scholarly journals Cyclodextrins, Natural Compounds, and Plant Bioactives—A Nutritional Perspective

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 401
Author(s):  
Svenja Wüpper ◽  
Kai Lüersen ◽  
Gerald Rimbach
Keyword(s):  
Intestinal Flora ◽  
Aqueous Solubility ◽  
Outer Wall ◽  
Natural Compounds ◽  
Model Organisms ◽  
Laboratory Model ◽  
Internal Cavity ◽  
Pentacyclic Triterpenoids ◽  
Starch Derivatives ◽  
Improved Stability

Cyclodextrins (CDs) are a group of cyclic oligosaccharides produced from starch or starch derivatives. They contain six (αCD), seven (βCD), eight (γCD), or more glucopyranose monomers linked via α-1,4-glycosidic bonds. CDs have a truncated cone shape with a hydrophilic outer wall and a less hydrophilic inner wall, the latter forming a more apolar internal cavity. Because of this special architecture, CDs are soluble in water and can simultaneously host lipophilic guest molecules. The major advantage of inclusion into CDs is increased aqueous solubility of such lipophilic substances. Accordingly, we present studies where the complexation of natural compounds such as propolis and dietary plant bioactives (e.g., tocotrienol, pentacyclic triterpenoids, curcumin) with γCD resulted in improved stability, bioavailability, and bioactivity in various laboratory model organisms and in humans. We also address safety aspects that may arise from increased bioavailability of plant extracts or natural compounds owing to CD complexation. When orally administered, α- and βCD—which are inert to intestinal digestion—are fermented by the human intestinal flora, while γCD is almost completely degraded to glucose units by α-amylase. Hence, recent reports indicate that empty γCD supplementation exhibits metabolic activity on its own, which may provide opportunities for new applications.

scholarly journals Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

2019 ◽  
Author(s):  
E. Ng’oma ◽  
P.A. Williams-Simon ◽  
A. Rahman ◽  
E.G. King
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Sequence Data ◽  
Nutrient Sensing ◽  
Gene Set Enrichment Analysis ◽  
Tissue Type ◽  
Model Organisms ◽  
Laboratory Model ◽  
Fisher Exact Test ◽  
Tissue Samples

AbstractBackgroundEnvironmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear.ResultsTo describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, Padj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (false discovery rate, FDR Padj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing a large number of cellular and nuclear processes (Fisher exact test, Padj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, known key genes such as InR, chico, insulin peptide genes, and the nutrient-sensing pathways were not observed.ConclusionsOur results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

scholarly journals Selective disappearance of individuals with high levels of glycated haemoglobin in a free-living bird

2016 ◽  
Vol 12 (8) ◽  
pp. 20160243 ◽  
Author(s):  
Charlotte Récapet ◽  
Adélaïde Sibeaux ◽  
Laure Cauchard ◽  
Blandine Doligez ◽  
Pierre Bize
Keyword(s):  
Glycated Haemoglobin ◽  
Protein Glycation ◽  
Model Organisms ◽  
Laboratory Model ◽  
Lower Probability ◽  
Poor Control ◽  
Free Living ◽  
Glucose Homoeostasis ◽  
Age Related ◽  
Individual Probability

Although disruption of glucose homeostasis is a hallmark of ageing in humans and laboratory model organisms, we have little information on the importance of this process in free-living animals. Poor control of blood glucose levels leads to irreversible protein glycation. Hence, levels of protein glycation are hypothesized to increase with age and to be associated with a decline in survival. We tested these predictions by measuring blood glycated haemoglobin in 274 adult collared flycatchers of known age and estimating individual probability of recapture in the following 2 years. Results show a strong decrease in glycated haemoglobin from age 1 to 5 years and an increase thereafter. Individuals with high levels of glycated haemoglobin had a lower probability of recapture, even after controlling for effects of age and dispersal. Altogether, our findings suggest that poor control of glucose homoeostasis is associated with lower survival in this free-living bird population, and that the selective disappearance of individuals with the highest glycation levels could account for the counterintuitive age-related decline in glycated haemoglobin in the early age categories.

scholarly journals Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

2019 ◽  
Author(s):  
Enoch Ng'oma ◽  
Patricka A. Williams-Simon ◽  
Aniqa Rahman ◽  
Elizabeth G. King
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Sequence Data ◽  
Nutrient Sensing ◽  
Gene Set Enrichment Analysis ◽  
Tissue Type ◽  
Model Organisms ◽  
Laboratory Model ◽  
Fisher Exact Test ◽  
Tissue Samples

Abstract Background: Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results: To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, P adj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (false discovery rate, FDR P adj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing a large number of cellular and nuclear processes (Fisher exact test, P adj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5 , Rheb , and Sirt2 showed significant elevation in expression, known key genes such as InR , chico , insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions: Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

scholarly journals Ras inhibition by trametinib treatment in Drosophila attenuates gut pathology in females and extends lifespan in both sexes

2018 ◽  
Author(s):  
Jennifer C Regan ◽  
Yu-Xuan Lu ◽  
Ekin Bolukbasi ◽  
Mobina Khericha ◽  
Linda Partridge
Keyword(s):  
Mek Inhibitor ◽  
Model Organisms ◽  
Laboratory Model ◽  
Lifespan Extension ◽  
Parallel Mechanisms ◽  
Beneficial Effects ◽  
Age Related ◽  
Ras Inhibition ◽  
Female Specific ◽  
Female Lifespan

AbstractFemales of most species live longer than do males. Furthermore, lifespan-extending interventions in laboratory model organisms are often more effective in females (Regan and Partridge 2013). For instance, genetic and pharmacological suppression of activity of the insulin/insulin-like signalling - target of rapamycin (IIS-TOR) network generally extends female lifespan more than that of males in both Drosophila and mice (Clancy et al. 2001; Selman et al. 2009). We previously showed that attenuation of Ras-dependent IIS signalling by treatment with the FDA-approved MEK inhibitor, trametinib extends lifespan in females (Slack et al. 2015). Here, we demonstrate that trametinib treatment has beneficial effects on female-specific, age-related gut pathologies, similar to those obtained through dietary restriction (Regan et al. 2016). Importantly, we identify Ras inhibition as an effective lifespan-extending manipulation in males as well as females, pointing to parallel mechanisms of lifespan extension by trametinib in both sexes.

scholarly journals The evolution of ovary-specific gene expression in Hawaiian Drosophilidae

2021 ◽  
Author(s):  
Samuel H Church ◽  
Catriona Munro ◽  
Casey Dunn ◽  
Cassandra G. Extavour
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Model Organisms ◽  
Laboratory Model ◽  
Developmental Genetics ◽  
Specific Gene ◽  
Ancestral State ◽  
Phylogenetic Distance ◽  
Evolutionary Changes

As detailed data on gene expression become accessible from more species, we have an opportunity to test the extent to which our understanding of developmental genetics from model organisms helps predict expression patterns across species. Central to this is the question: how much variation in gene expression do we expect to observe between species? Here we provide an answer by comparing RNAseq data between twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that there exists a cohort of ovary-specific genes that is stable across species, and that largely corresponds to described expression patterns from laboratory model Drosophila species. However, our results also show that, as phylogenetic distance increases, variation between species overwhelms variation between tissues. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression profiles, and use this to identify gains and losses of ovarian expression across these twelve species. We then use this distribution to calculate the correlation in expression evolution between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that have similar evolutionary trajectories, and we provide these as a dataset of novel testable hypotheses about genetic roles and interactions.

scholarly journals Gephebase, a Database of Genotype-Phenotype Relationships for natural and domesticated variation in Eukaryotes

2019 ◽  
Author(s):  
Virginie Courtier-Orgogozo ◽  
Laurent Arnoult ◽  
Stéphane R. Prigent ◽  
Séverine Wiltgen ◽  
Arnaud Martin
Keyword(s):  
Target Genes ◽  
Meta Analysis ◽  
Crop Improvement ◽  
Evolutionary Genetics ◽  
General Information ◽  
Model Organisms ◽  
Carotenoid Content ◽  
Laboratory Model ◽  
Phenotypic Change ◽  
Candidate Gene Approach

AbstractGephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes — mostly animals, plants and yeasts. Gephebase aims to compile studies where the genotype-phenotype association (based on linkage mapping, association mapping or a candidate gene approach) is relatively well supported or understood. Human disease and aberrant mutant phenotypes in laboratory model organisms are not included in Gephebase and can be found in other databases (eg. OMIM, OMIA, Monarch Initiative). Gephebase contains more than 1700 entries. Each entry corresponds to an allelic difference at a given gene and its associated phenotypic change(s) between two species or between two individuals of the same species, and is enriched with molecular details, taxonomic information, and bibliographic information. Users can easily browse entries for their topic of interest and perform searches at various levels, whether phenotypic, genetic, taxonomic or bibliographic (eg. transposable elements, cis-regulatory mutations, snakes, carotenoid content, an author name). Data can be searched using keywords and boolean operators and is exportable in spreadsheet format. This database allows to perform meta-analysis to extract general information and global trends about evolution, genetics, and the field of evolutionary genetics itself. Gephebase should also help breeders, conservationists and others to identify the most promising target genes for traits of interest, with potential applications such as crop improvement, parasite and pest control, bioconservation, and genetic diagnostic. It is freely available at www.gephebase.org.

scholarly journals Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

2019 ◽  
Author(s):  
Enoch Ng'oma ◽  
Patricka A. Williams-Simon ◽  
Aniqa Rahman ◽  
Elizabeth G. King
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Sequence Data ◽  
Nutrient Sensing ◽  
Gene Set Enrichment Analysis ◽  
Tissue Type ◽  
Model Organisms ◽  
Laboratory Model ◽  
Fisher Exact Test ◽  
Tissue Samples

Abstract Background Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, Padj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (false discovery rate, FDR Padj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing a large number of cellular and nuclear processes (Fisher exact test, Padj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, known key genes such as InR, chico, insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

scholarly journals Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

2019 ◽  
Author(s):  
Enoch Ng'oma ◽  
Patricka A. Williams-Simon ◽  
Aniqa Rahman ◽  
Elizabeth G. King
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Sequence Data ◽  
Nutrient Sensing ◽  
Gene Set Enrichment Analysis ◽  
Tissue Type ◽  
Model Organisms ◽  
Laboratory Model ◽  
Fisher Exact Test ◽  
Tissue Samples

Abstract Background: Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results: To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, Padj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (false discovery rate, FDR Padj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing a large number of cellular and nuclear processes (Fisher exact test, Padj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, known key genes such as InR, chico, insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions: Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

scholarly journals Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones

2011 ◽  
Vol 278 (1719) ◽  
pp. 2784-2790 ◽  
Author(s):  
Melanie G. Mayer ◽  
Ralf J. Sommer
Keyword(s):  
Natural Variation ◽  
Strong Association ◽  
Cross Reactivity ◽  
Model Organisms ◽  
Laboratory Model ◽  
Experimental Conditions ◽  
Pristionchus Pacificus ◽  
In The Wild ◽  
Dauer Formation ◽  
Dauer Larvae

Many free-living nematodes, including the laboratory model organisms Caenorhabditis elegans and Pristionchus pacificus , have a choice between direct and indirect development, representing an important case of phenotypic plasticity. Under harsh environmental conditions, these nematodes form dauer larvae, which arrest development, show high resistance to environmental stress and constitute a dispersal stage. Pristionchus pacificus occurs in a strong association with scarab beetles in the wild and remains in the dauer stage on the living beetle. Here, we explored the circumstances under which P. pacificus enters and exits the dauer stage by using a natural variation approach. The analysis of survival, recovery and fitness after dauer exit of eight P. pacificus strains revealed that dauer larvae can survive for up to 1 year under experimental conditions. In a second experiment, we isolated dauer pheromones from 16 P. pacificus strains, and tested for natural variation in pheromone production and sensitivity in cross-reactivity assays. Surprisingly, 13 of the 16 strains produce a pheromone that induces the highest dauer formation in individuals of other genotypes. These results argue against a simple adaptation model for natural variation in dauer formation and suggest that strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains. We therefore discuss intraspecific competition among genotypes as a previously unconsidered aspect of dauer formation.

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