duplication events. We computed Spearman’s correlation coefficient to measure gene expression pattern similarity between a pair of enzymes across Arabidopsis root cells. The coefficients computed based on single cell data were generally lower than that generated by bulk RNA-seq, which may be due to the sparseness of single cell transcriptomic profiles or high heterogeneity of gene expression across cells. Nonetheless, metabolic genes in the same pathway showed higher correlation than randomly sampled metabolic genes , which suggests functional coordination between genes involved in the same pathway at the cellular level. Isozymes were much less correlated than enzyme pairs catalyzing different reactions in the same pathway. This indicates that isozymes may have evolved divergent expression patterns in root cells . Since isozymes are often the results of gene duplication events, this diversified expression between isozymes may contribute to retaining duplicated genes through sub-functionalization or neofunctionalization and fine-tuning metabolic pathways at the cellular level . Recently we introduced the Pathway Co-Expression Viewer, which integrates information from PMN 15 and ATTED-II , a database of gene co-expression, to visualize co-expression of the genes in a pathway for species represented in ATTED-II , Solanumlycopersicum , Oryza sativa , Zea mays , Brassica rapa, Vitis vinifera , Populus trichocarpa , and Medicago truncatula. An example is shown in Supplemental Figure S4A-B; Lysine biosynthesis is currently known to occur via two distinct routes, utilizing either diaminopimelate or α- aminoadipate as an intermediate. Its biosynthetic pathway in plants, cyanobacteria, and certain archaebacteria converts tetrahydrodipicolinate to L,L-diaminopimelate via L,L-diaminopimelate aminotransferase and is distinct from that of other prokaryotes and of fungi . Lysine biosynthesis is of particular importance as it is both an essential amino acid not biosynthesized by mammals and it is the least abundant essential amino acid in cereals and legumes . The co-expression levels of six pairs of genes are in the top 1% of coexpressed gene pairs within ATTED-II, while an additional 10 gene pairs are in the top 5% . This tool provides a convenient way of visualizing the co-expression of genes in a pathway and thus provides clues as to how the pathway may be regulated. PMN 15 introduces an additional feature which provides a new way of visualizing pathways that span intracellular compartments and include transport reactions. For example, the glutamate-glutamine shuttle from AraCyc is a pathway in which glutamate and glutamine are exchanged between the mitochondria and chloroplast as a means of ridding the mitochondria of ammonium produced during photorespiration .

The bear’s habitat may also have included honeybees, but this is speculative. The genus appears to have originated in Europe dispersing into Asia, Africa as well as North America. In North America the fossil record of this lineage is represented by a single species from the Miocene of Nevada. The most likely route that the Apis lineage took to arrive in North America would have been via the Bering Isthmus, which was present throughout the Neogene until ~5–7Ma. This land connection would have allowed for the existence of expansive high-latitude terrestrial continuity, spanning the northern reaches of the Eurasian and North American continents. Thus Apis in North America may have originally inhabited this Arctic biome before dispersing southward into the mid-latitudes of North America. In which case, the polar P. abstrusus may have had opportunity to supplement its diet with honey. Aside from the Beaver Pond site fossil bear, all other basal ursines are known from the northern mid-latitudes of Eurasia and North America . The lack of fossil bears in the intervening latitudes reflects the scarcity of northern Neogene vertebrate fossil sites in these regions. Thus, the discovery of the Beaver Pond site P. abstrusus at 78°N fills a substantial geographical gap. The finding also shows that early ursines were adapted to northern forests with snowy winters. Moreover, the Beaver Pond site bear is a small-bodied bear with dental caries and associated with a polar forest, rich in seasonal fruits ,large pots with drainage suggesting that the northern populations of P. abstrusus likely consumed large amounts of sugar-rich foods in the fall, a pattern consistent with preparation for hibernation seen in modern bears.

If so, the Beaver Pond site bear represents the earliest known, and most primitive bear, to have hibernated. Modern ursid hibernators include high latitude/ altitude Asian black bears , northern American black bears , all brown bears , and female polar bears. Also, the fossil species of cave bears are inferred to have hibernated. All living bears also employ a reproductive strategy of embryonic diapause with implicit adaptive value of reducing the cost of reproduction by truncating embryonic development and of optimizing birth season at the most appropriate time. Furthermore, these reproductive cycles may regulate metabolism by facilitating earlier entry of pregnant females into winter-dormancy state. In the context of the phylogeny of modern bears the northern americanus-arctos-spelaeus-maritimus clade appears to have acquired hibernation from a single ancestor. The case for Asian black bear is ambiguous because its nearest relatives are not known to hibernate; namely the sloth bear of India, the sun bear of Southeast Asia. The early diverging spectacled bear of South America is also a non-hibernator . If the northern adapted Beaver Pond bear was a hibernator, then hibernation can be traced to the ancestor of all modern bears. This would imply that the Asian black bear retains the primitive condition, and the Eurasian ancestor of the spectacled bear, which would have passed through cold Beringian habitat when it first immigrated to North America, also employed hibernation as part of its repertoire for winter survival. In this evolutionary scenario modern non-hibernating bears, are interpreted to have secondarily lost this trait, in association with adaptation to warmer habitats.Fire-induced turbulence has considerable impact on scalar dispersion and momentum transport both during and after the passage of the fire-front across the fuel in wild land fire environments.

The dispersion of scalars such as smoke in turn affects visibility and human health, especially for residents in the wild land-urban interface, while the transport of firebrands poses a severe risk of spotting up to several kilometers away from the fire-front . Moreover, fire behavior is closely linked with the ambient turbulence . Depending on the environment, turbulence in the canopy or the atmospheric boundary layer demonstrably affects fire spread-rates , occasionally in unexpected ways. With a deep necessity to understand fire-induced turbulence both in grassland and forested environments, fire simulations as well as in-situ measurements from burns on small as well as management scales have gained importance. However, the excessive computational overhead involved in simulating fires in forested and grassland environments make them less amenable for extended use. While a fast-running simulation platform like QUIC-fire is able to circumvent this issue, its wind solver outputs the time-averaged flow field, which makes it difficult to analyze the turbulence-driving fire behavior. Given these constraints on computational models, careful examination of observed data from burn experiments can be useful in investigating the coherent motions that characterize fire-induced turbulence. Such examination can potentially also allow for the simplification of the governing equations describing fire behavior based on the relative importance of the different terms involved. In the past, empirically derived models based on the widely used model by Rothermel have been successful in simplifying the complex set of governing equations for successful operational use via the parameterization of several physical quantities. However, these models are based on laboratory experiments so that their application on management scales is limited.

Another limitation is their inability to provide insights into the complex turbulent environment arising from fire-atmosphere interaction. Despite their usefulness in understanding the physics underlying fire-induced turbulence, studies relying on experimental data have only recently gathered momentum because of the high risk of damage posed to equipment during data collection in the presence of a flame . Here, we review the key findings of some of the few leading empirical studies that attempted to untangle the complex dynamics underlying fire-atmosphere interaction. Recent studies by Heilman et al. explored turbulent kinetic energy levels at different heights of a 20 m measurement tower, the energy spectrum of the velocity components, and patterns in the turbulent heat and momentum fluxes for two different backing surface fires in the New Jersey Pinelands National Reserve , one of high intensity in 2011 and the other of lower intensity in 2012. For the higher intensity fire, fire-induced TKE near the canopy top was found to be much more substantial compared to the lower heights, making turbulent diffusion of smoke near the canopy top more important than mixing at lower heights within the canopy. Analysis of 1 minute averaged turbulent momentum fluxes showed that vertical turbulent fluxes contributed 40%–80% to the net momentum flux before, during, and after fire-front-passage . The relative contribution of the vertical turbulent heat and momentum fluxes to the net heat and momentum fluxes was found to be highest at the mid-canopy height when compared to near the surface or the canopy top. Estimates of the turbulence anisotropy obtained by Heilman et al. demonstrated the significance of horizontal velocity perturbations over vertical velocity perturbations pre- and post-FFP as well as during FFP periods at all measurement heights. Analysis of the relative contribution of the terms in the TKE budget equations showed that shear production was higher than the buoyancy production at all measurement heights within the over story vegetation layer pre- and post-FFP. Furthermore,square pot the turbulent transport term resulted in a loss of TKE at all measurement heights during FFP in 2011, while its effect was found to be greatly diminished in the lower-intensity 2012 burn. In a separate study, Heilman et al. studied the contribution to turbulent fluxes of sweep-ejection events before, during, and after the passage of a heading surface fire-front through a network of 20 m measurement towers during an operational burn in the New Jersey Pine Barren. It was found that pre-FFP and post-FFP periods were characterized by sweeps and ejections, while FFP periods were characterized by sweeps and outward interactions . These studies encapsulate some of the most recent turbulence analyses on experimental surface fires in forested regions. The FireFlux experiment was a pioneering study on fire–atmosphere interactions in a grassland fire and set a benchmark for similar studies in the future . It comprised a heading experimental grassland fire conducted at the Houston Coastal Center in Texas on 23 February, 2006. Temperature and velocity measurements taken during the experiment by a 43 m instrumented tower were utilized by Clements et al. for a first-order analysis. Derived quantities such as the velocity spectra, turbulent momentum fluxes, and TKE were analyzed to comment on the turbulence levels induced by the fire-front passage. The turbulence intensity generated by the fire was found to be four to five times greater than the ambient atmospheric turbulence. Furthermore, turbulent fluxes demonstrated a downward transfer of high momentum downstream of the fire-front. Heilman et al. took the analysis further with their study of sweep-ejection-like events, which also included results from the three prescribed fires in the New Jersey Pinelands described above.

Their focus was on examining how the frequencies of occurrence of sweep-ejection-like events and their contributions to the mean vertical turbulent fluxes of heat and momentum were modulated by the vicinity or presence of the fire. Contrary to conditions in the absence of surface fires, it was found that ejections were completely dominant in their contribution to heat-flux events and outward interaction events substantially overshadowed the contribution of sweeps and ejections to momentum-flux events in both environments. The most frequent events during FFP were heat-flux inward interaction events and momentum-flux outward interaction events in grassland and forested environments, respectively. As seen above, previous empirical and semi-empirical studies have taken a keen interest in exploring turbulent fluxes and terms of TKE budget equation pre-, during, and post-FFP for insights into the dominant physical processes characterizing fire-induced turbulence. However, the interpretation of coherent structures inferred from the turbulent fluxes and the TKE budget terms is sensitive to the averaging scheme employed to decompose turbulent signals into the mean and turbulent fluctuations from the mean. Additionally, the effect of the fire on the mean kinetic energy budget terms remains to be explored using the existing data. Furthermore, several differences in the fire-turbulence behavior between surface fires in forested and grassland environments remain to be articulated. For instance, we expect the nature of the turbulent transport term to be different, considering that it assumes different levels of importance within the canopy and in the open atmospheric boundary layer in no-fire conditions . Heilman et al. also reflected on the need to understand differences in the behavior of turbulent fluxes for backing and heading fires across all the measurement heights in the canopy. Evidently, there is a need to unify and synthesize observations from burn experiments that have already been conducted via an inter-comparison to develop an over-arching description of the process involved. The analyses presented by Clements et al. and Heilman et al. for four experimental management scale burns conducted in Texas in 2006 , in the New Jersey Pinelands National Reserve in 2011 and 2012, and in the New Jersey Pinelands National Reserve in 2019 are synthesized and re-investigated in this study. Here, we aim to fill the gaps in the previous analyses on these data regarding the coherent motions arising out of fire-atmosphere interaction when juxtaposed with the background canopy turbulence or open atmospheric turbulence, depending on the surface-fire environment. High-frequency 10 Hz measurements in the case of the sub-canopy fires and 20 Hz measurements in the case of the grassland fire for velocity and temperature are utilized. We first introduce the data by exploring the slowly-varying parts of the velocity components and temperature for changes occurring in the flow over relatively longer time scales. We then investigate pre-, during, and post- FFP wind-rose statistics for a visual representation of the combined changes induced by the presence of the fire and ambient wind shifts. Finally, we compute the turbulent fluxes and terms of the TKE budget equation; we comment on the effect of the former on the latter and on the physical significance of both. From these quantities, computed at different heights above ground level , we seek insights into the more persistent coherent structures, the key fire-spread mechanisms, and the dominant turbulence generation and TKE redistribution processes, along with the relevant vertical length scales. Another important and relatively unexplored question of interest is the effect of FFP on the terms of the MKE budget equation, which is investigated here for the sub-canopy surface fires. We aim to draw a comparison of insights among all the three scenarios considered here: heading surface fire beneath the canopy, backing surface fire beneath the canopy, and heading surface fire in a grassland.

The Food Rating Log included a 9-Point Hedonic Scale for each food item consumed, on which participants rated each food from 1 = “dislike extremely” to 9 = “like extremely.” This Hedonic Scale was originally developed by the U.S. Armed Forces to measure soldiers’ food preferences , but is now used by NASA to assess astronauts’ food preferences, as well. For each participant, I averaged their daily food ratings so that each participant had 8 average daily food rating scores, with 1 being the lowest possible rating and 9 being the highest possible rating. I also conducted exploratory analyses in which I evaluated each food item’s average rating. These exploratory analyses provided insight into which individual food items should be replaced, but these analyses were not included in the study’s main analyses. Every evening , participants completed the Food Monotony Scale , adapted from questions previously used by Redden in NASA-funded studies. The scale included three questions, with two questions asking participants to rate their satisfaction with food variety from 1 to 9 . The remaining question asked participants to rate their boredom with food from 1 to 9 . However, this question was sometimes negatively correlated with the other two questions, suggesting that participants misread the wording of the response options and interpreted 9 as indicating high boredom. Consequently, only the first two items were used in analyses. This resulted in consistent positive correlation between the two items every day. These two items were averaged to calculate 8 average daily satisfaction with variety scores, with 1 indicating lowest satisfaction with variety and 9 indicating highest satisfaction with variety.

If a participant ate half of a food item on Monday and finished that food item on Wednesday,nft vertical farming only their Monday rating was included when calculating that participant’s daily average food rating. On two instances, one participant ate half of a food item in the morning and the other half of that food item in the afternoon. In these instances, I averaged the food ratings and counted them as a single rating. If a participant smelled or tasted but did not eat a food item, the ratings were included in analyses, just as if the food had been eaten. Three participants requested and ate additional food items during days 3 and 4 of the experimental condition. Providing these additional food items was considered acceptable because the trading and sharing of food would likely be common during spaceflight. One participant was provided with another Asian Noodle and Indian Potato Entrée, one participant was provided with two more BBQ Chicken Sandwiches, and one participant was provided with two more applesauce pouches and two more yogurt pouches. Participants’ ratings of these additional food items were included when calculating participants’ daily food ratings. When computing the average rating a particular food item, I averaged ratings if one participant rated the food twice in one day. However, I used only the first rating if a participant rated the same food item on two separate days. This is the same way that I assessed ratings when computing participants’ daily food ratings. However, when computing average ratings of particular food items, I did not include the ratings of any additional items that were requested by participants, so that each participant’s evaluations were weighted the same . Two items were provided twice in the experimental condition. All ratings for the Italian-Style Sandwiches were averaged together to compute its average food rating.

The same approach was used for Turkey Jerky. Eight individuals participated in the study. One participant had a medical emergency on Thursday of the Control week, leading to extreme changes in diet , the inability to weigh the participant in-person, and the delayed completion of surveys. Additionally, it was unknown if the medical event led to altered eating on the other days of the study. Consequently, this participant was excluded from all analyses, leaving a sample size of N = 7.The remaining seven participants were comprised of four females and three males . Participants were not asked to report their precise age, but they all appeared to be in their late 20’s to early 30’s – largely mirroring NASA selected astronaut candidates, whose average age is 34 . The seven participants were of Caucasian descent. A sample that more accuracy reflected the U.S. population would have been preferred, but the sample nevertheless reflected NASA’s former astronaut population . Prior to participating in the study, participants reported they ate the breakfast that was served at work a mean of 2.43 times a week , the lunch a mean of 3.86 times a week , and the dinner a mean of 3.00 times a week . Prior to participating in the study, participants reported most commonly eating their meals at the cafeteria/Mezz at work , at their desks , and at home . No participant reported that they ate foods such as juice or meal replacement bars most days. However, participants did report having food patterns, such as eating protein shakes or oatmeal most days. The anonymous personality survey that participants completed on the last Friday of the study revealed that participants did not have extremely unusual personalities, as compared to norms based on 1,813 respondents . Compared to these norms, participants in this study scored 1.42 points higher on Extroversion, 0.60 points higher on Emotional Stability, and within a half point of every other measured personality trait. These comparisons were computed using the worksheet designed by DeNeui to compare TIPI scores to TIPI norms . These comparisons are shown in Table 5, with each participant depicted as a number.The primary aims of this study were to investigate the impact of a possible commercial space food diet on nutrient intake, food satisfaction, psychological health, and physical health. These aims were investigated by having a sample of aerospace employees eat a diet of commercial, ready-to-eat food for four days one week, and comparing their outcomes to when they ate essentially as normal for four days another week. The seven employees that participated in this study were an ideal sample, given that they had a high workload and represented the type of space enthusiast that will likely seek out commercial space flights, once they become more readily available.

These employees had relatively ordinary eating habits and average personalities, being just slightly more extraverted and emotionally stable than a normedsample. Their adherence to the study was extremely high, largely driven by their desire to contribute to the future of space food.The experimental diet was designed to meet nearly all nutrient recommendations set forth by NASA and to be highly satisfying. Consequently, I had hypothesized that while in the experimental condition, participants would consume the same amount of calories as they did while in the control condition. I had also hypothesized that there would be no significant decline in caloric intake across the four days of each condition. The results of this study coincided with these hypotheses. When caloric intake was computed based on participants’ self-reported food intake, there was no significant difference in caloric intake between conditions and no significant change in caloric intake over time. Although the experimental diet was designed to be highly satisfying, it was nevertheless made entirely of commercial, ready-to-eat food. Consequently, I had hypothesized that while in the experimental condition, participants would rate the food as being slightly less hedonically rewarding and slightly more monotonous, with “slightly” being defined as less than 2-point decreases on the 9-point scales assessing hedonic food ratings and satisfaction with variety. In line with these hypotheses,vertical tower for strawberries the experimental food, as compared to the control food, was rated 1.345 points lower on the hedonic food rating scale and 1.750 points lower on the scale assessing satisfaction with variety. In both instances, these differences between conditions were statistically significant . Consequently, as predicted, the experimental diet was rated as being slightly less hedonically rewarding and slightly more monotonous.I had also hypothesized there would be no significant decline in food satisfaction over the four days. In line with this hypothesis, there was no significant interaction between condition or time and no significant main effect of time on either hedonic food ratings or on satisfaction with variety. Thus, although participants rated the experimental diet as being slightly less hedonically rewarding and slightly more monotonous, the diet did not become less rewarding or more monotonous over time. Because the diet was comprised of long shelf-life, ready-to-eat food, it contained few vegetables and was a relatively sweet, salty diet. Consequently, I had hypothesized that during the experimental condition, as compared to during the control condition, participants would show higher cravings for vegetables, lower cravings for salty food, and lower cravings for sweets. The results showed that, in line with the hypothesis regarding sweets, participants reported lower cravings for sweets while in the experimental condition. However, contrary to my hypotheses regarding cravings for vegetables and salt, there were no significant differences between conditions on cravings for vegetables or salt. In post study interviews, some participants reported they would have liked to have seen more vegetables and more salty food. Unexpectedly, there was a significant interaction between condition and time on cravings for meat, with participants in the experimental condition craving meat significantly more than participants in the control condition on day 2.

Although cravings for meat were not significantly different on the other days of the week, this significant result coincides with participants’ qualitative feedback that they would have liked to have seen more meat in the experimental condition. The experimental condition was designed to be nutritious and highly satisfying, and was therefore expected to meet participants’ psychological needs. Consequently, I had hypothesized that while in the experimental condition, participants would show psychological health that was equivalent to their psychological health while in the control condition, as indicated by no significant differences in mood, perceptions of social disconnection, and perceived stress. I also hypothesized there would be no significant decline in psychological health over the four days, as indicated by non-significant time by interaction terms. In line with these hypotheses, participants showed no significant differences in perceptions of social disconnection, perceived stress, or mood between conditions. There were also no significant differences in perceptions of social disconnection or perceived stress over time. The only mood that changed significantly over time was fatigue; participants reported being less fatigued on the fourth day of each week than they were on the first day of each week. The time term was also significant for the mood of vigor, however pairwise comparisons showed no significant differences on any particular day. Thus, there was no significant decline in psychological health over the four days. The experimental diet was designed to be nutritious, and I had anticipated participants would consume equivalent calories in both the experimental and control conditions. Consequently, I had hypothesized that while in the experimental condition, participants would have physical health that was equivalent to their health while in the control condition, as indicated by no significant differences in sleep or self-reported health and no significant weight loss. I also hypothesized there would be no significant change in self-reported health or weight over time. In line with my hypotheses for sleep and self-reported health, participants showed no significant differences in global sleep scores or self-reported health between conditions, and no significant decline in self-reported health over time. However, contrary to my hypothesis for weight, participants in the experimental condition lost significantly more weight than participants in the control condition. In the control condition, participants lost just 0.071 pounds from Monday to Friday, a change that was not significant. Conversely, in the experimental condition, participants lost 2.157 pounds from Monday to Friday, a change that was statistically significant. Why did participants lose more weight in the experimental condition if they didn’t eat fewer calories? There are many possible explanations. It is possible that participants lost fat mass or lean mass due to eating less in the experimental condition. However, given that there were no significant differences in caloric intake between the two conditions, and that my visual checks of the leftovers showed that participants accurately reported their food intake, this is unlikely. Participants were not asked to record their exercise, and consequently, it is possible that participants exercised more during the experimental week, resulting in weight loss. However, there were no significant differences in vigor or fatigue between the two conditions, and consequently this is also considered unlikely.

Small molecules have a long history of acting as drugs for the treatment of hypertension, infections, heart failure, diabetes, asthma, rhinitis, and tumors and comprise approximately 75% of the anticancer drugs approved by the FDA from 1981 to 2014.Recently, many small molecules target EMT and exhibit good therapeutic effects on retarding progressive tissue fibrosis and cancer in experimental conditions.In addition, it is worth noting that many small molecules, such as tivantinib, trametinib, linsitinib, nintedanib, and binimetinib, are in ongoing clinical trials for the treatment of tumors.These cases show promising prospects for treating fibrosis and cancer, which encourages researchers to find effective small molecule drugs for treating fibrosis and cancer. In this review, we describe some important transcription factors, signaling pathways, RNA‐binding proteins and microRNAs and several novel regulators that contribute to EMT and further present some small molecules that exhibit therapeutic effects against EMT. Targeting these mediators with these compounds may be a promising therapeutic strategy to treat fibrosis and cancer.Briefly, histological and pathological analyses show that epithelial cells are present in single cell layers or multilayers and show apical‐basal polarity. Epithelial cells not only interact with the basement membrane with integrins but also communicate with each other via specialized intercellular junctions,round plastic pots including desmosomes, subapical tight junctions, adherens junctions and scattered gap junctions.

These interactions help maintain epithelium integrity and function. However, some stimuli drive EMT in pathological conditions. During the process of EMT, epithelial cell‐cell junctions are dissolved, and the epithelial cells lose their apical‐basal polarity and acquire front‐rear polarity. In addition, the cytoskeletal architecture is reorganized, and E‐cadherin expression is replaced by N‐cadherin expression, which enhances cell motility and invasiveness. In fibrosis, mesenchymal‐like cells transform into myofibroblasts, which can be activated to produce excessive collagen, and in tumors, these mesenchymal‐like cells migrate along with the circulatory system to a secondary location where they form a secondary tumor via mesenchymal‐epithelial transition .It is worth noting that tissue fibrosis and tumors share the common process of EMT, which suggests that targeting EMT may be an effective strategy to treat both fibrosis and tumors . EMT is regulated by various mediators such as transcription factors, signaling pathways, RNA‐binding proteins, and miRNAs. In addition, there are many small molecules that exhibit effective therapeutic effects on tissue fibrosis and tumors by suppressing EMT via targeting these mediators.Snail is a zinc‐finger transcriptional repressor that consists of three isoforms, Snail1, Snail2, and Snail3. Among them, Snail1 and Snail2 are activated in the EMT during development, fibrosis, and cancer. The upregulation of Snail1 is found in many different types of cancer such as gastric, colorectal, and prostate cancer.In addition, the over expression of Snail1 enhanced the motility and invasion of prostate cancer cells, and the silencing of Snail remarkedly suppressed the adhesion, migration, and invasion of Hep‐2 cells.Further study revealed that the knockdown of Snail blocked the EMT, which was accompanied by the down regulation of the expression of MMP‐2, MMP‐9, vimentin, N‐cadherin, and fibronectin.

Moreover, Snail expression was demonstrated at different stages of kidney fibrosis, and the reactivation of Snail‐induced renal fibrosis20 . Furthermore, hypoxia‐inducible factor 1α mediated EMT by regulating Snail and the β‐catenin signaling pathway in early pulmonary fibrosis induced by paraquat.Based on these findings, it was suggested that Snail played a key role in the EMT during fibrosis and cancer, and the targeted inhibition of Snail expression might be an effective therapy to treat fibrosis and tumors.Metformin is a first‐line drug for treating type II diabetes mellitus that has shown a therapeutic effect on many cancers. Further study revealed that metformin increased the expression of E‐cadherin, miR‐200a, miR‐200c, and miR‐429 and decreased the expression of miR‐34a, vimentin, Snail1 and ZEB1 in transforming growth factor‐β ‐induced EMT in the colorectal cancer cell lines SW480 and HCT‐116 .In addition, some compounds derived from natural products have also shown significant intervention in fibrosis and tumors by targeting Snail . Toosendanin, a triterpenoid isolated from Melia toosendan Sieb. et Zucc , isused to prevent and control agricultural pests.Recently, it was reported that toosendanin significantly inhibited TGF‐β1‐induced EMT in lung cancer cells via the extracellular signal‐regulated kinase /Snail pathway and suppressed EMT and tumor growth in pancreatic cancer by deactivating the RAC‐α serine/threonine‐protein kinase /mechanistic target of rapamycin pathway , which suggests that toosendanin is a promising pharmacological agent for the treatment of cancer.A recent study revealed that neferine enhanced oxaliplatin sensitivity by inhibiting EMT via the Snail pathway.In addition, ponicidin is a major diterpenoid compound extracted from Rabdosia rubescens Hara that exhibited a therapeutic effect on TNF‐α‐induced EMT and the metastasis of colorectal cancer by targeting the Akt/glycogen synthase kinase‐3 β /Snail pathway. Moreover, ferulic acid is a bioactive component derived from Ligusticum chuanxiong Hort that suppressed EMT induced by TGF‐β1 via inhibiting the Smad/integrin‐linked kinase/Snail signaling pathway in a renal proximal tubular epithelial cell line , suggesting that ferulic acid might be potent fibrosis antagonist.The two ZEB family members, ZEB1 and ZEB2, are transcriptional inhibitors that are involved in cell proliferation, migration, invasion, and apoptosis.

Extensive studies have confirmed that ZEB1 is upregulated in the EMT and plays a key role in the development of tumors and fibrosis.It was reported that the Np63‐miR‐205 axis increased epithelial marker gene expression and decreased mesenchymal marker gene expression in oral squamous cell carcinoma by down regulating ZEB1 and ZEB2.Moreover, the heterogeneous expression of ZEB1 induced by EMT played an important role in metastasis through the regulation of miR‐200c.In addition, miR‐302a‐3p exerted a protective role via inhibiting ZEB1 and EMT in diabetic kidney disease.These results suggest thatvarious mediators contribute to EMT via the ZEB signaling pathway, suggesting that ZEB is a promising target for the treatment of fibrosis and tumors. Decitabine is a drug used to treat myelodysplastic syndromes that inhibited EMT by regulating the miR‐200/ ZEB signaling pathway in non–small‐cell lung cancer PC9 cells.In addition, a phase Ib/II clinical trial revealed that low‐dose decitabine enhanced the efficacy of immunotherapy in patients with drug‐resistant relapsed/refractory alimentary tract cancer, making it an attractive therapy for cancers.104 Silibinin, a bio-active component from Silybum marianum Gaertn., exhibited anticancer properties in multiple types of cancer, such as bladder and lung cancer . Recent studies revealed that silibinin reversed EMT by inhibiting the expression of ZEB1, vimentin, and MMP‐2 as well as the transactivation of β‐ catenin in bladder cancer metastasis.Furthermore, the combined treatment of silibinin with trichostatin A or decitabine suppressed EMT in non–small‐cell lung cancer.These studies suggest that silibinin is an important candidate anticancer drug. Honokiol was extracted from the seed cones of Magnolia grandiflora L. and showed a therapeutic effect on various cancers. Honokiol effectively inhibited EMT in breast cancer through the STAT3/ZEB1/E‐cadherin axis and reversed EMT in renal cell carcinoma via miR‐141/ZEB2 .STAT3, a member of the STAT protein family, can be phosphorylated as a transcription factor and plays a key role in various cellular processes, including cell growth, apoptosis, and differentiation. Hypoxia is a key mediator that induces EMT during tumor initiation and metastasis, and STAT3 promotes HIF‐1α expression to induce EMT by binding to the promoter of HIF‐1α. In addition, STAT3 was identified as a positive regulator that aggravated TGF‐β1‐induced EMT.In particular, the JAK2/STAT3 signaling pathway had a significant effect on the EMT in multiple cancers. In addition, STAT3 cooperated with other transcription factors promoting EMT, such as Twist and ZEB1.For example, the expression of p‐STAT3 and ZEB1 was positively associated with metastasis, and they cooperatively enhanced EMT in colorectal carcinoma Moreover, STAT3 was upregulated in TGF‐β1‐induced EMT during renal fibrosis, implying that STAT3 is an innovative target for the prevention of fibrosi.Furthermore, there are many mediators that induce EMT through the activation of STAT3, such as Pin1, HOXB8, miR‐30d, and IL‐6.Sepantronium bromide is an inhibitor of survivin that exhibits anticancer properties in multiple cancer types. A recent study revealed that sepantronium bromide reduced the invasion of glioblastoma induced by radiation and reversed EMT by targeting STAT3.Tanshinone IIA is a major bioactive component from the famous medical herb Salvia miltiorrhiza that was reported to attenuate the proliferation of bladder cancer cells . Further study revealed that tanshinone IIA suppressed EMT in bladder cancer cells via the modulation of the STAT3‐CCL2 signaling pathway.In addition,hydroponic bucket tanshinone IIA blocked EMT by regulating the TGF‐β/Smad pathway in peritoneal fibrosis.From these data, it was suggested that compounds that target EMT might have both anti-fibrotic and anticancer properties. In addition, polyphyllin I, a steroidal saponin derived from Paris polyphylla, has shown anti inflammatory and anticancer properties. It was suggested that polyphyllin I, which reversed EMT by modulating the IL‐6/STAT3 pathway, served as a novel solution to conquer EGFR‐TKI resistance in non–small‐cell lung cancer. Therefore, combined treatment with polyphyllin I and erlotinib is a promising therapy for lung cancer patients to strengthen drug efficacy and reduce drug resistance.The other compound, quercetin, is a flavonoid widely distributed in fruits, vegetables, and beverages that shows antioxidative, anti inflammatory, and anticancer properties.

Quercetin reversed IL‐6‐induced EMT in pancreatic cancer cells through STAT3.Collectively, the data indicate that the use of compounds targeting STAT3 might be an effective approach for curing fibrosis and cancer.TGF‐β1 plays a crucial role in various cellular functions, including cell growth, proliferation, differentiation, and apoptosis, and is considered a key mediator in EMT during the processes of tumor formation and fibrosis.Many components contribute to EMT through the TGF‐β1 signaling pathway, which indicates that the inhibition of the TGF‐β1 signaling pathway may be effective in the treatment of cancer and fibrosis. Several excellent reviews have discussed the role of the TGF‐β1 signaling pathway in tumors and fibrosis well. Here, we present several important small molecules that suppress EMT in tumors and fibrosis by targeting the TGF‐β1 signaling pathway . Galunisertib, also known as LY2109761, is a TGF‐β receptor kinase inhibitor that specifically down regulated the phosphorylation of Smad2 and upregulated E‐cadherin expression in cultured human hepatocellular carcinoma cell lines, implying that it could suppress the EMT.Galunisertib is now in ongoing clinical trials in patients with glioblastoma, pancreatic cancer, and hepatocellular carcinoma.Nobiletin is a flavonoid compound isolated from Citrus depressa that suppressed EMT by antagonizing the TGF‐β1/Smad signaling pathway in human non–small‐cell lung cancer cells.In addition, oridonin is a diterpenoid from Rabdosia rubescens Hara that inhibited EMT via blocking TGF‐β1/ Smad2/3 in osteosarcoma.Moreover, GW788388 is a novel inhibitor of TGF‐β type I receptor that inhibited TGF‐β‐ induced EMT and fibrogenesis in db/db mice that showed significant diabetic nephropathy.Furthermore, oxymatrine, a bioactive alkaloid from Sophora japonica L., alleviated EMT induced by high glucose through inhibiting the TGF‐β1/ Smad signaling pathway in NRK‐52E cells, indicating that oxymatrine might be a therapeutic agent for diabetic nephropathy.Isoviolanthin, a flavonoid isolated from Dendrobium officinale Kimura et Migo, suppressed TGF‐β1‐ induced EMT through inhibiting the TGF‐β1/Smad and phosphatidylinositol 3‐kinase /Akt/mTOR signaling pathways in hepatocellular carcinoma cells.In addition, vitamin D, a well‐known inhibitor of EMT, inhibited EMT by negatively regulating the TGF‐β1 signaling pathway in human bronchial epithelial cells, and MART‐10 suppressed metastasis via down regulating EMT in pancreatic cancer cells.The NF‐κB signaling pathway is widely involved in multiple cellular activities, such as cell proliferation, apoptosis, invasion, and inflammation. NF‐κB plays a vital role in the inflammation of tissue fibrosis, and inhibiting NF‐κB activity reduced inflammation and enhanced recovery from CCl4‐induced liver fibrosis.In addition, NF‐κB contributed to inflammation, apoptosis, growth, migration, and invasion of cancer cells.Recently, it was found that the mediator of RNA polymerase II transcription, subunit 28 modulated EMT through NF‐κB in human breast cancer cells, which suggests that the NF‐κB signaling pathway also plays a key role in the process of EMT.Therefore, targeting the NF‐κB signaling pathway may be a good choice to treat fibrosis and tumors. Osthole, a dominant component in Cnidium monnieri Cuss., exhibited various biological activities including neuroprotective, osteogenic, cardiovascular protective, immunomodulatory, hepatoprotective, and antimicrobial effects. Osthole was found to block TGF‐β1‐induced EMT, adhesion, migration, and invasion by the inactivation of the NF‐κB/Snail pathways in A549 cells .In addition, osthole also attenuated insulin‐like growth factor‐ 1‐induced EMT by the PI3K/Akt pathway and inhibited hepatocyte growth factor‐induced EMT via the c‐Met/Akt/ mTOR pathway in human brain cancer cells.Pterostilbene is a stilbene containing in blueberries hat effectivelyblocked the EMT in breast cancer stem cells by the NF‐κB/miR‐488 circuit.Moreover, pterostilbene negatively regulated EMT and inhibited triple‐negative breast cancer metastasis via inducing the expression of miR‐205.

A far less common practice is to determine the effects of pesticides via oral exposure, in which the study organism is provided with a pesticide-treated food source. This approach has more frequently been used for testing pesticide toxicity among pollinators. Pesticides are added to a diet of sugar water and fed to pollinators, such as honey bees and bumbles bees . This type of bio-assay may be used to determine acute toxicity and/or effects on foraging behavior. With respect to natural enemies, a treated diet may be used to assess oral exposure. For instance, treated honey has been used to assess oral toxicity of several insecticides on parasitoids . Cryptolaemus montrouzieriis a mealybug predator used in integrated pest management programs for citrus. To determine non-target effects of acaricides, C. montrouzieri was provided treated prey, the citrus mealy bug Planococcus citri. Another key natural enemy in IPM programs is Coccinella undecimpunctata , a generalist predator of aphids. In order to evaluate how the neuroactive pesticides pirimicarb and pymetrozine may affect C. undecimpunctata consumption of aphids, the predator was provided a diet of treated Myzus persicae. As some pesticides are specifically designed for ingestion, oral exposure of natural enemies is an important factor to consider when assessing pesticide impacts. Historically, one of the most common toxicological measurements of pesticide exposure is the median lethal dose or the lethal concentration . Though acute toxicity assays are a good method for beginning to understand the effects of pesticides,stacking pots they are limited to the measurement of survivor ship only. Pesticides can induce a much wider range of sublethal effects that impair physiology or behavior .

Studies which consider sublethal effects are viewed as more accurately measuring toxic effects than those which only measure acute effects . For instance, when the parasitoid Aphidius erviwas exposed to lambda-cyhalothrin, the LD20 was found to be 50 times lower than the recommended field rate . Additionally, the study found, that even at such low concentrations, exposure to lambdacyhalothrin decreased the response of A. ervi females to its host aphid, M. persicae. This same parasitoid species also exhibited a change in response to plant-host odor when exposed to triazamate . Although it is worthwhile to determine lethal doses of pesticides for natural enemies relative to applied field rates, this measurement alone could not have predicted the disruptive behavioral effects on A. ervi females. Studies on sublethal effects can be used determine changes in all aspects of the life history performance of natural enemies that result from pesticide exposure. For instance, pesticides have been shown to significantly affect reproduction in the predatory mirid bugs, Nesidiocoris tenuis and M. pygmaeus . For N. tenuis, fresh residues of azadirachtin reduced fertility but those of spinosad did not. Conversely, for M. pygmaeus, spinosad reducedfertility, but azadirachtin did not. Another study found that methoxyfenozide significantly reduced fecundity of Aphidius colemani , while exposure to pure azadirachtin had no significant effect . Interestingly, a pesticide may display chronic toxicity, yet have no significant effects on reproduction. For example, exposure to any one of three insect growth regulators caused an 80% reduction in adult emergence of the lacewing C. externa, but there was no significant impact on the number of eggs laid per female or hatch rates . In this case, solely examining sublethal reproductive effects would have been misleading as a measure of potential demographic effects because the low adult emergence indicates otherwise. Therefore, it is best practice to link several effects of pesticides, lethal and sublethal, to estimate changes in the demography of natural enemy populations.

Demographic toxicology was initially used in 1962 to study the effects of gamma radiation on the intrinsic rate of increase Daphnia pulex . Since then, demographic toxicology has been increasingly employed, as it provides a more complete determination of the effects of a toxicant on the population growth rate of an organism rather than simply the acute effects on individuals . For example, using life table data , critical extinction thresholds were estimated for four economically important parasitoids: Diachasmimorpha longicaudata, Psyttalia fletcheri, Fopius arisanus, and Diaeretiella rapae . Though all species are braconid parasitoids, D. rapae was far less vulnerable to pesticide exposure, suggesting that risk assessments cannot be generalized for an entire guild. Another demographic study found that imidacloprid exposure reduced adult emergence of the egg parasitoid Trichogramma cacoeciae , yet mean longevity of emerged females or the mean number of female offspring per female was not significantly different from controls . In order to more fully understand the effects of pesticides, it is useful to measure both lethal and sublethal effects on natural enemies. Acute toxicity studies can be a useful starting point for determining lethal doses relative to recommended field rates. This is especially necessary when maximum field rates cause 100% mortality, making it difficult to study sublethal effects. Moreover, by determining both lethal and sublethal effects, we can begin to measure how these effects translate to changes in population dynamics. The accuracy of these tests can be increased even further by incorporating multiple routes of exposure, thereby predicting what actually may occur to natural enemies in a field setting. Taken together, the aforementioned bio-assays yield a more complete assessment of pesticide impacts on natural enemies, ultimately informing more effective integrated pest management strategies. The purpose of this dissertation was to assess the effects of reduced-risk pesticides on Hippodamia convergens. This coccinellid is an important predator in high-value tree crops in western North America, namely apples, pears, and walnuts. Hence, the pesticides included in this study are those that are commonly used in these cropping systems. In order to more fully understand pesticide impacts, several different assessment methods were used and are described below.

There were three primary objectives, each one addressed in a different chapter. For more than a decade, regulatory limitations have caused a reduction in the use of organophosphates in the U.S. as successive products have been restricted or can celled according to the Food Quality Protection Act . Additionally, the U.S. EPA’s Reduced-Risk Initiative has created a shift away from OPs toward other classes of insecticides . The goal of this initiative was to encourage the development and registration of insecticides that, compared to OPs, pose lower human and environmental health risks. This included lower health risks to mammals, aquatic organisms, birds, and other non-target organisms, such as beneficial insects . In principle, this initiative would be expected to enhance the potential for biological control of arthropod pests by the natural enemies that had previously been limited by the use of OPs. However, while reduced-risk insecticides may lower human and environmental health risks, they do not necessarily have lower toxicity to natural enemies . It is important to determine the selectivity of insecticide alternatives to OPs, particularly to natural enemies that contribute effectively to pest management . For instance, several reduced-risk insecticides showed acute toxicity to important natural enemies in high-value tree crops in western North America. Spinetoram and spirotetremat were toxic at recommended field concentrations to the predatory mite Galendromus occidentalis. Acetamiprid was toxic to Deraeocoris brevis, a natural enemy of pear psylla, Cacopsylla pyricola. Furthermore,strawberry gutter system novaluron and lambda-cyhalothrin were highly toxic to larvae of two different green lacewing species, Chrysoperla carneaand Chrysoperla johnsoni Henry, Wells and Pupedis . On the other hand, some reduced-risk insecticides appear to be compatible with certain natural enemy species, demonstrating low toxicity. Chlorantraniliprole had no significant effects on survival, parasitism rates, or emergence of seven different species of parasitoid wasps, including two sensitive indicator species, Aphidius rhopalosiphiand Trichogramma dendrolimi. In addition, it had no significant impact on the mortality of the predatory ground beetle Harpalus pennsylvanicus DeGeer when fed treated food or on parasitism rates of the ectoparasitoid, Tiphia vernalis Rohwer when treated directly. Another diamide insecticide, cyantraniliprole, had no significant impact on the mortality of Tamarixia triozaeexposed to residue on either a glass or leaf surface , and caused only 23% mortality of nymphs and no significant mortality of adults of the predatory mirid, D. brevis . For many natural enemies, the selectivity of insecticide chemistries is not yet clear. The primary objective of this study was to determine the acute toxicity of a range of pesticides for Hippodamia convergens, a well-known generalist aphid predator in a wide variety of agricultural systems . H. convergens is especially prevalent in western North America , where it serves as an indigenous biological control agent for aphid pests in high-value tree crops .

As for other natural enemy species, reduced-risk pesticides have also shown acute toxicity to H. convergens. In laboratory and greenhouse bio-assays, the two neonicotinoid insecticides, acetamiprid and imidacloprid, were toxic to H. convergens , and indoxacarb residue was highly toxic even when aged for 14 days . In this study, seven pesticides were tested that are commonly used in high-value tree crops in western North America . These included five insecticides used for management of key pests such as codling moth, Cydia pomonella, plus two pesticides used for management of bacterial or fungal pathogens in these crops. Each pesticide was tested for acute toxicity using laboratory bio-assays for each of three different exposure routes. Natural enemies, such as H. convergens, can experience topical exposure from direct applications of pesticides, residual exposure from a treated plant surface, and/or oral exposure from ingestion of a treated food source . The objectives of this study were 1) to assess the acute toxicity of selected pesticides on two life stages of H. convergensand 2) to determine the difference in acute toxicity through three different exposure routes: oral, residual, and topical. Adult H. convergens were obtained from a commercial source and stored for up to two months in a screened wooden cage at 6 °C in order to maintain them in a state of overwintering hibernation. To prevent desiccation, several 8.5 cm petri dishes lined with cotton wool were included in the cage and sprayed with distilled water on a weekly basis. Prior to use in the laboratory bio-assays, adults were removed from hibernation storage and placed into an incubator maintained at 22 °C, 60-70% RH, and a 16:8 h photoperiod. Males and females were identified and approximately 20 adults were placed into 96.1 ml plastic cups . Cups were lined with cotton wool soaked in a 1:1 honey-water solution and covered with a perforated plastic lid to allow for ventilation. After a period of 24 h under these conditions, adults were then used for bio-assays. To obtain larvae of H. convergens for the laboratory bio-assays, adults were removed from cold storage, sexed, and individual mating pairs were placed into 96.1 ml cups, capped with perforated plastic lids for ventilation, and assigned to the same incubator. These adults were reared on a diet of pea aphids, Acrythosiphum pisum, which are known to provide a high quality diet for H. convergens . 20 adult A. pisum were provided to each mating pair every day. After 3-4 days, males were removed from the cups and the remaining females were fed approximately 20 adult A. pisum per day. When a female oviposited, it was moved to a new plastic cup, and when eggs hatched, the first instar larvae were fed a diet of A. pisum, ad libitum, for a period of 48 h before being used in bio-assays. For each of the seven pesticides tested in comparison to a control, three variables were manipulated 1) life stage , 2) pesticide concentration , and 3) exposure route . For each bio-assay, a minimum of 28 replicates was used. In bio-assays using adults, the gender ratio was 1:1 . 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. Bioassays lasted for a period of 48 h, after which acute effects were recorded. Acute effects were estimated as the number of live and dead or moribund insects , where moribund insects were those that were unable to right themselves. For adult bio-assays, acute effects were recorded separately for each gender.

Targeted application of insecticide has the potential to reduce pesticide usage in conventional farming systems yet maintain an effective control over agricultural pests. Focusing spray along field borders can also potentially address the issue of spray coverage, one of the main problems faced in field-wide treatment of pesticides that severely reduce the efficacy of applied chemicals . An example of successful targeted application of insecticides would be the recent efforts to control brown marmorated stink bug, Halyomorpha halys Stål , in Northeastern USA by focus spraying along edges in peach orchards instead of orchard-wide application . The results are promising as pesticide usage was reduced by 25–61% using this method and the damage on peach caused by brown mamorated stink bugs was also reduced when compared with the common standard practices. In addition, better understanding of edge-biased distributions may be used to optimize deployments of anti-insect nets in the orchard industry . Finally, there is a growing body of literature on the potential use of banker plant systems . In these agricultural systems, the agroecological landscape is manipulated through integration of special plants along crop banks. These banker plants serve several purposes, including nectar and pollen for natural enemies, host plants for alternative prey of natural enemies, and shelter and oviposition sites for natural enemies. Thus,hydroponic nft banker plant systems represent ways to enhance the performance of biological control of crop pest. A very important aspect of banker plant systems is that the landscape manipulation is conducted along field edges, so edge-biased distributions of many insect pests are a contributing factor to the growing interest in this type of agricultural systems.

There are multiple ways in which removal of infected host plant tissue can be employed as an element of disease management. These include removal of reservoir hosts to limit pathogen spillover onto a focal host , roguing of infected focal hosts to limit secondary spread , and removal of localized infections within hosts to limit further infection or to retrain an unproductive plant . Studies of bacterial pathogens in perennial crops have evaluated the utility of pruning as a disease management tool, with mixed results . The removal of infected plant tissues is analogous to measures used for management of trunk diseases, often referred to as “remedial surgery,” as an alternative to replacing infected plants . In this study, we investigated whether severe pruning of Xylella fastidiosa-infected grapevines in commercial vineyards could clear vines of existing infections. Pierce’s disease is a lethal vector-borne disease of grapevines caused by the bacterium X. fastidiosa . After susceptible plants are inoculated by X. fastidiosa, pathogen populations multiply and move through the xylem network, leading to symptoms of reduced water flow , including leaf scorch, cluster desiccation, vine die back, and eventually death. There is no cure for grapevines infected with this bacterium; current strategies for management of PD in California vineyards involve limiting pathogen spread to uninfected vines by controlling vector populations, disrupting transmission opportunities, and eliminating pathogen sources in the surrounding landscape . PD is notable for the numerous sources of variability in infection levels and symptom severity in plants. X. fastidiosa infection levels vary among plant species , grapevine cultivars , seasons , and as a function of temperature .

Like other bacterial plant pathogens , X. fastidiosa is often irregularly distributed within individual hosts. For example, X. fastidiosa infection levels in grapevines may vary by more than 10-fold between grapevine petioles and stems ; in other hosts, infection levels may vary by more than 100-fold between basal and apical sections of shoots . This within-host heterogeneity may be epidemiologically significant if it affects pathogen acquisition efficiency . Moreover, if such variation is associated with protracted localized infection near inoculation points, such heterogeneity may facilitate other disease management tactics. In addition to grapevines, other plant species that are susceptible to X. fastidiosa infection include citrus in South America . Management of the resulting disease in C. sinensis relies on clean nursery stock, vector control, and pruning infected plant tissue from established trees or roguing young plants . The concept of pruning of infected plant material is based on the fact that, in established trees , tissue with early symptoms of infection can be pruned ~1 m proximal to the most symptomatic basal leaf, effectively eliminating infections, as the remaining tissue is free of X. fastidiosa . However, pruning is not adequate for young trees or for removing bacterial infections if any symptoms are present in fruit . X. fastidiosa multiplies and spreads through the xylem vessels, reaching the roots of perennial hosts such as citrus , peach , alfalfa , and blueberry . Nonetheless, under field conditions, chronic infection of grapevines is temperature and season dependent. In regions with freezing winter temperatures, infected plants can recover in winter, curing previously infected and symptomatic grapevines . Infections that occur during spring lead to chronic disease ; however, infections that occur during late summer and fall may cause disease symptoms in the current year, but a high proportion of vines lack symptoms of X. fastidiosa infection in the following year . The biological mechanism behind this winter recovery has been studied but is not fully resolved.

Nonetheless, models that incorporate low temperatures have substantial explanatory power in predicting rates of winter curing of X. fastidiosa infections in grapevine . Infections that occur early in the season may have a longer period during which X. fastidiosa can colonize and reach high infection levels, which may increase the likelihood of the disease surviving over the winter. Following this rationale, if most late-season infections remain in the distal ends of shoots and have lower infection levels, removing the symptomatic portion of the vine might eliminate X. fastidiosa. In other words, the efficacy of pruning infected grapevine tissue could depend on both the time of year in which the plant was infected and on winter temperature. A potential benefit of severe pruning versus replanting is that pruning leaves a mature root stock in place, which is likely to support more vigorous regrowth compared to the developing root stock of a young transplant . Recent attempts to increase vine productivity by planting vines with more well-developed root systems are based on this presumption. However, even if severe pruning can clear vines of infection,hydroponic channel it removes a substantial portion of the above ground biomass of the vine. Thus, a method for encouraging rapid regrowth of the scion after aggressive pruning is needed. We studied the efficacy of pruning infected vines immediately above the root stock graft union—the most aggressive pruning method—for clearing grapevines of infection by X. fastidiosa. We reasoned that if such severe pruning was ineffective at clearing vines of infection, less severe pruning would not be warranted; if severe pruning showed promise, less severe pruning could then be tested. We use the term “severe pruning” to refer to a special case of strategic pruning for disease management, analogous to the use of “remedial surgery” for trunk diseases . To test the efficacy of clearing vines of X. fastidiosa infection, we followed the disease status of severely pruned versus conventionally pruned vines over multiple years, characterized the reliability of using visual symptoms of PD to diagnose infection, and compared two methods of restoring growth of severely pruned vines.Pruning trials were established in Napa Valley, CA in commercial vineyards where symptoms of PD were evident in autumn of 1998. The vineyards used for these trials varied in vine age, cultivar, and initial disease prevalence . All study vines were cordon-trained and spur-pruned. We mapped the portions of the six vineyards selected for study according to evaluation of vines for disease symptoms. The overall severity of PD symptoms for each vine was recorded as follows: 0 = no symptoms, apparently healthy; 1 = marginal leaf scorch on up to four scattered leaves total; 2 = foliar symptoms on one shoot or on fewer than half of the leaves on two shoots on one cordon, no extensive shoot die back, and minimal shriveling of fruit clusters; and 3 = foliar symptoms on two or more shoots occurring in the canopy on both cordons; dead spurs possibly evident along with shriveled clusters. To test the reliability of the visual diagnosis of PD, petiole samples were collected from the six vineyard plots when symptom severity was evaluated for vines in each symptom category; these samples were assayed using polymerase chain reaction . Petioles were collected from symptomatic leaves on 25, 56, and 30 vines in categories 1, 2, and 3, respectively.Next, severe pruning was performed between October 1998 and February 1999 in the six vineyard plots by removing trunks of symptomatic vines ~10 cm above the graft union.

During a vineyard survey, severe pruning was conducted on 50% of vines in each symptom category; the other 50% of vines served as conventionally pruned controls. Sample sizes for control and severely pruned vines in each disease category ranged between six and 62 vines depending on the plot, with at least 38 total vines per plot in each control or pruned treatment. In spring 1999, multiple shoots emerged from the remaining section of scion wood above the graft union on severely pruned vines. When one or more shoots were ~15 to 25 cm long, a single shoot was selected and tied to the stake to retrain a new trunk and cordons, and all other shoots were removed at this time. We evaluated the potential of severe pruning to clear vines of infection, by reinspecting both control and severely pruned vines in all six plots for the presence or absence of PD symptoms in autumn 1999 and 2000. In all plots, category 3 vines were inspected in a third year ; in plot 6, vines were inspected an additional two years . Finally, in plot 6 we investigated chip-bud grafting as an alternate means of ensuring the development of a strong replacement shoot for retraining. To do this, 78 category 3 vines were selected for severe pruning, 39 of which were subsequently chip-bud grafted in May 1999. An experienced field grafter chip budded a dormant bud of Vitis vinifera cv. Merlot onto the root stock below the original graft union, and the trunk and graft union were removed. The single shoot that emerged from this bud was trained up the stake and used to establish the new vine. The other 39 vines were severely pruned above the graft union and retrained in the same manner as vines in plots 1 to 5. Development of vines in plot 6, with and without chip-bud grafting, was evaluated in August 1999 using the following rating scale: 1) “no growth”: bud failed to grow, no new shoot growth; 2) “weak”: multiple weak shoots emerging with no strong leader; 3) “developing”: selected shoot extending up the stake, not yet topped; and 4) “strong”: new trunk established, topped, and laterals developing.All analyses were conducted using R version 3.4.1 . We used a generalized linear model with binomial error to compare the relative frequency of X. fastidiosa-positive samples from vines in the different initial disease severity categories . Next, we analyzed the effectiveness of chip budding versus training of existing shoots as a means for restoring vines after severe pruning. This analysis used multi-nomial logistic regression that compared the frequency of four vine growth outcomes the following season: strong, developing, weak, or no growth. This main test was followed by pairwise Fisher exact tests of the frequency of each of the individual outcomes between chip budded-trained and trained vines . We analyzed the effect of severe pruning on subsequent development of PD symptoms using two complementary analyses. First, we compared symptom return between severely pruned and control vines in the three symptom severity categories for two years after pruning. To appropriately account for repeated measurements made over time, our analysis consisted of a linear mixed-effects model with binomial error, a random effect of block, and fixed effects of treatment , year , and symptom severity category . Next, we analyzed the rate at which PD reappeared in only severely pruned vines from category 3 in subsequent years using a survival analysis. Specifically, we used a Cox proportional hazards model with a fixed effect of plot .

Consumption of a 30% fructose diet for 8weeks resulted in a decrease in serotonin reuptake transporter protein levels in mouse duodenum. Interestingly, SERT-deficient mice are used as a relevant model for depression, suggesting a link between fructose consumption and psychological effect. Experimental evidence indicates that consumption of a high-fructose diet starting during juvenile life promotes a pro-inflammatory state involving both the Central and Peripheral Nervous Systems, and resulting in psychiatric-like disorders in adulthood. Obese phenotype in female rats caused by high fructose consumption is associated with an increase in IL-1β production, microglial reactivity and hyperphosphorylation of tau in the hippocampus, concomitant to neuronal loss and neurological dysfunction at 48 h post-stroke. Fructose-induced insulin resistance is closely associated with the two neuropathological biomarkers of Alzheimer’s disease namely senile plaques and neurofibrillary tangles. Under fructose induced hyperinsulinemic conditions, insulin competes with amyloid b protein for insulin-degrading enzyme, leading to the accumulation of Aβ and deposition of SPs. In addition, the fructose-induced impairment of the insulin receptor signaling culminates in loss of insulin-mediated activation of phosphoinositide 3-kinase /Akt pathway,nft hydroponic and subsequent dephosphorylation of glycogen synthase kinase-3b , which potentiates the phosphorylation and formation of NFTs. The significant correlation between Akt activity/ protein levels found in human Alzheimer’s disease indicates a timedependent and insulin-stimulated PI3-K signaling.

Experimental studies have demonstrated that fructose consumption aggravates the effects of brain trauma on molecular systems engaged in cell energy homeostasis and synaptic plasticity in the hippocampus. Fructose also aggravates the effects of brain trauma on spatial memory in association with a decrease in hippocampal insulin receptor signaling. High fructose consumption under the threshold for establishment of MetS exacerbates the disruptive effects of brain trauma on inflammation and lipid peroxidation in the liver. These effects seem to engage the neuroendocrine growth hormone system with increases of a metabolic/ inflammatory cascade and lipid peroxidation, and disruption of cell energy homeostasis and insulin signaling. Diet-induced metabolic disorders pose a risk for incidence of post-stroke depression, and exacerbate damage caused by ischemic stroke in cerebral vessels. These events result in an increase in BBB permeability and proinflammatory response that may exacerbate infarct volume. The period of fructose exposure seems a critical factor for the involvement of systemic metabolism and subsequent effects on brain. A minimum of 6 weeks of fructose in rodents is crucial for development of MetS with concomitant effects on brain function and cognition. Long-term high fructose consumption in rodents results in decrements in brain plasticity and learning and memory performance. Fructose alters brain molecular pathways involved in mitochondrial bio-energetics and plasma membrane homeostasis, neuronal signaling, and synaptic plasticity. Nevertheless, several studies indicate that a short period of fructose feeding for a duration insufficient to disrupt peripheral metabolism can also affect the brain by reducing cerebral blood flow, myelin basic protein, and the axonal growth-associated protein , concomitant with a decline in hippocampal weight.

Two weeks fructose diet induce inflammation, oxidative stress, impairment of insulin signaling as well as a significant decrease in mitochondrial function in the hippocampus . Although the greater amount of fructose is intuitively worse for systemic physiology, information derived from animal studies is not conclusive since animals adjust their own fructose consumption based on caloric contents. Although the BBB has low affinity for fructose, a short term fructose consumption seem to enable neuronal cells to metabolize fructose as evidenced by increased levels of GLUT5 in hippocampal microglia and cerebellar Purkinje cells . Short fructose consumption also produces insulin signaling alterations accompanied by neurite and synaptic reduction and astroglial activation in the rat hippocampus . Also, the hippocampus and hypothalamus contains the enzyme Ketohexokinase that degrades fructose reinforcing the possibility that fructose can be metabolized in the brain. The phylum Negarnaviricota, composed of viruses with negative-stranded RNA genome, includes species characterized by non-segmented or segmented genomes, the presence or absence of a membrane enveloping the capsid, and a diverse host range including plants and animals. Examples of nsRNA viruses associated with economically important diseases in plants are rose rosette virus, rice stripe virus, citrus psorosis virus, and blueberry mosaic associated virus. Historically, only a relatively small number of nsRNA viruses infecting plants as their primary host have been reporte. Recently, however, more novel viruses infecting plants have been discovered around the world. In the last few years, the use of high throughput sequencing technology has allowed the identification and characterization of new nsRNA viruses in pistachio, citrus, watermelon, and apple. Interestingly, most of these novel nsRNA viruses were classified under the family Phenuiviridae . To date, there are fifteen recognized genera integrating the family Phenuiviridae : Banyangvirus, Beidivirus, Goukovirus, Horwuvirus, Hudivirus, Hudovirus, Kabutovirus, Laulavirus, Mobuvirus, Phasivirus, Phlebovirus, Pidchovirus, Tenuivirus, Wenrivirus, and Wubeivirus.

Except for members of the genus Tenuivirus that are plant-infecting viruses, the members of the other genera infect vertebrates, including humans, and arthropods. Viruses belonging to the recently established genus Coguvirus also infect plants and, although this genus has not been included yet in the family Phenuiviridae, many structural and molecular features and phylogenetic relationships with other phenuiviruses support its classification in this family. With respect to nsRNA viruses, there is only one preliminary report of tomato spotted wilt virus in this host ; however, later studies failed to transmit TSWV to grapevine. During the screening of two selections of Garan dmak and Muscat rose grapevines via HTS, partial sequences with homology to apple rubbery wood viruses 1 and 2 were identified. ARWV1 and ARWV2 are two novel nsRNA viruses with tri-segmented genomes recently discovered in apple trees displaying rubbery wood symptoms in Canada. Based on sequence identity and phylogenetic analysis, ARWV1 and ARWV2 were proposed to be representative members of a new genus, tentatively named Rubodvirus, within the family Phenuiviridae. Here, we report the natural occurrence and discovery of two novel nsRNA viruses, named grapevine Muscat rose virus and grapevine Garan dmak virus , in grapevine plants. Even more, this is the first evidence for the natural occurrence of phenui-like viruses in grapevine. Later, reverse transcription PCR -based assays for the specific detection of both viruses were designed to investigate the prevalence in different grapevine populations. Phylogenetics and transmission of GMRV and GGDV were also investigated.HTS analysis was performed as described by Al Rwahnih et al.. Briefly, aliquots of TNA from source samples were subjected to rRNA depletion and complementary DNA library construction. Later, cDNA libraries were sequenced using the Illumina NextSeq 500 platform using a single-end 75-bp regime. Illumina reads were demultiplexed and adapter trimmed prior to analysis using Illumina bcl2fastq v2.20.0.422. Trimmed reads were subsequently de novo assembled into contigs using SPAdes v3.13. Generated contigs were compared against the viral database of the National Center for Biotechnology Information using tBLASTx. Novel virus contigs were initially identified by their conserved protein domains. Open reading frames were annotated using HMMER v3.1 to look for Pfam protein domains associated with viruses infecting land plants. In the case of Phenuiviridae-like contigs,nft system the large RNAs were annotated with the bunyavirus RNA-dependent RNA polymerase domain. The medium RNAs were annotated with the viral movement protein domain. The small RNAs were annotated with the Tenuivirus/Phlebovirus nucleocapsid protein domain. The association between the small and the medium RNAs was investigated by BLASTn sequence similarity of their 50 ends. These contig sequences were subsequently confirmed by BLASTx hits to the NCBI nucleotide database which produced top hits to different accessions of ARWV2 and ARWV1. To complete the 50 end of each RNA segment present in GMRV and GGDV, the SMARTer RACE 5 0 /3 0 Kit was employed following the instructions provided by the manufacturer. In the case of the 30 ends, the methodology described by Navarro et al.was used, which involved the addition of a poly tail to the RNA template.

A total of 1732 samples collected in three different grapevine populations were screened for GMRV and GGDV using the above-described assays. The NCGR , located in Winters, California, includes selections of table and wine grapevines originated from around the world; the Davis Virus Collection , which is integrated by plants infected with different viruses; and the FPS pipeline of foreign and domestic introductions. The last two mentioned collections belonging to the University of California-Davis. To determine the transmissibility of GMRV and GGDV, plants infected by these viruses were used as an inoculum source in a biological assay. Following the methodology described by Al Rwahnih et al., bud chips from the Garan dmak and Muscat rose grapevines were grafted onto Cabernet franc indicator plants . Grafted plants were maintained in an insect-proof greenhouse for one month to allow the graft to heal before planting in the field. One year later, indicator plants were sampled for virus detection. Likewise, non-graft Cabernet franc plants were used as negative controls. An ML phylogenetic tree was inferred using the RdRp core sequence of the two novel viruses from grapevine reported here, the two viruses recently identified in apple , representative members of all the genera in the family Phenuiviridae and the plant infecting nsRNA viruses in the genera Emaravirus, Orthotospovirus, and Coguvirus . In this tree, GMRV, GGDV, and the rubodviruses ARWV1 and ARWV2 form a monophyletic group with high bootstrap support . In addition, this tentative rubodvirus clade is contained in a superclade that also contains coguvirus and laulavirus clades. The coguvirus clade consists of two members and two tentative members of the genus Coguvirus infecting plants. The trivial laulavirus clade contains the arthropod-associated Laurel Lake virus . The same superclade was observed when the phylogenetic tree was generated from the putative NPs encoded byGGDV, GMRV, and different recognized/tentative members of the family Phenuiviridae ; with GGDV, GMRV, ARWV1 and ARWV2 as a monophyletic group, and the same phylogenetic relationship between the rubodviruses, coguviruses, and LLV. Interestingly, in the ML tree inferred using the MPs of diverse nsRNA viruses , rubodviruses and coguviruses are clustered in two distantly related clades.In the last few years, as a consequence of the increasing application of HTS, many novel nsRNA viruses have been identified, most of which are from invertebrates. Thus, the classification of these viruses has been recently reassessed, with plant-infecting viruses now classified in the order Bunyavirales, Serpentoviralesand Mononegavirales . Recently, the tentative genus Rubodvirus has been officially proposed to classify two novel nsRNA viruses from apple trees, with a suggested species demarcation criteria of <95% aa identity for the RdRp. In the present study, HTS allowed the identification of two novel plant-infecting viruses with segmented nsRNA genome, GMRV, and GGDV, which are also the first nsRNA viruses identified and transmitted in grapevine. Although these viruses infect the same host species, the aa sequence identity between the putative proteins encoded by their genomic RNAs is always below 75% , indicating that GMRV and GGDV are two different viruses. Their genomes encode proteins showing the highest sequence identity with ARWV1 and ARWV2. GGDV and GMRV also share other traits with these viruses, including the number of genomic components, limited to three nsRNAs, identical terminal nucleotides in the genomic RNAs, and the lack of any ORF coding for glycoproteins. Moreover, close phylogenetic relationships between these four viruses are supported by the ML phylogenetic trees reported here, in which, independently of the considered protein , they always clustered in the same clade, which is significantly separated from all the other nsRNA viruses included in the analyses. Altogether these data support the classification of GMRV and GGDV as two novel species in the tentative genus Rubodvirus. When the other bunyavirales are considered, the ML phylograms inferred from the RdRps or the NPs show a close phylogenetic relationship between rubodviruses and coguviruses, which together with the arthropod-infecting LLV, form a superclade nested at a basal node, in closer proximity to arthropod-infecting viruses than other plant-infecting viruses. These data are consistent with the hypothesis, previously advanced for the coguviruses, that all the members of this super clade evolved from a common ancestor virus infecting arthropods. In this evolutionary scenario, the acquisition of the MP gene appears to be the key step in the adaptation of the ancestor virus to plants, an event that likely happened through the typical modular genome evolution process proposed for most eukaryotic viruses. However, the clustering of rubodviruses and coguviruses in two distant clades, observed in the ML tree inferred with MPs , supports the independent acquisition of the MP gene by the ancestor of the viruses included in these two taxa.

Yan et al. demonstrated a 3 week acute effect following alcohol administration in mice that resulted in bacterial overgrowth, as well as an expansion of Bacteroidetes and Verrucomicrobia bacteria while decreasing Firmicutes, with no difference observed after only 1 day or 1 week.For example, daily alcohol consumption for 10 weeks in a rat alters the colonic mucosa-associated bacterial micro-biota fingerprint pattern.Similarly, chronic ethanol feeding for 8 weeks increased fecal pH and decreased abundance of both Bacteriodetes and Firmicutes phyla with a remarkable expansion of Proteobacteria and Actinobacteria phyla in mice.In a human trial, chronic alcohol consumption resulted in the alteration of the mucosa-associated colonic bacterial composition in a subset of alcoholics, with lower median abundances of Bacteroides and higher Proteobacteria. Furthermore, measurement of serum endotoxin suggests a change in microbial function, rather than abundance, which may lead to increased levels of gut-derived pro-inflammatory factors in chronic alcohol consumption. It is noted that the inability to detect clear differences between alcoholics with and without liver disease suggests that chronic alcohol consumption, rather than the disease physiology, is the most important event that appears to alter micro-biota composition.It is now well established that host diet alters the gut micro-biome. Changes in the gut micro-biota composition are also considered an important factor in health and disease.

Dietary assessment has provided us with a window to discover a way to reconfigure the gut micro-biome. In this regard,hydroponic channel the nutritional manipulation of the gut micro-biome serves as a basis for formulating therapeutic approaches that are feasible and acceptable to the general population as a promising way to promote health in the era of personalized nutrition and medicine. Understanding the impact of foods and nutrients on host− microbe coevolution supports the essential role of a mutualistic relationship for intestinal homeostasis, but there remain challenges for nutritionists and scientific investigators alike to determine the “ideal” diet. This review collectively maintains the emerging view that diet supports a specific bacterial community structure and further suggests that a suboptimal dietary composition/quality may promote the development of diseases through introducing intestinal microbial dysbiosis. Major shifts in intestinal microbial composition are often observed when dietary differences between groups are extreme. Only a few population-wide studies are available to date, but some of them support a role of food diversity as a potential mechanism for altering gut microbial diversity. Although it is difficult to determine the causality of observed fecal micro-biota shift with respect to many lifelong changes, generally, an adequate control over influential factors is important for the success of clinical studies to eliminate the drastic effects of unnecessary confounding variables. Many of the studies reviewed here rely on the assumption of equivalence between the term “fecal micro-biome” and “intestinal micro-biome”. Further studies are necessary to elucidate more clearly the exact impact of the selection of different diets on qualitative changes in the gut micro-biota. Some nutrients that have been studied, such as dietary fiber, are a possible option for the maintenance of intestinal homeostasis and improvement of gut health, whereas others may contribute an opposite effect.

Therefore, future research must be focused on looking to improve the effectiveness of diets with an underlying long-term “targeted approach” that allows improvement of intestinal microbial composition and functional activities. In other instances, when dietary differences are small and on a short time scale, gut micro-biota changes are not as obvious, but that is not to say that changes do not occur. An alteration of the gut micro-biota at lower taxonomic levels is still likely to have important functional consequences for the host. Notably, gut micro-biota varies dramatically from individual to individual in lower taxonomic levels. Even small dietary changes may have impacts on the gut micro-biota and altered metabolic activities in the microbial profile that are not easily detected by the phylogenetic/taxonomic methods. Metabolic alterations induced by diet may result in varying the microbial capability of synthesizing substances in the intestinal tract. It appears that measurement of bacterial enzyme activities may be a more sensitive indicator of diet induced changes in the gut micro-biota than taxonomic-based methods. Arguably, absolute microbial population densities are more important than the relative proportion, because these determine the absolute production rates and concentrations of metabolites and signals of microbial origins. Rates of production of fermentation products need to be measured as an index of microbial community function. Further research into the characterization and metabolic activity of the gut micro-biota may provide the key to the influence of the environment on colonic health and disease. Integrating the gut micro-biome data with clinical nutritional assessment, food consumption monitoring, and host phenotyping measurements in future investigations are needed to focus on the identification of metabolic impacts that mediate the effect of diet on gut micro-biota as well as their synergistic effect on host immune function, metabolism, and homeostasis.

Organized by Allison Carruth and Rachel Lee,“The Cultural Politics of Seeds” symposium will look at how gender, ethnicity, and race shape contemporary cultural and political movements related to seeds. Conceived as a forum for integrating research, policy, activism, and art practice, this event will include day-long event with 3 panels and two keynote talks and a related art exhibit at UCLA’s Art/Sci Center featuring Fallen Fruit, the Los Angeles–based art collaborative. By bringing together farmers, artists, academics, and political organizers, the symposium demonstrates that to adequately examine seeds’ diverse functions in culture, taking a multifaceted approach is fundamental. “Moving into a century of 9 billion people and unprecedented pressures on the environment, there is nothing more important than how we will feed ourselves and the sustainability and equity of that enterprise,” says Glen M. MacDonald, Director and Distinguished Professor at the UCLA Institute of the Environment and Sustainability about the upcoming event. “Here is a thoughtful and multifaceted exploration of that challenge.” Participants in the symposium come from across the country, including farmers, artists, academics, and political organizers. Several participants take several of these titles. For example, Stephen S. Jones, a professor, collaborates with graduate students to develop wheat for organic and small farms that are underserved by traditional research programs. Elaine Gan, an artist, lecturer, and Ph.D. student studying Film & Digital Media, is working on a multimedia web project that maps different varieties of rice and the ways in which they bring together biocultural entanglements and political economies. Artist-writer-critic Mathias Viegener will give a presentation on “Feral, Wild, Domestic and Social.” The symposium will include an installation by Fallen Fruit at UCLA Art/Sci Center + Lab . The event’s diverse presenters illuminate the inter-connections between individuals’ experiences working with seeds, and broader social and cultural systems. For example, Lucilia Martinez will give a co-presentation about her family’s development of a successful maize farm with ethnoecologist Daniela Solieri. Solieri works collaboratively with scientists and practitioners to analyze small-scale, local food systems,hydroponic dutch buckets identifying key biological and sociocultural processes that may increase their resilience. The symposium will examine the ways in which seeds lead to the creation of social, political and artistic movements that intertwine with issues of gender, ethnicity, and race. It will explore how seeds become entangled with issues such as globalization, global climate change, and developments in genetic engineering and commodity markets. Finally, it will provide a forum for integrating research, policy, activism, and art practice. According to Carruth, “The symposium brings together an exciting group of scholars in the fields of cultural geography, gender studies, comparative literature, anthropology, environmental studies and science, and plant science along with the three co-founders of LA-based Fallen Fruit as well as longtime urban agriculture and food justice activist Tezozomoc. We are fortunate to have had support from across campus to make this interdisciplinary conversation on the cultural politics of seeds possible.” “The Cultural Politics of Seeds” symposium is part of CSW’s multi-year “Life Ltd” research project, which is addressing the question of what impact recent developments inthe biosciences and biotechnology have had on feminist studies. In this year, the group, led by Principal Investigator Rache Lee, is exploring the rich connections between food, ecology, propagation, and metabolism.

Cosponsors of the symposium include University of California Humanities Research Initiative, Institute for Society and Genetics, Division of Life Sciences, Division of Humanities, Division of Social Sciences, Institute of American Cultures, Department of English, Institute of the Environment and Sustainability, School of Law, Chicano Studies Research Center, and Charles E. Young Research Library.How do people engage with fruit, and how does fruit engage with us? In what ways does fruit erect or problematize social boundaries? How can fruit bring people together, or tell us about the lives and behaviors of individuals? If fruit is endlessly intertwined with social and cultural politics, how can it become a means of positive change? These are some of the many questions raised by Fallen Fruit, a long-term art collaboration between visual artist David Burns, artist-writer-critic Mathias Viegener, and portrait photographervideo artist Austin Young. Viegener will speak about one of the collaboration’s latest projects at the “Cultural Politics of Seeds” symposium hosted by CSW on May 17. Concurrently, an exhibition by Fallen Fruit will open at UCLA Art/Sci Center + Lab. Fallen Fruit began when the members of the group mapped fruit trees growing on or over public property in Los Angeles and it remains one of their core projects. In order to map local fruit, they explore neighborhoods to which they have been invited, creating maps of all the publically available fruit. The maps are hand drawn and distributed free from copyright as jpgs and PDFs. Several of these maps will be on display at Art/Sci. Since first embarking on the fruit mapping project, the collaboration has expanded to include serialized public projects, site-specific installations, and happenings in cities throughout the world. Fallen Fruit’s projects cover all media . Through its happenings and museum exhibitions, the group takes particular interest in working with public space and those who travel through it. At the symposium, Viegener will talk about Fallen Fruit’s pending public art project titled “Feral, Wild, Domestic and Social,” a one quarter-acre watermelon patch in the center of a small town in rural Alabama. During a brief residency in Fall 2012, the group learned that watermelons had once grown on vacant lots throughout the town, partly as the result of people spitting watermelon seeds in the vicinity. Over the years the lots became bare as the result of industrially produced seedless minimelons , sold in supermarkets nationwide. “Mother Patch” will be a public watermelon patch in which visitors will be encouraged to “spit their seeds” as they please, in the hopes that the land’s legacy of natural, community rooted watermelon production may begin again. “This narrative links to the variety of feral stone fruit we’ve found growing in Copenhagen, Northern California and Santa Fe, New Mexico,” says Viegener, in correspondence. “These plants have a symbiotic relationship with us, but a happier one than feral dogs or cats. We’re interested in this kind of peripatetic communal culture that not only links communities but also plants, animals and humans in significant relationships.” In addition to creating public spaces and events built upon the growing and harvesting of natural fruit, Fallen Fruit comments on the broad social implications of these events through the use of mixed media. Fallen Fruit’s 2008 video Double Standard, currently featured on their website, exemplifies how the collaboration melds real time public happenings with various forms of media in order to chart different ways in which fruit functions in society’s social and geographical structures, illuminating issues of sexuality, race, class, and the mediation of “public interaction.” The video juxtaposes unedited footage from two video cameras, documenting one of Fallen Fruit’s Neighborhood Fruit Forages, an event at which people gathered to take a tour of Los Angeles, exploring public places where fruit grows. The videos are overlaid with a text block of comments from a short public television video of the same event that was posted on YouTube. The comments range from insightful to homophobic and racist, creating what the group’s website calls “an alternative, cynical narrative to the events.” The Neighborhood Fruit Forage was an effort to bring peopletogether and consider the roles that fruit plays in public urban space. Double Standard incorporates the event with mixed media in order to challenge participants’ and viewers’ experiences.

Additionally, clinical studies are needed, since in vitro and animal studies, while potentially relevant as preclinical models, do not directly assess outcomes such as the vascular effects in humans. Clinical and mechanistic data on the biological effects of polyphenols derived from dates are limited . Such evidence is crucial for agriculture, health professionals and consumers, particularly as the concept of personalized nutrition grows more popular. In addition to randomized clinical trials on the fruit in general, more data is needed to identify which polyphenols are the most vasculoprotective and then determine how best to cultivate, harvest and process the fruit for maximum bio-activity. The efficacy of date consumption also needs further interrogation in various at-risk groups such as those with lipid disorders, hypertension, obesity or diabetes. Since all fruits are not equal in composition, identification of unique bio-active compounds or fractions in dates would help define benefits that may not be obtained from other fruits or plant-based foods. Beyond polyphenols, dates contain cardiovascular-protective nutrients including potassium, magnesium, folate, selenium, fiber, and vitamin C . Most date varieties are rich in potassium and low in sodium, both of which are important dietary factors that help maintain blood pressure in the normal range.Dates contain folic acid and vitamin C. Folic acid is required to metabolize homocysteine to methionine. Elevated levels of serum homocysteine have been associated with increased risk for CVD . Although the mechanisms by which increased homocysteine promotes CVD are incompletely defined,blueberry packaging box suggested alterations include impaired vascular tone due to decreases in NO bio-availability and increases in ET-1, promotion of damaging ROS, and endothelial inflammation and the activation of the coagulation cascade.

The vitamin C in dates, while modest in amount compared to most citrus fruits, can nonetheless help to scavenge free radicals via enzymatic and non-enzymatic activities, and help protect lipoproteins from oxidative damage. In addition, vitamin C can improve measures such as arterial stiffness and endothelial function, and low serum concentrations of vitamin C have been linked to increased CVD risk and mortality. Some of the cardioprotective effects of dates have been ascribed to dietary fibers, which have a well-established lipid-lowering effect. Serum triacylglycerol, total cholesterol, and LDL-C levels were significantly lowered in rats given 100 g/kg of date dietary fibers. Most of the fibers in dates are insoluble. These fibers can bind to cholesterol and triacylglycerols in the intestine and facilitate their excretion, which helps lower circulating cholesterol levels. As a result, less lipoprotein is also susceptible to oxidation, thus reducing the impact on atherogenesis. Further, fiber-rich foods can promote production of beneficial commensal bacteria while limiting the growth of known opportunistic pathogens. A high-fiber diet was reported to increase acetateproducing micro-biota, lower blood pressure and decrease cardiac hypertrophy and fibrosis in hypertensive mice. Bacterial fermentation of prebiotic soluble fiber generates short chain fatty acids, which are thought to exert several beneficial effects including differentiation of immune regulatory T cells, and decreasing the expression and activation of peroxisome proliferator-activated receptor-γ . Downregulation of PPAR-γ activates a mitochondrial uncoupling protein 2 and an AMP-activated protein kinase network, shifting metabolism in adipose and liver tissue from lipogenesis to fatty acid oxidation. Conversely, activation of PPAR-γ has been shown to have anti-inflammatory effects, promote the expression of genes for fatty acid oxidation, and decrease lipotoxicity in macrophages .

The gut micro-biota are critical for enhanced bio availability and activity of ingested polyphenols, as most parent compounds are not well absorbed in the small intestine. Following the ingestion of polyphenols, typically in their glycosylated forms, bacteria in the gastrointesti-nal tract metabolize these molecules to low-molecular-weight phenolic compounds that are then absorbed by intestinal epithelial cells. Polyphenols have been shown to undergo a variety of enzymatic processes by bacterial populations in the gastrointestinal tract, including the hydrolysis of glycosylated flavonoids, acylation of flavanol-3-ols and esterification of hydroxycinnamic acids . A detailed description of these mechanisms can be found elsewhere. While the health promoting cardiovascular benefits of a number of fruits, nuts and berries rich in select polyphenols have been characterized through animal and human studies, no such data exists for dates to our knowledge. Given the polyphenol and fiber content of dates, vascular function and gut micro-biome studies would be useful. Vascular function is commonly assessed by two noninvasive techniques: flow-mediated dilation of the brachial artery and peripheral arterial tonometry in the fingertip. Both methods have demonstrated prognostic value for the assessment of cardiovascular risk factor burden. High dietary intakes of select polyphenols, such as the flavanols and PACs found in berries, tea, red grapes, and cocoa have been reported to significantly improve FMD and PAT in various population groups. Importantly, no data exists with respect to the impact of date products and their polyphenols on vascular dysfunction via measurement of FMD and PAT. An inherent challenge with most nutrition studies is the identification of suitable controls. This is particularly difficult when examining the potential health effects of whole foods that contain a multitude of compounds that are bio-active either separately or through their interaction with other constituents in the food matrix.

One model for testing foods or extracts is to use a control product that is closely matched in calories, macro- and micronutrients, taste, and color, but devoid of the test fraction or compound. This model has been used successfully in studies that assess the effects of a dietary strawberry powder and a flavanol-rich cocoa drink . Another model is to employ a no-intervention control group, although operationally, this may skew the results since a number of those assigned to the control group may withdraw from the study prior to its completion, and those remaining may not fully represent the population initially enrolled. Future human research on dates must select the study population carefully, and focus mainly on groups at risk for CVD. Accordingly, hormonal status, age and sex are factors that can produce significant interindividual variability in cardiometabolic responses to phenolic compounds and must be considered. Factors such as microbial metabolism and genetic polymorphisms may be other contributors to outcome variability. Recent attention has also emphasized the challenge of reproducibility and accuracy in human nutrition research. As noted above, more complete compositional profiles of dates are needed rather than simply recognizing the total amount of GAEs, a gross index of flavonoid content. A more detailed characterization of products, reagents, and model systems used, as well as better rigor and reporting of experimental designs, protocols, and data analysis, will help achieve this goal. Worthy of note, many of these elements were limiting factors in the in vitro and in vivo animal reports discussed above. While dates have positive biological effects, concerns have been raised about their potential concentrations of heavy metals. Exposure to heavy metals can result in cardiovascular diseases, encephalopathy, renal dysfunction, dementia, and certain cancers. A recent study of seven date varieties collected from different locations in Saudi Arabia noted that aluminum, chromium, and antimony were within a safe range based on the maximum allowable levels set by the World Health Organization, while arsenic, lead, and cadmium exceeded the upper limit in some of the date cultivars. Numerous environmental factors can increase concentrations of heavy metals such as mining, fertilizer applications and industrial emissions,blueberry packaging containers as well as naturally occurring amounts normally found in some soils. An increasing body of evidence suggests that the gut micro-biota has a profound impact on human health. While the micro-biome of a healthy individual is relatively stable, gut microbial dynamics can be influenced by host lifestyle and dietary choices. An acute change in dietary pattern from animal-based to plant-based diet alters gut microbial populations within 24 h and then reverts to baseline within 48 h of returning to the baseline dietary pattern. Studies that involve intake of a specific dietary component demonstrate how certain micro-biota tend to respond to nutrient-specific challenges. Protein, fats, digestible and non-digestible carbohydrates, probiotics, and dietary polyphenols all induce shifts in the micro-biome with secondary effects on host immunological and metabolic markers. An emerging and rapidly growing scientific literature is implicating the micro-biome in a number of conditions and disorders including inflammatory bowel disease, obesity, type 2 diabetes mellitus, cardiovascular disease, cancer, autism, mood and neurodegenerative disorders. The consumption of polyphenol-rich foods, including fruits and vegetables, has been reported to reduce pathogenic Clostridia and to enrich beneficial bacteria such as Bifidobacterium and Lactobacillus species in human studies. In conjunction with these changes, reductions in plasma triglycerides and C-reactive protein have been noted. Dietary polyphenols have been shown to help maintain intestinal health by preserving the gut microbial balance through the stimulation of the growth of beneficial bacteria and the inhibition of pathogenic bacteria, exerting prebiotic-like effects.

We have previously demonstrated the effect of water extract of culinary spices, including cinnamon, Mediterranean oregano, ginger, rosemary, black and cayenne pepper, on the growth of 33 Bifidobaterium and Latobacillus spp., and its antimicrobial activity against 88 intestinal, pathogenic, and toxigenic bacterial strains in an in vitro model. These spices promoted the growth of Bifidobaterium and Latobacillus spp. Cinnamon, ginger, oregano, black pepper, and cayenne pepper showed activity against several pathogenic Fusobaterium and Ruminococcus spp. and selected Clostridium difficile strains. The present pilot study was designed to investigate the effects of mixed spices at culinary doses consumed over 2 weeks in a standardized 5 g capsule on the production of gut micro-biota and short-chain fatty acids in healthy subjects compared to a placebo maltodextrin capsule in a parallel randomized controlled clinical trial. The pilot study was conducted in accordance with the guidelines of the Office of the Human Research Protection Programs of the University of California, Los Angeles. The clinical protocol was approved by the UCLA Internal Review Board and the study was registered at the NIH Clinical Trial Registry . A total of 66 healthy women and men aged 18 to 65 were screened in 2017 through local advertisement. Participants with a history of gastrointestinal surgery, diabetes mellitus, or other serious medical conditions such as chronic hepatic or renal disease, bleeding disorder, congestive heart disease, chronic diarrhea, myocardial infarction, coronary artery bypass graft, angioplasty within 6 months prior to screening, current diagnosis of uncontrolled hypertension or chronic gastrointestinal disorders, bulimia, anorexia, laxative abuse, or endocrine disorders were excluded. Participants who were consuming a high-fiber/polyphenol diet; taking any medication or dietary supplement interfering with the absorption of polyphenols; pregnant or breastfeeding; frequently using prebiotics, probiotics, yogurt, or fiber supplements; taking antibiotics or laxatives within the previous 3 months; or currently using tobacco products were also excluded. Thirty-one subjects meeting enrollment criteria were recruited and provided written informed consent before the study began. A randomized, placebo-controlled, double-blind pilot study was conducted. Subjects were randomized according to an algorithm modified from a previous publication. The study was divided into two periods: an initial run-in period of 1 week and an intervention period of 2 weeks. After the run-in period, 31 subjects were randomly allocated to consume either 5 g capsules of spice mixture containing 1 g cinnamon, 1.5 g oregano, 1.5 g ginger, 0.85 g black pepper, and 0.15 g cayenne pepper, or 5 g capsules containing maltodextrin daily for 2 weeks. The individual spices were purchased from local grocery stores. At the start of study, participants received a diet instructional handout and were counseled by a registered dietitian on compliance. During the run-in and intervention period, all participants consumed a beige diet . The beige diet handout advised participants to eat foods beige in color and rich in simple carbohydrates like white breads/bagels, crackers, granola bars, rice, macaroni/pasta, yogurt, dairy, poultry, cereal, and bananas and to avoid foods high in polyphenols and/or fiber. Participants were also provided with weekly checklists to track their fruit and vegetable intake throughout the study with a limit of three servings per day. This checklist included a list of higher fiber/polyphenol foods to avoid as well as a list of lower fiber/polyphenol fruits and vegetables theycould consume as a part of their three servings per day, with a serving size estimation tool included. At the baseline and final visits, participants also completed and returned 3-day food records that were evaluated by the dietitian for compliance with the beige diet.

There is a growing interest in better understanding factors affecting agroecosystem functions and services. One key property of agroecosystems that has received much attention in recent years is the diversity of crop species. National crop species diversity has been associated with the stability of food production and used as a proxy for pollination services partly because local crop diversity enhances associated biodiversity . However, it is unclear how national crop diversity is related to local-scale diversity, and assuming that inferences made at one scale are maintained at other scales can be misleading. Crop species diversity also has a temporal dimension of great importance resulting from farmers’ crop rotations. These crop rotations can reduce pressure from pathogens, pests, and weeds and improve soil quality and yield stability . Yet, the temporal dimension of crop diversity is frequently ignored in most diversity assessments, mainly because it is hard to measure , and it is not clear how diversity in space and time relates. Therefore, a better understanding and treatment of the scale dependency of spatial crop species diversity and its relation with temporal diversity is needed to develop comprehensive theories of crop diversity effects on agroecosystem function. Most calls for more diverse farming systems do not consider regional differences that might limit farmers’ diversification opportunities or demand-side constraints . Moreover,wholesale grow bags most studies on crop species diversity used variation in diversity to explain other phenomena but there has been less progress in understanding factors that shape crop diversity .

Thus, to gain a quantitative understanding of diversity patterns and processes and improve comparisons between regions and countries, environmental and crop demand constraints to crop diversity must be identified. The first two chapters of this dissertation deal with some fundamental aspects of crop species diversity. The first chapter explores how crop diversity can be measured, depending on the dimension and scale considered and how these relate, using data for the conterminous United States. The second chapter examines which factors define and limit crop diversity. It outlines a framework for quantifying potential and attainable levels of crop species diversity, which is then applied at the global level. Crop species diversity in the USA increased during the first half of the 20th century, but it has gradually declined over the past 50 years in most of the country . This specialization, together with increasing use of inputs, allowed substantial yield gains, but it was also associated with important negative environmental impacts . Consequently, there is an interest in developing more diverse and sustainable cropping systems . Most studies on diversified cropping systems consider crop rotation diversification a key management practice to be developed and implemented . However, there have been no comprehensive efforts to analyze crop rotation diversity across the US, probably because it needs to be observed at a very high spatial resolution . The first chapter analyzes temporal and spatial crop species diversity patterns in the conterminous US and how they relate. It shows that crop rotation diversity is tightly associated with local diversity at a spatial resolution close to typical US farm size. It also shows that this diversity is lower for rotations that include major crops. The observable patterns in the spatial distribution of crop species and their subsequent diversity are realizations of underlying processes that need to be elucidated .

While drivers of current crop genetic diversity patterns have been studied , there is very little knowledge on processes shaping the diversity of crop species. However, some concepts from macroecology and bio geography might be applicable . For instance, one of the most established patterns in Ecology, latitudinal biodiversity gradients , can also be expected to regulate crop species diversity. But crop diversity depends on both natural and human-mediated processes. Thus, while some tropical regions might be suitable for many crop species , current diversity patterns are also affected by individual and structural factors shaping farming decisions and resulting in different specialization levels . The second chapter sets a theoretical framework of hierarchical levels of crop diversity that considers crop-specific environmental requirements and the demand for agricultural products. This framework is then used to analyze the environmental drivers of potential and attainable crop diversity and quantify diversity gaps. The results show that potential and attainable crop diversity are lower in temperate and continental areas than in tropical and coastal regions. Although current diversity follows these patterns to some extent, other processes also affect it, resulting in high spatial variability in diversity gaps. The third chapter of this dissertation is on a different topic. It contributes to a project to better understand the opportunities for improved management of acid soils in Africa. One of the initial steps of the project is developing a spatially-explicit analysis of the costs and benefits of liming in Africa. This analysis is founded on models for lime requirement estimation. However, the literature on lime requirement estimation methods is sparse and inconsistent, particularly for acid tropical soils. Thus, the third chapter focused on a comparison of lime requirement models. Acid tropical soils can have several problems affecting crop growth, such as aluminum and manganese toxicity and calcium and magnesium deficiencies .

These issues can be addressed by applying liming materials . The amount of agricultural lime required is often estimated with locally calibrated soil tests . Both soil testing and liming might be relatively cheap and easy to access for intensive commercial farmers, but that is not the case for most smallholder farmers in tropical developing countries . Lime application is relatively expensive in many tropical regions, and the experimental evidence on lime response is also limited. Furthermore, soil tests that work elsewhere cannot be assumed to work for these places and must be re-calibrated. Therefore, general models to estimate lime requirements from generally available soil data could be useful as a starting point in developing locally optimal liming recommendations and for strategic research on future lime use. The third chapter compares and evaluates different models for lime requirement estimation that can be used in acid tropical soils with readily available soil data and introduces an outperforming model developed based on past experiences and clear principles. It shows that there are important differences in model accuracy and prediction values and that liming estimates largely depend on the target soil chemical property of the model. Therefore, the most important soil acidity problems affecting crop yields must be identified to formulate liming recommendations in acid tropical soils. However,grow bags for gardening models for other acidity problems than aluminum toxicity still need to be developed.Low soil pH is associated with a high concentration of toxic elements in the soil solution, such as aluminum and manganese, and with low availability of phosphorus, calcium, and other plant nutrients . Soil acidity problems can be addressed with liming, the application of calcium or magnesium-rich materials that react as a base . Liming has been practiced for centuries , and its use is still expanding, particularly in tropical areas with acid soils. For example, it played a key role in the recent expansion of agriculture in the Brazilian Cerrado region . The amount of lime required to adjust soil acidity depends on the soil, the target crop, and the liming material used. In temperate regions, lime requirements are commonly estimated with locally calibrated quick tests using buffer solutions . These tests can be developed by comparing the buffer’s response to the soil with the soil response to lime in field or incubation studies or by slow titrations. Both the soil testing and the lime application may be a relatively small expense in intensively managed commercial farms, partly because lime is cheap and partly because the use of lime, when needed, increases the use efficiency of other inputs . Moreover, applying a bit more lime than needed means its benefits will last longer . Thus, blanket applications that err on the higher side are not very risky , so there is no need for a highly accurate determination of the amount of lime to apply. This situation is different for smallholder farmers in sub-Saharan Africa and other tropical regions . Lime may be relatively expensive, and its benefit may be relatively small if fertilizer use is low. Under these circumstances, it would be helpful to have accurate estimates of lime requirements. However, empirical evidence from these tropical regions is limited, and laboratory-based soil testing is often inaccessible. Furthermore, methods that depend on direct measurements of soil acidity in each field with buffer solutions cannot be assumed to work elsewhere and would have to be redeveloped. Models to estimate lime requirements from generally available soil data are needed for strategic research of potential lime use across tropical regions.

They can be particularly useful for subSaharan Africa, where the impact of soil acidity on crop productivity and nutrient-use efficiency is poorly understood . Lime requirement models could serve as a starting point to develop locally optimal liming recommendations for farmers and development practitioners and provide strategic information to national governments and the private sector on potential market sizes for lime for a region of interest. The latter is now possible thanks to the availability of high-resolution spatial products for most soil properties across the continent . Here we provide a comprehensive review of general lime requirement models for tropical acid soils that can be used with readily available soil data. We first introduce key concepts related to estimating lime requirements that have been a source of confusion and inconsistency. We then describe and discuss published lime requirement models for tropical soils and introduce a new model to estimate lime requirements. Finally, we show substantial differences in the estimated lime requirement for acid tropical soils when using these models and discuss their implications. Soils can be naturally acidic or become acidic because of agricultural practices such as the use of acidifying fertilizer and the removal of elements with harvested products. In the tropics, many soils in humid areas are inherently acidic because intense weathering processes have resulted in the displacement and leaching of basic exchangeable cations and the accumulation of exchangeable acidity . The main problem with soil acidity in the tropics is not the low pH as such, but rather the associated aluminum toxicity that constrains crop growth . The purpose of liming should be, therefore, to remove Al toxicity, considering the sensitivity of the target crops, together with other possible constraints such as Ca and Mg deficiencies , but not to increase pH for its own sake . Acidity saturation is the fraction of the effective cation exchange capacity of the soil occupied by exchangeable acid cations . In tropical soils, nearly all exchangeable acidity comprises exchangeable Al3+ and, thus, Al saturation approximates acidity saturation . For that reason, acidity saturation is often used as a proxy for Al toxicity . Many lime requirement models estimate the lime rate required to lower the acidity saturation to a target level that does not affect crop yield . The terms exchangeable acidity and exchangeable Al3+ have been used interchangeably in tropical soil literature, with the term exchangeable Al3+ more commonly used in older literature . Indeed, several authors of the lime requirement models reviewed here measured acidity saturation but referred to it as Al saturation . Consequently, some models were originally formulated for exchangeable Al3+ but derived from exchangeable acidity measurements. Some highly weathered acid soils can have very low ECEC and, thus, low exchangeable Ca2+ and Mg2+ but low acidity saturation, resulting in Ca and Mg deficiencies without Al toxicity problems . Therefore, some lime requirement models based on acidity saturation also estimate the lime rate needed to cover such deficiencies . Such mineral deficiencies can also be addressed with compost or inorganic fertilizers such as calcium nitrate, which might be more convenient in soils with no Al toxicity problems. An alternative approach to alleviating soil acidity problems aims to raise the “base saturation” to a certain level rather than focusing on acidity saturation . Base saturation is the sum of all exchangeable bases divided by the Cation Exchange Capacity at pH 7 . CEC7 is different from ECEC, especially in acid soils, where CEC7 ≫ ECEC. For ECEC, exchangeable acid cations are extracted with a neutral unbuffered salt. In contrast, a pH 7 buffer solution is used for CEC7, which extracts both exchangeable and non-exchangeable acidity , comprising the potential acidity.