VProtein: identifying optimal amino acid complements from plant-based foods.
ABSTRACT: BACKGROUND: Indispensible amino acids (IAAs) are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions, but many plant-based foods provide different proportions of IAAs. To explore how these plant-based foods can be better used in human nutrition, we have created the computational tool vProtein to identify optimal food complements to satisfy human protein needs. METHODS: vProtein uses 1251 plant-based foods listed in the United States Department of Agriculture standard release 22 database to determine the quantity of each food or pair of foods required to satisfy human IAA needs as determined by the 2005 daily recommended intake. The quantity of food in a pair is found using a linear programming approach that minimizes total calories, total excess IAAs, or the total weight of the combination. RESULTS: For single foods, vProtein identifies foods with particularly balanced IAA patterns such as wheat germ, quinoa, and cauliflower. vProtein also identifies foods with particularly unbalanced IAA patterns such as macadamia nuts, degermed corn products, and wakame seaweed. Although less useful alone, some unbalanced foods provide unusually good complements, such as Brazil nuts to legumes. Interestingly, vProtein finds no statistically significant bias toward grain/legume pairings for protein complementation. These analyses suggest that pairings of plant-based foods should be based on the individual foods themselves instead of based on broader food group-food group pairings. Overall, the most efficient pairings include sweet corn/tomatoes, apple/coconut, and sweet corn/cherry. The top pairings also highlight the utility of less common protein sources such as the seaweeds laver and spirulina, pumpkin leaves, and lambsquarters. From a public health perspective, many of the food pairings represent novel, low cost food sources to combat malnutrition. Full analysis results are available online at http://www.foodwiki.com/vprotein.
Project description:The current model of auxin-inducible transcription describes numerous regulatory interactions between AUXIN RESPONSE FACTORs (ARFs) and Aux/IAAs. However, specific relationships between individual members of these families in planta remain largely uncharacterized. Using a systems biology approach, the entire suite of Aux/IAA genes directly regulated by the developmentally pivotal ARF MONOPTEROS (MP) was recently determined for multiple Arabidopsis tissue types. This study showed that MP directly targets distinct subclades of Aux/IAAs, revealing potential regulatory modules of redundantly acting Aux/IAAs involved in MP-dependent processes. Further, functional analyses indicated that the protein products of these targeted Aux/IAAs negatively feedback on MP. Thus, comprehensive identification of Aux/IAAs targeted by individual ARFs will generate biologically meaningful networks of ARF-Aux/IAA regulatory modules controlling distinct plant pathways.
Project description:BACKGROUND:The types of food in complementary feeding of infants and young children are important for growth and development. Food protein quality, as measured by the Digestible Indispensable Amino Acid Score (DIAAS), requires the determination of true ileal digestibility of indispensable amino acids (IAAs) in children. OBJECTIVES:First, the aim of this study was to measure the true ileal IAA digestibility of 4 (rice, finger millet, mung bean, and hen egg) commonly consumed complementary foods in children aged <2 y using the dual-isotope tracer method. Second, we calculated the DIAAS of complementary feeding diets and their relation to stunting in a representative Indian rural population. DESIGN:Rice, finger millet, and mung bean were intrinsically labeled with deuterium oxide (2H2O), whereas egg was labeled through oral dosing of hens with a uniformly 2H-labeled amino acid mixture. True ileal IAA digestibility was determined by the dual-isotope tracer technique. The DIAAS of complementary food protein was calculated in children aged 1-3 y from a nationally representative survey to evaluate its relation with stunting. RESULTS:True ileal IAA digestibility was lowest in mung bean (65.2% ± 7.1%), followed by finger millet (68.4 %± 5.3%) and rice (78.5% ± 3.5%), and was highest for egg (87.4% ± 4.0%). There was a significant inverse correlation of complementary food DIAAS with stunting in survey data (r = -0.66, P = 0.044). The addition of egg or milk to nationally representative complementary diets theoretically improved the DIAAS from 80 to 100. CONCLUSIONS:The true ileal IAA digestibility of 4 foods commonly consumed in complementary diets showed that the DIAAS was associated with stunting and reinforces the importance of including animal source food (ASF) in diets to improve growth. This trial was registered at http://ctri.nic.in/clinicaltrials/login.php as CTRI/2017/02/007921.
Project description:Vegetarian diets are defined by the absence of meat and fish, but differences in the intake of other foods between meat-eaters and low or non-meat eaters are also important to document. We examined intakes of high-protein foods (meat, poultry, fish, legumes, nuts, vegetarian protein alternatives, dairy products, and eggs) and other major food groups (fruit, vegetables, bread, pasta, rice, snack foods, and beverages) in regular meat-eaters, low meat-eaters, poultry-eaters, fish-eaters, vegetarians, and vegans of white ethnicity participating in UK Biobank who had completed at least one web-based 24-h dietary assessment (n = 199,944). In regular meat-eaters, around 25% of total energy came from meat, fish, dairy and plant milk, cheese, yogurt, and eggs. In vegetarians, around 20% of energy came from dairy and plant milk, cheese, yoghurt, eggs, legumes, nuts, and vegetarian protein alternatives, and in vegans around 15% came from plant milk, legumes, vegetarian alternatives, and nuts. Low and non-meat eaters had higher intakes of fruit and vegetables and lower intakes of roast or fried potatoes compared to regular meat-eaters. The differences in the intakes of meat, plant-based high-protein foods, and other foods between meat-eaters and low and non-meat eaters in UK Biobank may contribute to differences in health outcomes.
Project description:The plant hormone auxin can regulate gene expression by destabilizing members of the Aux/IAA family of transcriptional repressors. Auxin-induced Aux/IAA degradation requires the protein-ubiquitin ligase SCF(TIR1), with auxin acting to enhance the interaction between the Aux/IAAs and SCF(TIR1). SKP1, Cullin, and an F-box-containing protein (SCF)-mediated degradation is an important component of many eukaryotic signaling pathways. In all known cases to date, the interaction between the targets and their cognate SCFs is regulated by signal-induced modification of the target. The mechanism by which auxin promotes the interaction between SCF(TIR1) and Aux/IAAs is not understood, but current hypotheses propose auxin-induced phosphorylation, hydroxylation, or proline isomerization of the Aux/IAAs. We found no evidence to support these hypotheses or indeed that auxin induces any stable modification of Aux/IAAs to increase their affinity for SCF(TIR1). Instead, we present data suggesting that auxin promotes the SCF(TIR1)-Aux/IAA interaction by affecting the SCF component, TIR1, or proteins tightly associated with it.
Project description:The plant hormone auxin regulates many aspects of plant growth and development. Auxin signaling involves hormone perception by the TRANSPORT INHIBITOR RESPONSE/AUXIN F-BOX (TIR1/AFB)-Aux/IAA co-receptor system, and the subsequent degradation of the Aux/IAA transcriptional repressors by the ubiquitin proteasome pathway. This leads to the activation of downstream gene expression and diverse physiological responses. Here, we investigate how the structural elements in the Aux/IAAs determine their function in Auxin perception and transcriptional repression. We took advantage of the facile genetics of the moss Physcomitrella patens to determine the activity of wild-type and mutant PpIAA1a proteins in a ?aux/iaa null background. In this way, Aux/IAA function was characterized at the molecular and physiological levels without the interference of genetic redundancy. We identified and characterized degron variants in Aux/IAAs that affect their stability and Auxin response. We also demonstrated that neither the Aux/IAA EAR motif nor Aux/IAA oligomerization is essential for the repressive function of Aux/IAA. Our study demonstrates how key elements within the Aux/IAA proteins fine tune stability and repressor activity, as well as the long-term developmental outcome.
Project description:Auxin influences nearly every aspect of plant biology through a simple signaling pathway; however, it remains unclear how much of the diversity in auxin effects is explained by variation in the core signaling components and which properties of these components may contribute to diversification in response dynamics. Here, we recapitulated the entire Arabidopsis thaliana forward nuclear auxin signal transduction pathway in Saccharomyces cerevisiae to test whether signaling module composition enables tuning of the dynamic response. Sensitivity analysis guided by a small mathematical model revealed the centrality of auxin/indole-3-acetic acid (Aux/IAA) transcriptional corepressors in controlling response dynamics and highlighted the strong influence of natural variation in Aux/IAA degradation rates on circuit performance. When the basic auxin response circuit was expanded to include multiple Aux/IAAs, we found that dominance relationships between coexpressed Aux/IAAs were sufficient to generate distinct response modules similar to those seen during plant development. Our work provides a new method for dissecting auxin signaling and demonstrates the key role of Aux/IAAs in tuning auxin response dynamics.
Project description:The coordinated action of the auxin-sensitive Aux/IAA transcriptional repressors and ARF transcription factors produces complex gene-regulatory networks in plants. Despite their importance, our knowledge of these two protein families is largely based on analysis of stabilized forms of the Aux/IAAs, and studies of a subgroup of ARFs that function as transcriptional activators. To understand how auxin regulates gene expression we generated a Physcomitrella patens line that completely lacks Aux/IAAs. Loss of the repressors causes massive changes in transcription with misregulation of over a third of the annotated genes. Further, we find that the aux/iaa mutant is blind to auxin indicating that auxin regulation of transcription occurs exclusively through Aux/IAA function. We used the aux/iaa mutant as a simplified platform for studies of ARF function and demonstrate that repressing ARFs regulate auxin-induced genes and fine-tune their expression. Further the repressing ARFs coordinate gene induction jointly with activating ARFs and the Aux/IAAs.
Project description:Iso-?-acids (IAAs) are hop-derived bitter acids of beer. Epidemiologic studies suggest that moderate alcohol consumption is beneficial for cognitive function, but they do not show the ingredients in alcoholic beverages. Previously, we reported that long-term consumption of IAAs prevents inflammation and Alzheimer pathologies in mice, but their effects on cognitive function have not been evaluated. In the present study, we demonstrated that the consumption of IAAs improves spatial and object recognition memory functions not only in normal Crl:CD1(ICR) male mice but also in mice with pharmacologically induced amnesia. IAA consumption increased the total and extracellular levels of dopamine in the hippocampus of mice and Sprague-Dawley male rats, respectively. Dopamine D<sub>1</sub> receptor antagonist treatment and knockdown of dopamine D<sub>1</sub> receptor expression in the hippocampus attenuated IAA-induced spatial memory improvement. Furthermore, vagotomy attenuated the effects of IAAs in improving spatial and object recognition memory functions and increasing the total level of dopamine in the hippocampus. These results suggest that the consumption of IAAs activates dopamine D<sub>1</sub> receptor-signaling in the hippocampus in a vagus nerve-dependent manner and, consequently, improves spatial and object recognition memory functions. Vagal activation with food components including IAAs may be an easy and safe approach to improve cognitive functions.-Ano, Y., Hoshi, A., Ayabe, T., Ohya, R., Uchida, S., Yamada, K., Kondo, K., Kitaoka, S., Furuyashiki, T. Iso-?-acids, the bitter components of beer, improve hippocampus-dependent memory through vagus nerve activation.
Project description:Mushrooms are fungi, biologically distinct from plant- and animal-derived foods (fruits, vegetables, grains, dairy, protein [meat, fish, poultry, legumes, nuts, and seeds]) that comprise the US Department of Agriculture food patterns operationalized by consumer-focused MyPlate messages. Although mushrooms provide nutrients found in these food groups, they also have a unique nutrient profile. Classified into food grouping systems by their use as a vegetable, mushrooms' increasing use in main entrées in plant-based diets is growing, supporting consumers' efforts to follow dietary guidance recommendations. Mushrooms' nutrient and culinary characteristics suggest it may be time to reevaluate food groupings and health benefits in the context of 3 separate food kingdoms: plants/botany, animals/zoology, and fungi/mycology.
Project description:Background:The Norwegian food-based dietary guidelines (FBDG) aim at reducing the risk of developing chronic diseases and promote overall health. We studied the effect of the Norwegian FBDG in colorectal cancer (CRC) patients. There is a need for a time-efficient dietary assessment tool measuring adherence to these guidelines in patients treated for dietary dependent cancer, such as CRC patients. Objective:To evaluate a new short food frequency questionnaire (NORDIET-FFQ), developed to estimate adherence to the Norwegian FBDG among CRC patients. Design:Eighty-one CRC patients from both study groups in the Norwegian Dietary Guidelines and Colorectal Cancer Survival study, an ongoing dietary intervention, completed both the short 63-item NORDIET-FFQ and a 7-day weighed food record. Results:The NORDIET-FFQ was on group level able to estimate intakes of fruits, vegetables, unsalted nuts, fish, fatty fish, high fat dairy products, unprocessed meat, processed meat, red meat, water, sugar-rich beverages, alcoholic drinks, and sugar- and fat-rich foods. Ranking of individuals according to intake was good (r = 0.31-0.74) for fruits and vegetables, fruits, unsalted nuts, whole grain products, sugar-rich cereals, fish, fatty fish, dairy products, red meat, water, sugar-rich beverages, alcoholic beverages, and sugar- and fat-rich foods. The NORDIET-FFQ was able to identify the individuals who did not fulfil the recommendations of fruits, vegetables, unsalted nuts, whole grains, low-fat dairy products, processed meat, water, alcoholic beverages, and sugar- and fat-rich foods (sensitivity: 67-93%). Conclusions:The NORDIET-FFQ showed good ability in to estimate intakes of plant-based foods, fish, dairy products, meat, and energy-dense foods; adequate ranking of individuals according to intake of most recommendations except for unprocessed meat, processed meat, and vegetables; and importantly a good ability to identify those patients in need of dietary counselling for foods that are known to modulate the risk of CRC. Trial registration:National Institutes of Health ClinicalTrials.gov; Identifier: NCT01570010.