Food proteins and maturation of small intestinal microvillus membranes (MVM). III. Food protein binding and MVM proteins in rats from newborn to young adult age.

PubMed

Stern, M; Gellermann, B; Wieser, H

1990-10-01

To investigate postnatal maturational profiles of functional and biochemical properties of rat small intestinal microvillus membranes (MVM), we did a longitudinal study in rats from birth to the age of 12 weeks. In parallel, we studied binding of cow's milk proteins and of the wheat gliadin peptide B 3142, as well as MVM proteins (SDS-PAGE). Changes in MVM fluidity and lipid composition exhibited early (0-4 weeks) and intermediate and late (6-12 weeks) patterns, as has been published earlier. Postnatal changes of food protein and peptide binding occurred early during the observation period, not related to weaning. There was not much further change in binding after 6-8 weeks. Developmental profiles of MVM protein and some lipid changes resembled, but did not equal, changes in food protein binding. We conclude that changes in MVM biochemical composition affect MVM binding characteristics. In particular, high molecular weight MVM proteins (susceptible to trypsin treatment) appear to play a role in postnatal maturational differences in MVM food protein binding.

Whey proteins in the regulation of food intake and satiety.

PubMed

Luhovyy, Bohdan L; Akhavan, Tina; Anderson, G Harvey

2007-12-01

Whey protein has potential as a functional food component to contribute to the regulation of body weight by providing satiety signals that affect both short-term and long-term food intake regulation. Because whey is an inexpensive source of high nutritional quality protein, the utilization of whey as a physiologically functional food ingredient for weight management is of current interest. At present, the role of individual whey proteins and peptides in contributing to food intake regulation has not been fully defined. However, Whey protein reduces short-term food intake relative to placebo, carbohydrate and other proteins. Whey protein affects satiation and satiety by the actions of: (1) whey protein fractions per se; (2) bioactive peptides; (3) amino-acids released after digestion; (4) combined action of whey protein and/or peptides and/or amino acids with other milk constituents. Whey ingestion activates many components of the food intake regulatory system. Whey protein is insulinotropic, and whey-born peptides affect the renin-angiotensin system. Therefore whey protein has potential as physiologically functional food component for persons with obesity and its co-morbidities (hypertension, type II diabetes, hyper- and dislipidemia). It remains unclear, however, if the favourable effects of whey on food intake, subjective satiety and intake regulatory mechanisms in humans are obtained from usual serving sizes of dairy products. The effects described have been observed in short-term experiments and when whey is consumed in much higher amounts.

High pressure effects on allergen food proteins.

PubMed

Somkuti, Judit; Smeller, László

2013-12-15

There are several proteins, which can cause allergic reaction if they are inhaled or ingested. Our everyday food can also contain such proteins. Food allergy is an IgE-mediated immune disorder, a growing health problem of great public concern. High pressure is known to affect the structure of proteins; typically few hundred MPa pressure can lead to denaturation. That is why several trials have been performed to alter the structure of the allergen proteins by high pressure, in order to reduce its allergenicity. Studies have been performed both on simple protein solutions and on complex food systems. Here we review those allergens which have been investigated under or after high pressure treatment by methods capable of detecting changes in the secondary and tertiary structure of the proteins. We focus on those allergenic proteins, whose structural changes were investigated by spectroscopic methods under pressure in correlation with the observed allergenicity (IgE binding) changes. According to this criterion we selected the following allergen proteins: Mal d 1 and Mal d 3 (apple), Bos d 5 (milk), Dau c 1 (carrot), Gal d 2 (egg), Ara h 2 and Ara h 6 (peanut), and Gad m 1 (cod). Copyright © 2013 Elsevier B.V. All rights reserved.

Polyphenol-enriched berry extracts naturally modulate reactive proteins in model foods.

PubMed

Lila, Mary Ann; Schneider, Maggie; Devlin, Amy; Plundrich, Nathalie; Laster, Scott; Foegeding, E Allen

2017-12-13

Healthy foods like polyphenol-rich berries and high quality edible proteins are in demand in today's functional food marketplace, but it can be difficult to formulate convenient food products with physiologically-relevant amounts of these ingredients and still maintain product quality. In part, this is because proteins can interact with other food ingredients and precipitate destabilizing events, which can disrupt food structure and diminish shelf life. Proteins in foods can also interact with human receptors to provoke adverse consequences such as allergies. When proteins and polyphenols were pre-aggregated into stable colloidal particles prior to use as ingredients, highly palatable food formulations (with reduced astringency of polyphenols) could be prepared, and the overall structural properties of food formulations were significantly improved. All of the nutritive and phytoactive benefits of the proteins and concentrated polyphenols remained highly bioavailable, but the protein molecules in the particle matrix did not self-aggregate into networks or react with other food ingredients. Both the drainage half-life (a marker of structural stability) and the yield stress (resistance to flow) of model foams made with the protein-polyphenol particles were increased in a dose-dependent manner. Of high significance in this complexation process, the reactive allergenic epitopes of certain proteins were effectively blunted by binding with polyphenols, attenuating the allergenicity of the food proteins. Porcine macrophages produced TNF-α proinflammatory cytokine when provoked with whey protein, but, this response was blocked completely when the cells were stimulated with particles that complexed whey protein with cinnamon-derived polyphenols. Cytokine and chemokine production characteristic of allergic reactions were blocked by the polyphenols, allowing for the potential creation of hypoallergenic protein-berry polyphenol enriched foods.

Impact of dietary protein and gender on food reinforcement

USDA-ARS?s Scientific Manuscript database

Recent evidence suggests that increasing dietary protein may alter reward-driven eating behavior. However, the link between protein and food reinforcement is not known. We sought to determine the extent to which increasing dietary protein alters food reinforcement in healthy adults. In a randomized ...

Food Protein-Induced Enterocolitis Syndrome.

PubMed

Bingemann, Theresa A; Sood, Puja; Järvinen, Kirsi M

2018-02-01

Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy that usually presents in infancy. Cow's milk, soy, and grains are the most common food triggers. FPIES can present as a medical emergency with symptoms including delayed persistent emesis or diarrhea that can lead to severe dehydration and hemodynamic instability with abnormal laboratory markers. Diagnosis can often be made based on clinical history and noted improvement in symptoms once the suspected triggers have been removed from the diet, with oral food challenge as the gold standard for confirmation of diagnosis in unclear cases. Copyright © 2017 Elsevier Inc. All rights reserved.

Immunochemical analytical methods for the determination of peanut proteins in foods.

PubMed

Whitaker, Thomas B; Williams, Kristina M; Trucksess, Mary W; Slate, Andrew B

2005-01-01

Peanut proteins can cause allergenic reactions that can result in respiratory and circulatory effects in the body sometimes leading to shock and death. The determination of peanut proteins in foods by analytical methods can reduce the risk of serious reactions in the highly sensitized individual by allowing for the detection of these proteins in a food at various stages of the manufacturing process. The method performance of 4 commercially available enzyme-linked immunosorbent assay (ELISA) kits was evaluated for the detection of peanut proteins in milk chocolate, ice cream, cookies, and breakfast cereals: ELISA-TEK Peanut Protein Assay, now known as "Bio-Kit" for peanut proteins, from ELISA Technologies Inc.; Veratox for Peanut Allergens from Neogen Corp.; RIDASCREEN Peanut Kit from R-Biopharm GmbH; and ProLisa from Canadian Food Technology Ltd. The 4 test kits were evaluated for accuracy (recovery) and precision using known concentrations of peanut or peanut proteins in the 4 food matrixes. Two different techniques, incurred and spiked, were used to prepare samples with 4 known concentrations of peanut protein. Defatted peanut flour was added in the incurred samples, and water-soluble peanut proteins were added in the spiked samples. The incurred levels were 0.0, 10, 20, and 100 microg whole peanut per g food; the spiked levels were 0.0, 5, 10, and 20 microg peanut protein per g food. Performance varied by test kit, protein concentration, and food matrix. The Veratox kit had the best accuracy or lowest percent difference between measured and incurred levels of 15.7% when averaged across all incurred levels and food matrixes. Recoveries associated with the Veratox kit varied from 93 to 115% for all food matrixes except cookies. Recoveries for all kits were about 50% for cookies. The analytical precision, as measured by the variance, increased with an increase in protein concentration. However, the coefficient of variation (CV) was stable across the 4 incurred

The Ontario Food and Nutrition Strategy: identifying indicators of food access and food literacy for early monitoring of the food environment.

PubMed

Boucher, Beatrice A; Manafò, Elizabeth; Boddy, Meaghan R; Roblin, Lynn; Truscott, Rebecca

2017-09-01

To address challenges Canadians face within their food environments, a comprehensive, multistakeholder, intergovernmental approach to policy development is essential. Food environment indicators are needed to assess population status and change. The Ontario Food and Nutrition Strategy (OFNS) integrates the food, agriculture and nutrition sectors, and aims to improve the health of Ontarians through actions that promote healthy food systems and environments. This report describes the process of identifying indicators for 11 OFNS action areas in two strategic directions (SDs): Healthy Food Access, and Food Literacy and Skills. The OFNS Indicators Advisory Group used a five-step process to select indicators: (1) potential indicators from national and provincial data sources were identified; (2) indicators were organized by SD, action area and data type; (3) selection criteria were identified, pilot tested and finalized; (4) final criteria were applied to refine the indicator list; and (5) indicators were prioritized after reapplication of selection criteria. Sixty-nine potential indicators were initially identified; however, many were individual-level rather than system-level measures. After final application of the selection criteria, one individual-level indicator and six system-level indicators were prioritized in five action areas; for six of the action areas, no indicators were available. Data limitations suggest that available data may not measure important aspects of the food environment, highlighting the need for action and resources to improve system-level indicators and support monitoring of the food environment and health in Ontario and across Canada.

Patterns of Protein Food Intake Are Associated with Nutrient Adequacy in the General French Adult Population.

PubMed

Gavelle, Erwan de; Huneau, Jean-François; Mariotti, François

2018-02-17

Protein food intake appears to partially structure dietary patterns, as most current emergent diets (e.g., vegetarian and flexitarian) can be described according to their levels of specific protein sources. However, few data are available on dietary protein patterns in the general population and their association with nutrient adequacy. Based on protein food intake data concerning 1678 adults from a representative French national dietary survey, and non-negative-matrix factorization followed by cluster analysis, we were able to identify distinctive dietary protein patterns and compare their nutrient adequacy (using PANDiet probabilistic scoring). The findings revealed eight patterns that clearly discriminate protein intakes and were characterized by the intakes of one or more specific protein foods: 'Processed meat', 'Poultry', 'Pork', 'Traditional', 'Milk', 'Take-away', 'Beef' and 'Fish'. 'Fish eaters' and 'Milk drinkers' had the highest overall nutrient adequacy, whereas that of 'Pork' and 'Take-away eaters' was the lowest. Nutrient adequacy could often be accounted for by the characteristics of the food contributing to protein intake: 'Meat eaters' had high probability of adequacy for iron and zinc, for example. We concluded that protein patterns constitute strong elements in the background structure of the dietary intake and are associated with the nutrient profile that they convey.

Serum C-reactive protein in food protein-induced enterocolitis syndrome versus food protein-induced proctocolitis in Japan.

PubMed

Kimura, Mitsuaki; Shimomura, Masaki; Morishita, Hideaki; Meguro, Takaaki; Seto, Shiro

2016-09-01

Some infants with food protein-induced enterocolitis syndrome (FPIES) have increased serum C-reactive protein (CRP) and fever in Japan. The aim of this study was therefore to clarify and compare the incidence of this in patients with FPIES versus patients with food protein-induced proctocolitis (FPIP). One hundred and sixteen infants with non-IgE-mediated gastrointestinal food allergies were enrolled in this study and classified into three phenotypes: FPIES presenting with vomiting and/or diarrhea (n = 47); FPIP with bloody stool alone (n =19); and the mixed phenotype (MP), bloody stool with vomiting and/or diarrhea (n = 50). Serum CRP was increased in 55.3% of the FPIES group, similar to that in the MP group (54.0%), and significantly higher than in the FPIP group (15.8%; P < 0.01). Fever was observed in 29.8% of the FPIES group, significantly higher than in the MP group (8.0%; P < 0.01) and in the FPIP group (0%; P < 0.05). Patients with fever had significantly higher serum CRP than patients without fever (median, 12.8 vs <0.2 mg/dL, P < 0.00001). Serum CRP was significantly higher in the FPIES group than in the FPIP group. This suggests that serum CRP is a useful marker for differentiating the pathogenesis of FPIES from FPIP. From the perspective of serum CRP, the pathology of the intestinal inflammation in MP subjects is suggested to be similar to that of FPIES. © 2016 The Authors. Pediatrics International published by John Wiley & Sons Australia, Ltd on behalf of Japan Pediatric Society.

Bioactive Properties of Maillard Reaction Products Generated From Food Protein-derived Peptides.

PubMed

Arihara, K; Zhou, L; Ohata, M

Food protein-derived peptides are promising food ingredients for developing functional foods, since various bioactive peptides are released from food proteins. The Maillard reaction, which plays an important role in most processed foods, generates various chemical components during processing. Although changes of amino acids or proteins and reduced sugars by the Maillard reaction have been studied extensively, such changes of peptides by the Maillard reaction are still not resolved enough. Since food protein-derived peptides are widely utilized in many processed foods, it deserves concern and research on the changes of peptides by the Maillard reaction in foods during processing or storage. This chapter initially overviewed food protein-derived bioactive peptides. Then, Maillard reaction products generated from peptides are discussed. We focused particularly on their bioactivities. © 2017 Elsevier Inc. All rights reserved.

Dietary protein restriction for renal patients: don't forget protein-free foods.

PubMed

D'Alessandro, Claudia; Rossi, Andrea; Innocenti, Maurizio; Ricchiuti, Guido; Bozzoli, Laura; Sbragia, Giulietta; Meola, Mario; Cupisti, Adamasco

2013-09-01

The treatment of chronic kidney disease (CKD) consists of pharmacological, nutritional, and psychological-social approaches. The dietary therapy of CKD, namely a low-protein low-phosphorus diet, plays a crucial role in contributing to delay the onset of end-stage renal disease (ESRD) and to protect cardiovascular and nutritional status. The protein-free food products represent a very important tool for the implementation of a low-protein diet to ensure adequate energy supply, reducing the production of nitrogenous waste products. This survey included 100 consecutive CKD patients who were asked their opinion about the use of protein-free foods. Ninety-eight patients (98%) reported a regular daily intake of protein-free pasta (as macaroni, spaghetti, etc.), which was the preferred product consumed. Actually, the taste and texture of protein-free pasta were considered as "good" or "very good" by 70% of patients. Conversely, 43% of CKD patients perceived the taste and texture of protein-free bread as "bad" or "very bad", and 30% found it "acceptable". Therefore, the main concern for the implementation of low-protein diets is the use and palatability of the protein-free products, bread in particular. The use of these products may help in reducing protein, phosphorus, and sodium intake while supplying an adequate energy intake, which represents the basis for a nutritionally safe and successful dietary treatment of advanced CKD patients. Manufacturers and food technology should make more efforts to finding new solutions to improve the taste and texture of protein-free products. Copyright © 2013 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Physical properties of mixed dairy food proteins

USDA-ARS?s Scientific Manuscript database

Mixed food protein gels are complex systems, which changes functional behaviors such as gelling properties and viscosity depending on the miscibility of the proteins. We have noted that differences in co-solubility of mixed proteins created unique network structures and gel properties. The effects o...

Evaluation of canine adverse food reactions by patch testing with single proteins, single carbohydrates and commercial foods.

PubMed

Johansen, Cornelia; Mariani, Claire; Mueller, Ralf S

2017-10-01

Adverse food reaction (AFR) is an important differential diagnosis for the pruritic dog. It is usually diagnosed by feeding an elimination diet with a novel protein and carbohydrate source for eight weeks followed by subsequent food provocation. A previous study demonstrated that patch testing dogs with foods had a high sensitivity and negative predictability for selection of elimination diet ingredients. The aim of this study was to investigate patch testing with proteins, carbohydrates and dry commercial dog food in dogs to determine whether there was value in patch testing to aid the diagnosis of canine adverse food reaction. Twenty five privately owned dogs, with confirmed AFR, underwent provocation trials with selected food antigens and patch testing. For proteins, carbohydrates and dry dog food the sensitivity of patch testing was 100%, 70% and 22.2%, respectively; the negative predictive values of patch testing were 100%, 79% and 72%. The positive predictive values of patch testing for proteins and carbohydrates were 75% and 74%, respectively. This study confirmed that patch testing may be useful for the selection of a suitable protein source for an elimination diet in dogs with suspected AFR, but not as a diagnostic tool for canine AFR. Results for proteins are more reliable than for carbohydrates and the majority of positive patch test reactions were observed with raw protein. Patch testing with commercial dog food does not seem to be useful. © 2017 ESVD and ACVD.

Food protein-induced enterocolitis syndrome: a challenging diagnosis.

PubMed

Ribeiro, Andreia; Moreira, Diana; Costa, Cristina; Pinto Pais, Isabel

2018-02-08

Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated gastrointestinal food hypersensitivity triggered by food proteins. It may present acutely, with repetitive vomiting, diarrhoea and lethargy leading to dehydration and eventually shock or insidiously with intermittent emesis, chronic diarrhoea or failure to thrive. We describe a paediatric male patient with recurrent sepsis-like episodes of fever, lethargy, ashen-grey skin colouration and vomiting followed by diarrhoea. These episodes were triggered by cow's milk formula and grains. Laboratory tests revealed leucocytosis, thrombocytosis, metabolic acidosis and elevated C reactive protein. After exclusion of other differential diagnoses, the diagnosis of FPIES was established on clinical improvement with withdrawal of the offending food and positive oral food challenge. FPIES diagnosis requires a high index of suspicion and is frequently delayed, which contributes to an increased morbidity. This is due to the wide spectrum of clinical presentations and due to the absence of specific diagnostic tests. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Toxicological evaluation of proteins introduced into food crops

PubMed Central

Kough, John; Herouet-Guicheney, Corinne; Jez, Joseph M.

2013-01-01

This manuscript focuses on the toxicological evaluation of proteins introduced into GM crops to impart desired traits. In many cases, introduced proteins can be shown to have a history of safe use. Where modifications have been made to proteins, experience has shown that it is highly unlikely that modification of amino acid sequences can make a non-toxic protein toxic. Moreover, if the modified protein still retains its biological function, and this function is found in related proteins that have a history of safe use (HOSU) in food, and the exposure level is similar to functionally related proteins, then the modified protein could also be considered to be “as-safe-as” those that have a HOSU. Within nature, there can be considerable evolutionary changes in the amino acid sequence of proteins within the same family, yet these proteins share the same biological function. In general, food crops such as maize, soy, rice, canola etc. are subjected to a variety of processing conditions to generate different food products. Processing conditions such as cooking, modification of pH conditions, and mechanical shearing can often denature proteins in these crops resulting in a loss of functional activity. These same processing conditions can also markedly lower human dietary exposure to (functionally active) proteins. Safety testing of an introduced protein could be indicated if its biological function was not adequately characterized and/or it was shown to be structurally/functionally related to proteins that are known to be toxic to mammals. PMID:24164515

Immunochemical-based method for detection of hazelnut proteins in processed foods.

PubMed

Ben Rejeb, Samuel; Abbott, Michael; Davies, David; Querry, Jessica; Cléroux, Chantal; Streng, Christine; Delahaut, Philippe; Yeung, Jupiter M

2003-01-01

A competitive enzyme-linked immunosorbent assay (ELISA) was developed to detect hazelnut by using polyclonal antibodies generated against a protein extract of roasted hazelnut. No cross-reactivity was observed in tests against 39 commodities, including many common allergens, tree nuts, and legumes. Hazelnut protein standard solutions at 0.45 ng/mL [inhibition concentration (IC80) of the competitive test] were clearly identified by the ELISA. An extraction and quantification method was developed and optimized for chocolate, cookies, breakfast cereals, and ice cream, major food commodities likely to be cross-contaminated with undeclared hazelnut during food processing. No sample cleanup was required when extracts were diluted 10-fold. Recovery results were generated with blank matrixes spiked at 4 levels from 1 to 10 microg/g hazelnut protein. With the developed extraction and sample handling procedure, hazelnut proteins were recovered at 64-83% from chocolate and at 78-97% from other matrixes. A confirmatory technique was developed with sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western transfer. The developed methods were applied to a small market survey of chocolate products and allowed the identification of undeclared hazelnut in these products.

Barriers to and Facilitators of the Consumption of Animal-Based Protein-Rich Foods in Older Adults

PubMed Central

Appleton, K. M.

2016-01-01

Protein intakes in the older population can be lower than recommended for good health, and while reasons for low protein intakes can be provided, little work has attempted to investigate these reasons in relation to actual intakes, and so identify those of likely greatest impact when designing interventions. Questionnaires assessing: usual consumption of meat, fish, eggs and dairy products; agreement/disagreement with reasons for the consumption/non-consumption of these foods; and several demographic and lifestyle characteristics; were sent to 1000 UK community-dwelling adults aged 65 years and over. In total, 351 returned questionnaires, representative of the UK older population for gender and age, were suitable for analysis. Different factors were important for consumption of the four food groups, but similarities were also found. These similarities likely reflect issues of particular concern to both the consumption of animal-based protein-rich foods and the consumption of these foods by older adults. Taken together, these findings suggest intakes to be explained by, and thus that strategies for increasing consumption should focus on: increasing liking/tastiness; improving convenience and the effort required for food preparation and consumption; minimizing spoilage and wastage; and improving perceptions of affordability or value for money; freshness; and the healthiness of protein-rich foods. PMID:27043615

Food Protein-polysaccharide Conjugates Obtained via the Maillard Reaction: A Review.

PubMed

de Oliveira, Fabíola Cristina; Coimbra, Jane Sélia Dos Reis; de Oliveira, Eduardo Basílio; Zuñiga, Abraham Damian Giraldo; Rojas, Edwin E Garcia

2016-05-18

The products formed by glycosylation of food proteins with carbohydrates via the Maillard reaction, also known as conjugates, are agents capable of changing and improving techno-functional characteristics of proteins. The Maillard reaction uses the covalent bond between a group of a reducing carbohydrates and an amino group of a protein. This reaction does not require additional chemicals as it occurs naturally under controlled conditions of temperature, time, pH, and moisture. Moreover, there is growing interest in modifying proteins for industrial food applications. This review analyses the current state of art of the Maillard reaction on food protein functionalities. It also discusses the influence of the Maillard reaction on the conditions and formulation of reagents that improve desirable techno-functional characteristics of food protein.

Occupational protein contact dermatitis in food handlers.

PubMed

Hjorth, N; Roed-Petersen, J

1976-02-01

The preparation of food in restaurant kitchens carries a high risk of occupational dermatoses. Analysis of 33 cases revealed four different etiological types. Simple irritant dermatitis was rare (2 cases), plain contact dermatitis was more common (6 cases). Fifteen patients had relevant patch tests and scratch tests; ten had positive scratch tests only to explain the cause of their dermatitis. The last type was termed protein contact dermatitis. The major type IV allergens incriminated were metals, onion and garlic. The major proteinaceous allergens indicated by history and test results were fish and shell-fish. Open patch tests with the incriminated foods may cause erythema or oedema on normal skin after 20 minutes. Previously eczematous, now normal looking, skin often responds with a crop of dyshidrotic vesicles preceded by erythema and itching 30 minutes after the application of an open test. Examination for specific IgE is not always positive in such cases. Inhalant allergy was rare. The results indicate that food handlers are sensitized by the protein they touch, and then react to later contact with the proteins. Protein contact dermatitis is similarly common among veterinary surgeons, while the importance in other occupational groups remains to be studied.

Foods with increased protein content: A qualitative study on European consumer preferences and perceptions.

PubMed

Banovic, Marija; Arvola, Anne; Pennanen, Kyösti; Duta, Denisa E; Brückner-Gühmann, Monika; Lähteenmäki, Liisa; Grunert, Klaus G

2018-06-01

Foods with increased protein content have rapidly become one of the fastest-growing product categories targeting image- and health-focused consumers. However, it is not clear whether consumers really understand the difference between 'inherently rich in protein' and 'artificially increased protein'. This study used a qualitative focus group approach to investigate the consumer preferences and perceptions of foods with increased protein content among mixed-age and older population in four European countries. In total fifty-two participants were involved in the study. Understanding of the concept of foods with 'increased protein' content was limited. Both older and mixed-age participants could not differentiate between natural sources of protein and foods with increased protein content, no matter whether foods with animal or plant proteins were mentioned. Older participants expressed more scepticism towards foods with increased protein content than mixed-age participants. The combination of protein type and food carrier closer to conventional foods received more acceptance among both older and mixed-age participants. Future use and acceptance of foods with increased protein content will depend on the extent to which consumer concerns about incorporating additional protein into a diet can be responded. Copyright © 2018 Elsevier Ltd. All rights reserved.

A leukocyte activation test identifies food items which induce release of DNA by innate immune peripheral blood leucocytes.

PubMed

Garcia-Martinez, Irma; Weiss, Theresa R; Yousaf, Muhammad N; Ali, Ather; Mehal, Wajahat Z

2018-01-01

Leukocyte activation (LA) testing identifies food items that induce a patient specific cellular response in the immune system, and has recently been shown in a randomized double blinded prospective study to reduce symptoms in patients with irritable bowel syndrome (IBS). We hypothesized that test reactivity to particular food items, and the systemic immune response initiated by these food items, is due to the release of cellular DNA from blood immune cells. We tested this by quantifying total DNA concentration in the cellular supernatant of immune cells exposed to positive and negative foods from 20 healthy volunteers. To establish if the DNA release by positive samples is a specific phenomenon, we quantified myeloperoxidase (MPO) in cellular supernatants. We further assessed if a particular immune cell population (neutrophils, eosinophils, and basophils) was activated by the positive food items by flow cytometry analysis. To identify the signaling pathways that are required for DNA release we tested if specific inhibitors of key signaling pathways could block DNA release. Foods with a positive LA test result gave a higher supernatant DNA content when compared to foods with a negative result. This was specific as MPO levels were not increased by foods with a positive LA test. Protein kinase C (PKC) inhibitors resulted in inhibition of positive food stimulated DNA release. Positive foods resulted in CD63 levels greater than negative foods in eosinophils in 76.5% of tests. LA test identifies food items that result in release of DNA and activation of peripheral blood innate immune cells in a PKC dependent manner, suggesting that this LA test identifies food items that result in release of inflammatory markers and activation of innate immune cells. This may be the basis for the improvement in symptoms in IBS patients who followed an LA test guided diet.

Identifying Protein-Calorie Malnutrition Workshop.

ERIC Educational Resources Information Center

Walker, Susan S.; Barker, Ellen M.

Instructional materials are provided for a workshop to enable participants to assist in identifying patients at risk with protein-calorie malnutrition and in corrrecting this nutritional deficiency. Representative topics are nutrients; protein, mineral, and vitamin sources, functions, and deficiency symptoms; malnutrition; nutritional deficiency…

Determination of allergenic egg proteins in food by protein-, mass spectrometry-, and DNA-based methods.

PubMed

Lee, Ji-Yun; Kim, Chang Jong

2010-01-01

Egg allergy is one of the most common food allergies in both adults and children, and foods including eggs and their byproducts should be declared under food allergen labeling policies in industrial countries. Therefore, to develop and validate a sensitive and specific method to detect hidden egg allergens in foods, we compared immunochemical, DNA-based, and proteomic methods for detecting egg allergens in foods using egg allergen standards such as egg whole protein, egg white protein, egg yolk protein, ovomucoid, ovalbumin, ovotransferrin, lysozyme, and alpha-livetin. Protein-based immunochemical methods, including ELISA as an initial screening quantitative analysis and immunoblotting as a final confirmatory qualitative analysis, were very sensitive and specific in detecting potentially allergenic egg residues in processed foods in trace amounts. In contrast, the proteomics-based, matrix-assisted laser desorption/ionization time-of-flight MS and LC-tandem quadrupole time-of-flight MS methods were not able to detect some egg allergens, such as ovomucoid, because of its nondenaturing property under urea and trypsin. The DNA-based PCR method could not distinguish between egg and chicken meat because it is tissue-nonspecific. In further studies for the feasibility of these immunochemical methods on 100 real raw dietary samples, four food samples without listed egg ingredients produced a positive response by ELISA, but exhibited negative results by immunoblotting.

Food allergen protein families and their structural characteristics and application in component-resolved diagnosis: new data from the EuroPrevall project.

PubMed

Hoffmann-Sommergruber, Karin; Mills, E N Clare

2009-09-01

A large number of food allergens able to induce allergic symptoms in predisposed individuals, including severe, even life-threatening reactions, have been identified and characterized. However, proteins able to cause such IgE-mediated reactions can be assigned to only a limited number of protein families. Detailed knowledge about the characteristics of food allergens, their 3D structures, biological activity and stability, will help to improve diagnosis of food allergy, avoid unnecessary exclusion diets and assess the risk of cross-reactive allergies to other food sources. This review is dedicated to summarizing current knowledge about the most important food allergen protein families and to presenting data from the EuroPrevall allergen library, a proof-of-concept collection of highly purified, characterized and authenticated food allergens from animal and plant food sources to facilitate improved diagnosis of food allergies.

Unraveling novel broad-spectrum antibacterial targets in food and waterborne pathogens using comparative genomics and protein interaction network analysis.

PubMed

Jadhav, Ankush; Shanmugham, Buvaneswari; Rajendiran, Anjana; Pan, Archana

2014-10-01

Food and waterborne diseases are a growing concern in terms of human morbidity and mortality worldwide, even in the 21st century, emphasizing the need for new therapeutic interventions for these diseases. The current study aims at prioritizing broad-spectrum antibacterial targets, present in multiple food and waterborne bacterial pathogens, through a comparative genomics strategy coupled with a protein interaction network analysis. The pathways unique and common to all the pathogens under study (viz., methane metabolism, d-alanine metabolism, peptidoglycan biosynthesis, bacterial secretion system, two-component system, C5-branched dibasic acid metabolism), identified by comparative metabolic pathway analysis, were considered for the analysis. The proteins/enzymes involved in these pathways were prioritized following host non-homology analysis, essentiality analysis, gut flora non-homology analysis and protein interaction network analysis. The analyses revealed a set of promising broad-spectrum antibacterial targets, present in multiple food and waterborne pathogens, which are essential for bacterial survival, non-homologous to host and gut flora, and functionally important in the metabolic network. The identified broad-spectrum candidates, namely, integral membrane protein/virulence factor (MviN), preprotein translocase subunits SecB and SecG, carbon storage regulator (CsrA), and nitrogen regulatory protein P-II 1 (GlnB), contributed by the peptidoglycan pathway, bacterial secretion systems and two-component systems, were also found to be present in a wide range of other disease-causing bacteria. Cytoplasmic proteins SecG, CsrA and GlnB were considered as drug targets, while membrane proteins MviN and SecB were classified as vaccine targets. The identified broad-spectrum targets can aid in the design and development of antibacterial agents not only against food and waterborne pathogens but also against other pathogens. Copyright © 2014 Elsevier B.V. All rights

Protein Enrichment of Familiar Foods as an Innovative Strategy to Increase Protein Intake in Institutionalized Elderly.

PubMed

Beelen, J; de Roos, N M; de Groot, L C P G M

2017-01-01

To increase the protein intake of older adults, protein enrichment of familiar foods and drinks might be an effective and attractive alternative for oral nutritional supplements (ONS). We performed a pilot study to test whether these products could help institutionalized elderly to reach a protein intake of 1.2 gram per kg body weight per day (g/kg/d). Intervention study with one treatment group (no control group). Dietary assessment was done before and at the end of a 10-day intervention. Two care facilities in Gelderland, the Netherlands: a residential care home and a rehabilitation center. 22 elderly subjects (13 women, 9 men; mean age 83.0±9.4 years). We used a variety of newly developed protein enriched regular foods and drinks, including bread, soups, fruit juices, and instant mashed potatoes. Dietary intake was assessed on two consecutive days before and at the end of the intervention, using food records filled out by research assistants. Energy and macronutrient intake was calculated using the 2013 Dutch food composition database. Changes in protein intake were evaluated using paired t-tests. Protein intake increased by 11.8 g/d (P=0.003); from 0.96 to 1.14 g/kg/d (P=0.002). This increase is comparable to protein provided by one standard portion of ONS. The intake of energy and other macronutrients did not change significantly. At the end of the intervention more elderly reached a protein intake level of 1.2 g/kg/d than before (9 vs 4). Protein intake significantly increased during breakfast (+3.7 g) and during the evening (+2.2 g). Including familiar protein enriched foods and drinks in the menu helped to meet protein recommendations in institutionalized elderly.

Eliminating anti-nutritional plant food proteins: the case of seed protease inhibitors in pea.

PubMed

Clemente, Alfonso; Arques, Maria C; Dalmais, Marion; Le Signor, Christine; Chinoy, Catherine; Olias, Raquel; Rayner, Tracey; Isaac, Peter G; Lawson, David M; Bendahmane, Abdelhafid; Domoney, Claire

2015-01-01

Several classes of seed proteins limit the utilisation of plant proteins in human and farm animal diets, while plant foods have much to offer to the sustainable intensification of food/feed production and to human health. Reduction or removal of these proteins could greatly enhance seed protein quality and various strategies have been used to try to achieve this with limited success. We investigated whether seed protease inhibitor mutations could be exploited to enhance seed quality, availing of induced mutant and natural Pisum germplasm collections to identify mutants, whilst acquiring an understanding of the impact of mutations on activity. A mutant (TILLING) resource developed in Pisum sativum L. (pea) and a large germplasm collection representing Pisum diversity were investigated as sources of mutations that reduce or abolish the activity of the major protease inhibitor (Bowman-Birk) class of seed protein. Of three missense mutations, predicted to affect activity of the mature trypsin / chymotrypsin inhibitor TI1 protein, a C77Y substitution in the mature mutant inhibitor abolished inhibitor activity, consistent with an absolute requirement for the disulphide bond C77-C92 for function in the native inhibitor. Two further classes of mutation (S85F, E109K) resulted in less dramatic changes to isoform or overall inhibitory activity. The alternative strategy to reduce anti-nutrients, by targeted screening of Pisum germplasm, successfully identified a single accession (Pisum elatius) as a double null mutant for the two closely linked genes encoding the TI1 and TI2 seed protease inhibitors. The P. elatius mutant has extremely low seed protease inhibitory activity and introgression of the mutation into cultivated germplasm has been achieved. The study provides new insights into structure-function relationships for protease inhibitors which impact on pea seed quality. The induced and natural germplasm variants identified provide immediate potential for either halving

Advanced DNA- and Protein-based Methods for the Detection and Investigation of Food Allergens.

PubMed

Prado, M; Ortea, I; Vial, S; Rivas, J; Calo-Mata, P; Barros-Velázquez, J

2016-11-17

Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredients in food products. The present review addresses the recent developments regarding the application of DNA- and protein-based methods for the detection of allergenic ingredients in foods. The fitness-for-purpose of reviewed methodology will be discussed, and future trends will be highlighted. Special attention will be given to the evaluation of the potential of newly developed and promising technologies that can improve the detection and identification of allergenic ingredients in foods, such as the use of biosensors and/or nanomaterials to improve detection limits, specificity, ease of use, or to reduce the time of analysis. Such rapid food allergen test methods are required to facilitate the reliable detection of allergenic ingredients by control laboratories, to give the food industry the means to easily determine whether its product has been subjected to cross-contamination and, simultaneously, to identify how and when this cross-contamination occurred.

In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins.

PubMed

Acevedo-Pacheco, Laura; Serna-Saldívar, Sergio O

2016-01-01

One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. The aim was to determine and compare the essential amino acid (EAA) scores, protein digestibility corrected amino acid scores (PDCAAS), and in vivo protein quality (protein digestibility, protein efficiency ratio (PER), biological values (BV), and net protein utilization (NPU) values) of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. The proposed enrichment of cereal-based foods with soybean proteins greatly improved PDCAAS, animal growth, nitrogen retention, and PER primarily

In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

PubMed Central

Acevedo-Pacheco, Laura; Serna-Saldívar, Sergio O.

2016-01-01

Background One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective The aim was to determine and compare the essential amino acid (EAA) scores, protein digestibility corrected amino acid scores (PDCAAS), and in vivo protein quality (protein digestibility, protein efficiency ratio (PER), biological values (BV), and net protein utilization (NPU) values) of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions The proposed enrichment of cereal-based foods with soybean proteins greatly improved PDCAAS, animal

House dust mite (Der p 10) and crustacean allergic patients may react to food containing Yellow mealworm proteins.

PubMed

Verhoeckx, Kitty C M; van Broekhoven, Sarah; den Hartog-Jager, Constance F; Gaspari, Marco; de Jong, Govardus A H; Wichers, Harry J; van Hoffen, Els; Houben, Geert F; Knulst, André C

2014-03-01

Due to the imminent growth of the world population, shortage of protein sources for human consumption will arise in the near future. Alternative and sustainable protein sources (e.g. insects) are being explored for the production of food and feed. In this project, the safety of Yellow mealworms (Tenebrio molitor L.) for human consumption was tested using approaches as advised by the European Food Safety Authority for allergenicity risk assessment. Different Yellow mealworm protein fractions were prepared, characterised, and tested for cross-reactivity using sera from patients with an inhalation or food allergy to biologically related species (House dust mite (HDM) and crustaceans) by immunoblotting and basophil activation. Furthermore, the stability was investigated using an in vitro pepsin digestion test. IgE from HDM- and crustacean allergic patients cross-reacted with Yellow mealworm proteins. This cross-reactivity was functional, as shown by the induction of basophil activation. The major cross-reactive proteins were identified as tropomyosin and arginine kinase, which are well known allergens in arthropods. These proteins were moderately stable in the pepsin stability test. Based on these cross-reactivity studies, there is a realistic possibility that HDM- and crustacean allergic patients may react to food containing Yellow mealworm proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gonad differential proteins revealed with proteomics in oyster (Saccostrea cucullata) using alga as food contaminated with cadmium.

PubMed

Zhu, Bo; Gao, Kun-Shan; Wang, Ke-Jian; Ke, Cai-Huan; Huang, He-Qing

2012-04-01

As mercury and lead, cadmium (Cd) is one of the highly toxic metals in both the ocean and land environments, but its toxicological mechanism in organisms including human is still unclear because of the complex toxicological pathways in vivo. Here, the alga Chlorella vulgaris were cultivated at room temperature under the stress of cadmium (1 mg L(-1)) to obtain a toxic food, and then the contaminated food were directly supplied to oyster (Saccostrea cucullata) in seawater. After feeding with C. vulgaris contaminated with Cd (C. vulgaris-Cd), the differential proteins in the oyster gonad (OG) were effectively separated and identified with proteomic approaches. Eleven protein spots were observed to be significantly changed in the OG feeding with C. vulgaris-Cd, which seven spots of these differential proteins were down-regulated while four spots were up-regulated. These altered spots were further excised in gels and identified by a combined technique of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and database searching. A portion of these differential proteins were further proofed by real-time PCR and Western blotting. The results indicate that the major functions of these differential proteins were described as follows: binding, protein translocation, catalysis, regulation of energy metabolism, reproductive function and skeleton structure. These differential proteins in part may effectively provide a few novel biomarkers for the evaluation of Cd pollution level via a food pathway for harming halobios, mammal and human health, and for understanding the complex mechanisms of Cd toxicity in vivo. Copyright © 2011 Elsevier Ltd. All rights reserved.

Protein engineering and its applications in food industry.

PubMed

Kapoor, Swati; Rafiq, Aasima; Sharma, Savita

2017-07-24

Protein engineering is a young discipline that has been branched out from the field of genetic engineering. Protein engineering is based on the available knowledge about the proteins structure/function(s), tools/instruments, software, bioinformatics database, available cloned gene, knowledge about available protein, vectors, recombinant strains and other materials that could lead to change in the protein backbone. Protein produced properly from genetic engineering process means a protein that is able to fold correctly and to do particular function(s) efficiently even after being subjected to engineering practices. Protein is modified through its gene or chemically. However, modification of protein through gene is easier. There is no specific limitation of Protein Engineering tools; any technique that can lead to change the protein constituent of amino acid and result in the modification of protein structure/function is in the frame of Protein Engineering. Meanwhile, there are some common tools used to reach a specific target. More active industrial and pharmaceutical based proteins have been invented by the field of Protein Engineering to introduce new function as well as to change its interaction with surrounding environment. A variety of protein engineering applications have been reported in the literature. These applications range from biocatalysis for food and industry to environmental, medical and nanobiotechnology applications. Successful combinations of various protein engineering methods had led to successful results in food industries and have created a scope to maintain the quality of finished product after processing.

Knowledge, perceptions and preferences of elderly regarding protein-enriched functional food.

PubMed

van der Zanden, Lotte D T; van Kleef, Ellen; de Wijk, René A; van Trijp, Hans C M

2014-09-01

Promoting protein consumption in the elderly population may contribute to improving the quality of their later years in life. Our study aimed to explore knowledge, perceptions and preferences of elderly consumers regarding protein-enriched food. We conducted three focus groups with independently living (ID) elderly (N = 24, Mage = 67 years) and three with elderly living in a residential home (RH) (N = 18, Mage = 83 years). Both the ID and RH elderly were predominantly sceptical about functional food in general. Confusion, distrust and a perceived lack of personal relevance were main perceived barriers to purchasing and consuming these products, although a majority of the participants did report occasionally consuming at least one type of functional food. For the ID elderly, medical advice was an important facilitator that could overcome barriers to purchasing and consuming protein-enriched food, indicating the importance of personal relevance for this group. For the RH elderly, in contrast, sensory appeal of protein-enriched foods was a facilitator. Carrier preferences were similar for the two groups; the elderly preferred protein-enriched foods based on healthy products that they consumed frequently. Future studies should explore ways to deal with the confusion and distrust regarding functional food within the heterogeneous population of elderly. Copyright © 2014 Elsevier Ltd. All rights reserved.

The role of protein digestibility and antacids on food allergy outcomes

PubMed Central

Untersmayr, Eva; Jensen-Jarolim, Erika

2010-01-01

Digestion assays with simulated gastric fluid have been introduced for characterization of food proteins to imitate the effect of stomach proteolysis on dietary compounds in vitro. By using these tests, dietary proteins can be categorized as digestion-resistant class 1 (true allergens triggering direct oral sensitization) or as labile class 2 allergens (nonsensitizing elicitors). Thus the results of these digestion assays mirror situations of intact gastric proteolysis. Alterations in the gastric milieu are frequently experienced during a lifetime either physiologically in the very young and the elderly or as a result of gastrointestinal pathologies. Additionally, acid-suppression medications are frequently used for treatment of dyspeptic disorders. By increasing the gastric pH, they interfere substantially with the digestive function of the stomach, leading to persistence of labile food protein during gastric transit. Indeed, both murine and human studies reveal that antiulcer medication increases the risk of food allergy induction. Gastric digestion substantially decreases the potential of food proteins to bind IgE, which increases the threshold dose of allergens required to elicit symptoms in patients with food allergy. Thus antiulcer agents impeding gastric protein digestion have a major effect on the sensitization and effector phase of food allergy. PMID:18539189

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.

PubMed

Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L; Hallström, Björn M; Liu, Zihe; Petranovic, Dina; Uhlén, Mathias; Joensson, Haakan N; Andersson-Svahn, Helene; Nielsen, Jens

2015-08-25

There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV mutagenesis. Several screening and sorting rounds resulted in the selection of eight yeast clones with significantly improved secretion of recombinant α-amylase. Efficient secretion was genetically stable in the selected clones. We performed whole-genome sequencing of the eight clones and identified 330 mutations in total. Gene ontology analysis of mutated genes revealed many biological processes, including some that have not been identified before in the context of protein secretion. Mutated genes identified in this study can be potentially used for reverse metabolic engineering, with the objective to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could broadly facilitate design of novel cell factories.

Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

PubMed

Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

2017-05-01

The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of protein on biohydrogen production from starch of food waste.

PubMed

Ding, H B; Liu, X Y; Stabnikova, O; Wang, J-Y

2008-01-01

This study demonstrated the influence of protein on biohydrogen production from carbohydrates, especially starch, by using different combinations of two model food wastes, rice as starch-rich and soybean residue as protein-rich food waste. It was found the maximum specific hydrogen production potential, 0.99 mol H2/mol initial starch as glucose, and the maximum specific hydrogen production rate, 530 ml H2/h g-VS, occurred at a starch/protein ratio of 1.7. The protein content in the initial food waste not only provided buffering capacity to neutralize the volatile fatty acids as concurrent products but also enhanced the hydrogen production by providing readily available organic nitrogen such as soluble proteins and amino acids to microorganisms. Copyright IWA Publishing 2008.

The food colorant erythrosine is a promiscuous protein-protein interaction inhibitor.

PubMed

Ganesan, Lakshmi; Margolles-Clark, Emilio; Song, Yun; Buchwald, Peter

2011-03-15

Following our observation that erythrosine B (FD&C Red No. 3) is a relatively potent inhibitor of the TNF-R-TNFα and CD40-CD154 protein-protein interactions, we investigated whether this inhibitory activity extends to any other protein-protein interactions (PPI) as well as whether any other approved food colors possess such inhibitory activity. We found erythrosine, a poly-iodinated xanthene dye, to be a non-specific promiscuous inhibitor of a number of PPIs within the tumor necrosis factor superfamily (TNF-R-TNFα, CD40-CD154, BAFF-R-BAFF, RANK-RANKL, OX40-OX40L, 4-1BB-4-1BBL) as well as outside of it (EGF-R-EGF) with a remarkably consistent median inhibitory concentration (IC(50)) in the 2-20 μM (approximately 2-20mg/L) range. In agreement with this, erythrosine also showed cellular effects including clear cytotoxic effects around this concentration range (IC₅₀≈50 μM). Among the seven FDA-approved food colorants, only erythrosine showed consistent PPI inhibitory activity in the sub-100 μM range, which might also explain (at least partially) why it also has the lowest approved acceptable daily intake (ADI) (0.1 mg/kg body weight/day). Among a number of xanthene structural analogs of erythrosine tested for activity, rose Bengal, a food colorant approved in Japan, showed similar, maybe even more pronounced, promiscuous inhibitory activity, whereas fluorescein was inactive and gallein, phloxine, and eosin were somewhat active in some of the assays. Copyright © 2011 Elsevier Inc. All rights reserved.

[Evaluation of the adjusted amino acid score by digestibility for estimating the protein quality and protein available in food and diets].

PubMed

Pak, N; Vera, G; Araya, H

1985-03-01

The purpose of the present study was to evaluate the amino acid score adjusted by digestibility to estimate protein quality and utilizable protein in foods and diets, considering net protein utilization (NPU) as a biological reference method. Ten foods of vegetable origin and ten of animal origin, as well as eight mixtures of foods of vegetable and animal origin were studied. When all the foods were considered, a positive (r = 0.83) and highly significant correlation (p less than 0.001) between NPU and the amino acid score adjusted by digestibility was found. When the foods were separated according to their origin, this correlation was positive only for the foods of vegetable origin (r = 0.93) and statistically significant (p less than 0.001). Also, only in those foods were similar values found between NPU and amino acid score adjusted by digestibility, as well as in utilizable protein estimated considering both methods. Caution is required to interpret protein quality and utilizable protein values of foods of animal origin and mixtures of foods of vegetable and animal origin when the amino acid score method adjusted by digestibility, or NPU, are utilized.

Food Processing: The Influence of the Maillard Reaction on Immunogenicity and Allergenicity of Food Proteins

PubMed Central

Teodorowicz, Malgorzata; van Neerven, Joost

2017-01-01

The majority of foods that are consumed in our developed society have been processed. Processing promotes a non-enzymatic reaction between proteins and sugars, the Maillard reaction (MR). Maillard reaction products (MRPs) contribute to the taste, smell and color of many food products, and thus influence consumers’ choices. However, in recent years, MRPs have been linked to the increasing prevalence of diet- and inflammation-related non-communicable diseases including food allergy. Although during the last years a better understanding of immunogenicity of MRPs has been achieved, still only little is known about the structural/chemical characteristics predisposing MRPs to interact with antigen presenting cells (APCs). This report provides a comprehensive review of recent studies on the influence of the Maillard reaction on the immunogenicity and allergenicity of food proteins. PMID:28777346

Food Processing: The Influence of the Maillard Reaction on Immunogenicity and Allergenicity of Food Proteins.

PubMed

Teodorowicz, Malgorzata; van Neerven, Joost; Savelkoul, Huub

2017-08-04

The majority of foods that are consumed in our developed society have been processed. Processing promotes a non-enzymatic reaction between proteins and sugars, the Maillard reaction (MR). Maillard reaction products (MRPs) contribute to the taste, smell and color of many food products, and thus influence consumers' choices. However, in recent years, MRPs have been linked to the increasing prevalence of diet- and inflammation-related non-communicable diseases including food allergy. Although during the last years a better understanding of immunogenicity of MRPs has been achieved, still only little is known about the structural/chemical characteristics predisposing MRPs to interact with antigen presenting cells (APCs). This report provides a comprehensive review of recent studies on the influence of the Maillard reaction on the immunogenicity and allergenicity of food proteins.

Food protein induced enterocolitis syndrome caused by rice beverage.

PubMed

Caminiti, Lucia; Salzano, Giuseppina; Crisafulli, Giuseppe; Porcaro, Federica; Pajno, Giovanni Battista

2013-05-14

Food protein-induced enterocolitis syndrome (FPIES) is an uncommon and potentially severe non IgE-mediated gastrointestinal food allergy. It is usually caused by cow's milk or soy proteins, but may also be triggered by ingestion of solid foods. The diagnosis is made on the basis of clinical history and symptoms. Management of acute phase requires fluid resuscitation and intravenous steroids administration, but avoidance of offending foods is the only effective therapeutic option.Infant with FPIES presented to our emergency department with vomiting, watery stools, hypothension and metabolic acidosis after ingestion of rice beverage. Intravenous fluids and steroids were administered with good clinical response. Subsequently, a double blind placebo control food challenge (DBPCFC) was performed using rice beverage and hydrolyzed formula (eHF) as placebo. The "rice based formula" induced emesis, diarrhoea and lethargy. Laboratory investigations reveal an increase of absolute count of neutrophils and the presence of faecal eosinophils. The patient was treated with both intravenous hydration and steroids. According to Powell criteria, oral food challenge was considered positive and diagnosis of FPIES induced by rice beverage was made. Patient was discharged at home with the indication to avoid rice and any rice beverage as well as to reintroduce hydrolyzed formula. A case of FPIES induced by rice beverage has never been reported. The present case clearly shows that also beverage containing rice proteins can be responsible of FPIES. For this reason, the use of rice beverage as cow's milk substitute for the treatment of non IgE-mediated food allergy should be avoided.

Novel isoprenylated proteins identified by an expression library screen.

PubMed

Biermann, B J; Morehead, T A; Tate, S E; Price, J R; Randall, S K; Crowell, D N

1994-10-14

Isoprenylated proteins are involved in eukaryotic cell growth and signal transduction. The protein determinant for prenylation is a short carboxyl-terminal motif containing a cysteine, to which the isoprenoid is covalently attached via thioether linkage. To date, isoprenylated proteins have almost all been identified by demonstrating the attachment of an isoprenoid to previously known proteins. Thus, many isoprenylated proteins probably remain undiscovered. To identify novel isoprenylated proteins for subsequent biochemical study, colony blots of a Glycine max cDNA expression library were [3H]farnesyl-labeled in vitro. Proteins identified by this screen contained several different carboxyl termini that conform to consensus farnesylation motifs. These proteins included known farnesylated proteins (DnaJ homologs) and several novel proteins, two of which contained six or more tandem repeats of a hexapeptide having the consensus sequence (E/G)(G/P)EK(P/K)K. Thus, plants contain a diverse array of genes encoding farnesylated proteins, and our results indicate that fundamental differences in the identities of farnesylated proteins may exist between plants and other eukaryotes. Expression library screening by direct labeling can be adapted to identify isoprenylated proteins from other organisms, as well as proteins with other post-translational modifications.

Dietary proteins in the regulation of food intake and body weight in humans.

PubMed

Anderson, G Harvey; Moore, Shannon E

2004-04-01

This review presents 4 lines of evidence supporting a role for proteins in the regulation of food intake and maintenance of healthy body weights. It is concluded that the protein content of food, and perhaps its source, is a strong determinant of short-term satiety and of how much food is eaten. Although the role of protein in the regulation of long-term food intake and body weight is less clear, the evidence reviewed suggests that further research to define its role is merited. Such research has the potential to lead to new functional foods, food formulations, and dietary recommendations for achieving healthy body weights.

With Protein Foods, Variety Is Key: 10 Tips for Choosing Protein

MedlinePlus

... or seeds can be considered as 1 ounce-equivalent from the Protein Foods Group. Revised January 2016 ... Us Advanced Search Help Search Tips Privacy Policy Non-Discrimination Statement Information Quality USA.gov WhiteHouse.gov

Determination of egg proteins in snack food and noodles.

PubMed

Williams, Kristina M; Westphal, Carmen D; Shriver-Lake, Lisa C

2004-01-01

Egg is one of the 5 major allergenic foods that are responsible for more than 3/4 of food allergies in children. Food-allergic responses can be controlled by avoidance of the offending foods. The applicability of a commercial enzyme-linked immunosorbent assay (ELISA) kit for the detection of egg in food products such as cookies, crackers, pretzels, salad dressings, and raw and cooked noodles was evaluated. A preliminary evaluation of an antibody-based biosensor was also performed. A National Institute of Standards and Technology (NIST) whole dried egg powder reference material, SRM 8415, was used as a standard. A homogeneous and stable aqueous egg suspension was prepared for the evaluation of the performance of the Veratox for Egg Allergen Test (Neogen Corp., Lansing, MI). This test does not detect egg yolk proteins. Each gram of the aqueous dried egg suspension contained 643 microg whole dried egg, 0.5 mg thimerosal, and 2.5 mg bovine serum albumin. When cookies, crackers, salad dressings, noodles, and ice cream were spiked at a level of 24 mg/kg SRM 8415, recoveries for whole egg averaged about 28%. All foods containing egg as indicated on the ingredient label were found positive by the Veratox test. No false positives occurred in samples that did not contain eggs. Similar results were obtained using the Naval Research Laboratory (NRL) array biosensor, an evanescent wave fluoroimmunosensor. Results for cooked noodles showed that they contained <1% of the egg found in uncooked noodles. A comparison of extracts from cooked and uncooked noodles by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed differences in protein profiles. The boiling of the noodles could have reduced the immunoreactivity of the egg proteins to the antibodies used in the kit or rendered the egg proteins nonextractable.

Improved Functional Characteristics of Whey Protein Hydrolysates in Food Industry

PubMed Central

Jeewanthi, Renda Kankanamge Chaturika; Lee, Na-Kyoung; Paik, Hyun-Dong

2015-01-01

This review focuses on the enhanced functional characteristics of enzymatic hydrolysates of whey proteins (WPHs) in food applications compared to intact whey proteins (WPs). WPs are applied in foods as whey protein concentrates (WPCs), whey protein isolates (WPIs), and WPHs. WPs are byproducts of cheese production, used in a wide range of food applications due to their nutritional validity, functional activities, and cost effectiveness. Enzymatic hydrolysis yields improved functional and nutritional benefits in contrast to heat denaturation or native applications. WPHs improve solubility over a wide range of pH, create viscosity through water binding, and promote cohesion, adhesion, and elasticity. WPHs form stronger but more flexible edible films than WPC or WPI. WPHs enhance emulsification, bind fat, and facilitate whipping, compared to intact WPs. Extensive hydrolyzed WPHs with proper heat applications are the best emulsifiers and addition of polysaccharides improves the emulsification ability of WPHs. Also, WPHs improve the sensorial properties like color, flavor, and texture but impart a bitter taste in case where extensive hydrolysis (degree of hydrolysis greater than 8%). It is important to consider the type of enzyme, hydrolysis conditions, and WPHs production method based on the nature of food application. PMID:26761849

Improved Functional Characteristics of Whey Protein Hydrolysates in Food Industry.

PubMed

Jeewanthi, Renda Kankanamge Chaturika; Lee, Na-Kyoung; Paik, Hyun-Dong

2015-01-01

This review focuses on the enhanced functional characteristics of enzymatic hydrolysates of whey proteins (WPHs) in food applications compared to intact whey proteins (WPs). WPs are applied in foods as whey protein concentrates (WPCs), whey protein isolates (WPIs), and WPHs. WPs are byproducts of cheese production, used in a wide range of food applications due to their nutritional validity, functional activities, and cost effectiveness. Enzymatic hydrolysis yields improved functional and nutritional benefits in contrast to heat denaturation or native applications. WPHs improve solubility over a wide range of pH, create viscosity through water binding, and promote cohesion, adhesion, and elasticity. WPHs form stronger but more flexible edible films than WPC or WPI. WPHs enhance emulsification, bind fat, and facilitate whipping, compared to intact WPs. Extensive hydrolyzed WPHs with proper heat applications are the best emulsifiers and addition of polysaccharides improves the emulsification ability of WPHs. Also, WPHs improve the sensorial properties like color, flavor, and texture but impart a bitter taste in case where extensive hydrolysis (degree of hydrolysis greater than 8%). It is important to consider the type of enzyme, hydrolysis conditions, and WPHs production method based on the nature of food application.

Chemopreventive role of food-derived proteins and peptides: A review.

PubMed

Hernández-Ledesma, Blanca; Hsieh, Chia-Chien

2017-07-24

Cancer is one of the leading causes of mortality and disability worldwide. Although great advances in cancer treatments such as chemotherapy, surgery, and radiation are currently being achieved, their application is associated with numerous and expensive adverse side effects. Epidemiological evidence has demonstrated that the consumption of certain foods potentially prevents up to 35% of cancer cases. Bioactive components are ubiquitous in nature, also in dietary food, providing an essential link in health maintenance, promotion, and prevention of chronic diseases, such as cancer. Development of bioactive proteins and peptides is a current and innovative strategy for cancer prevention/cure. A growing body of anticancer protein and peptides from natural sources has shown the ability to reduce tumor progression through multiple mechanisms including apoptotic, antiproliferative, antiangiogenic, and immunomodulatory activities. This review is focused on proteins and peptides from different food sources including plants, milk, egg, and marine organisms in which chemopreventive properties have been demonstrated. Other aspects such as mechanism of action, bioavailability, and identification and characterization of food-derived peptides by advance separated technologies are also included. This review highlights the potential application of food-derived peptides as functional food ingredients and pharmaceutical candidates in the auxiliary therapy of cancer.

Review: Optimizing ruminant conversion of feed protein to human food protein.

PubMed

Broderick, G A

2017-11-20

Ruminant livestock have the ability to produce high-quality human food from feedstuffs of little or no value for humans. Balanced essential amino acid composition of meat and milk from ruminants makes those protein sources valuable adjuncts to human diets. It is anticipated that there will be increasing demand for ruminant proteins in the future. Increasing productivity per animal dilutes out the nutritional and environmental costs of maintenance and rearing dairy animals up to production. A number of nutritional strategies improve production per animal such as ration balancing in smallholder operations and small grain supplements to ruminants fed high-forage diets. Greenhouse gas emission intensity is reduced by increased productivity per animal; recent research has developed at least one effective inhibitor of methane production in the rumen. There is widespread over-feeding of protein to dairy cattle; milk and component yields can be maintained, and sometimes even increased, at lower protein intake. Group feeding dairy cows according to production and feeding diets higher in rumen-undegraded protein can improve milk and protein yield. Supplementing rumen-protected essential amino acids will also improve N efficiency in some cases. Better N utilization reduces urinary N, which is the most environmentally unstable form of excretory N. Employing nutritional models to more accurately meet animal requirements improves nutrient efficiency. Although smallholder enterprises, which are concentrated in tropical and semi-tropical regions of developing countries, are subject to different economic pressures, nutritional biology is similar at all production levels. Rather than milk volume, nutritional strategies should maximize milk component yield, which is proportional to market value as well as food value when milk nutrients are consumed directly by farmers and their families. Moving away from Holsteins toward smaller breeds such as Jerseys, Holstein-Jersey crosses or

INSOLUBILITY AND ALTERATION OF ALLERGENIC ACTIVITY OF WHEAT PROTEINS IN PROCESSED FOODS.

PubMed

Tanaka, Kajiyo; Kanie, Yuuki; Naitou, Michita; Suzuki, Misa; Umemura, Harue; Tagami, Kazunori; Sakai, Kazunori; Furuta, Tomoko; Yamada, Chikako; Izumi, Hidehiko; Yokooji, Tomoharu; Matsuo, Hiroaki; Ito, Komei

2017-01-01

Food processing causes decomposition, denaturation or polymerization of protein, which may alter an allergic reaction. This study aimed to investigate the insolubility and alteration of wheat allergens in processed foods and the reactivity to patient sera. We extracted proteins from wheat flour, udon and bread using different extracts and conducted SDS-polyacrylamide gel electrophoresis. IgE-immunoblotting was also conducted using sera from children with wheat allergy. Soluble protein was extracted from wheat flour, and gluten fractions were also extracted by adding SDS. However, no proteins were able to be extracted from udon or bread witout severing the disulfide bonds under reducing condition. Only trace amounts of protein were detected in the water after boiling udon noodles. The reactivity of IgE antibody to the extracted protein did not differ among the different processed food types. Wheat allergens became strongly insolubilized after gluten formation and heating. However, the reactivity of IgE antibody to each allergen was not affected by food processing. Further studies are needed for the effects on clinical symptoms.

Protein Beverage vs. Protein Gel on Appetite Control and Subsequent Food Intake in Healthy Adults.

PubMed

Zhang, Sha; Leidy, Heather J; Vardhanabhuti, Bongkosh

2015-10-21

The objective of this study was to compare the effects of food form and physicochemical properties of protein snacks on appetite and subsequent food intake in healthy adults. Twelve healthy subjects received a standardized breakfast and then 2.5 h post-breakfast consumed the following snacks, in randomized order: 0 kcal water (CON) or 96 kcal whey protein snacks as beverages with a pH of either 3.0 (Bev-3.0) or 7.0 (Bev-7.0) or gels as acid (Gel-Acid) or heated (Gel-Heated). In-vitro study showed that Bev-3.0 was more resistant to digestion than Bev-7.0, while Gel-Acid and Gel-Heated had similar digestion pattern. Appetite questionnaires were completed every 20 min until an ad libitum lunch was provided. Post-snack hunger, desire to eat, and prospective food consumption were lower following the beverages and gels vs. CON (all, p < 0.05), and post-snack fullness was greater following the snacks (except for the Bev-3.0) vs. CON (all, p < 0.05). Gel-Heated treatment led to lower prospective food consumption vs. Bev-3.0; however, no other differences were detected. Although all snacks reduced energy intake vs. CON, no differences were observed among treatments. This study suggested that whey protein in either liquid or solid form improves appetite, but the physicochemical property of protein has a minimal effect.

2S Albumin Storage Proteins: What Makes them Food Allergens?

PubMed

Moreno, F Javier; Clemente, Alfonso

2008-01-01

2S albumin storage proteins are becoming of increasing interest in nutritional and clinical studies as they have been reported as major food allergens in seeds of many mono- and di-cotyledonous plants. This review describes the main biochemical, structural and functional properties of these proteins thought to play a role in determining their potential allergenicity. 2S albumins are considered to sensitize directly via the gastrointestinal tract (GIT). The high stability of their intrinsic protein structure, dominated by a well-conserved skeleton of cysteine residues, to the harsh conditions present in the GIT suggests that these proteins are able to cross the gut mucosal barrier to sensitize the mucosal immune system and/or elicit an allergic response. The flexible and solvent-exposed hypervariable region of these proteins is immunodominant and has the ability to bind IgE from allergic patients sera. Several linear IgE-binding epitopes of 2S albumins spanning this region have been described to play a major role in allergenicity; the role of conformational epitopes of these proteins in food allergy is far from being understood and need to be investigated. Finally, the interaction of these proteins with other components of the food matrix might influence the absorption rates of immunologically reactive 2S albumins but also in their immune response.

2S Albumin Storage Proteins: What Makes them Food Allergens?

PubMed Central

Moreno, F. Javier; Clemente, Alfonso

2008-01-01

2S albumin storage proteins are becoming of increasing interest in nutritional and clinical studies as they have been reported as major food allergens in seeds of many mono- and di-cotyledonous plants. This review describes the main biochemical, structural and functional properties of these proteins thought to play a role in determining their potential allergenicity. 2S albumins are considered to sensitize directly via the gastrointestinal tract (GIT). The high stability of their intrinsic protein structure, dominated by a well-conserved skeleton of cysteine residues, to the harsh conditions present in the GIT suggests that these proteins are able to cross the gut mucosal barrier to sensitize the mucosal immune system and/or elicit an allergic response. The flexible and solvent-exposed hypervariable region of these proteins is immunodominant and has the ability to bind IgE from allergic patients´ sera. Several linear IgE-binding epitopes of 2S albumins spanning this region have been described to play a major role in allergenicity; the role of conformational epitopes of these proteins in food allergy is far from being understood and need to be investigated. Finally, the interaction of these proteins with other components of the food matrix might influence the absorption rates of immunologically reactive 2S albumins but also in their immune response. PMID:18949071

Study of quantitative changes of cereal allergenic proteins after food processing.

PubMed

Flodrová, Dana; Benkovská, Dagmar; Laštovičková, Markéta

2015-03-30

Within last few years, the occurrence of food allergens and corresponding food allergies has been increasing, therefore research into the individual allergens is required. In the present work, the effect of cereal processing on the amounts of allergenic proteins is studied by modern proteomic-based approaches. The most important wheat and barley allergens are low-molecular-weight (LMW) proteins. Therefore we investigated the relative quantitative changes of these proteins after food technological processing, namely wheat couscous production and barley malting. A comparative study using mass spectrometry in connection with the technique of isobaric tag for relative and absolute quantification (iTRAQ) revealed that the amount of wheat allergenic LMW proteins decreased significantly during couscous production (approximately to 5-26% of their initial content in wheat flour). After barley malting, the amounts of the majority of LMW proteins decreased as well, although to a lesser extent than in the case of wheat/couscous. The level of two allergens even slightly increased. Suggested proteomic strategy proved as universal and sensitive method for fast and reliable identification of various cereal allergens and monitoring of their quantitative changes during food processing. Such information is important for consumers who suffer from allergies. © 2014 Society of Chemical Industry.

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

DOE PAGES

Shatsky, Maxim; Dong, Ming; Liu, Haichuan; ...

2016-04-20

Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification ofmore » endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.« less

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shatsky, Maxim; Dong, Ming; Liu, Haichuan

Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification ofmore » endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.« less

Clinical-Community Partnerships to Identify Patients With Food Insecurity and Address Food Needs

PubMed Central

Siegel, Karen R.; Calhoun, Holly; Kim, Sonia A.; Garcia, Sandra P.; Hoeting, Natalie M.; Harris, Diane M.; Khan, Laura Kettel; Smith, Bryce; Blanck, Heidi M.; Barnett, Kevin; Haddix, Anne C.

2017-01-01

Introduction More than 42 million people in the United States are food insecure. Although some health care entities are addressing food insecurity among patients because of associations with disease risk and management, little is known about the components of these initiatives. Methods The Systematic Screening and Assessment Method was used to conduct a landscape assessment of US health care entity–based programs that screen patients for food insecurity and connect them with food resources. A network of food insecurity researchers, experts, and practitioners identified 57 programs, 22 of which met the inclusion criteria of being health care entities that 1) screen patients for food insecurity, 2) link patients to food resources, and 3) target patients including adults aged 50 years or older (a focus of this assessment). Data on key features of each program were abstracted from documentation and telephone interviews. Results Most programs (n = 13) focus on patients with chronic disease, and most (n = 12) partner with food banks. Common interventions include referrals to or a list of food resources (n = 19), case managers who navigate patients to resources (n = 15), assistance with federal benefit applications (n = 14), patient education and skill building (n = 13), and distribution of fruit and vegetable vouchers redeemable at farmers markets (n = 8). Most programs (n = 14) routinely screen all patients. Conclusion The programs reviewed use various strategies to screen patients, including older adults, for food insecurity and to connect them to food resources. Research is needed on program effectiveness in improving patient outcomes. Such evidence can be used to inform the investments of potential stakeholders, including health care entities, community organizations, and insurers. PMID:29144894

MALDI based identification of soybean protein markers--possible analytical targets for allergen detection in processed foods.

PubMed

Cucu, Tatiana; De Meulenaer, Bruno; Devreese, Bart

2012-02-01

Soybean (Glycine max) is extensively used all over the world due to its nutritional qualities. However, soybean is included in the "big eight" list of food allergens. According to the EU directive 2007/68/EC, food products containing soybeans have to be labeled in order to protect the allergic consumers. Nevertheless, soybeans can still inadvertently be present in food products. The development of analytical methods for the detection of traces of allergens is important for the protection of allergic consumers. Mass spectrometry of marker proteolytical fragments of protein allergens is growingly recognized as a detection method in food control. However, quantification of soybean at the peptide level is hindered due to limited information regarding specific stable markers derived after proteolytic digestion. The aim of this study was to use MALDI-TOF/MS and MS/MS as a fast screening tool for the identification of stable soybean derived tryptic markers which were still identifiable even if the proteins were subjected to various changes at the molecular level through a number of reactions typically occurring during food processing (denaturation, the Maillard reaction and oxidation). The peptides (401)Val-Arg(410) from the G1 glycinin (Gly m 6) and the (518)Gln-Arg(528) from the α' chain of the β-conglycinin (Gly m 5) proved to be the most stable. These peptides hold potential to be used as targets for the development of new analytical methods for the detection of soybean protein traces in processed foods. Copyright © 2011 Elsevier Inc. All rights reserved.

Identifying reliable predictors of protein-energy malnutrition in hospitalized frail older adults: A prospective longitudinal study.

PubMed

Sanson, Gianfranco; Bertocchi, Luca; Dal Bo, Eugenia; Di Pasquale, Carmen Luisa; Zanetti, Michela

2018-06-01

Decreased food intake is a risk factor for relevant complications (e.g. infections, pressure ulcers), longer hospital stays, higher readmission rates, greater health care costs and increased patient mortality, particularly in frail hospitalized older adults who are malnourished or at risk of malnutrition. Nurses are called to improve this criticality, starting from accurately identifying malnourished patients at hospital admission and effectively monitoring their food intake. The primary aim was to identify reliable predictive indicators of reduced food intake at hospital admission. The secondary aims were to assess the adequacy of daily energy and protein intake and the impact of nutrient intake on patient outcomes. Prospective observational longitudinal study. Internal Medicine Ward of an Academic Teaching University Hospital. Acute older adults who were malnourished or at risk of malnutrition (Nutritional Risk Score-2002 ≥ 3, middle-upper arm circumference <23.5 cm or impaired self-feeding ability) at admission. The effective energy and protein intake was monitored during the first 5 days of hospital stay by a photographic method and compared to the daily energy and protein requirement calculated by specific equations. Data on anthropometry, inflammation/malnutrition laboratory data and body composition (phase angle calculated using bioelectrical impedance analysis) were collected. Eighty-one subjects (age 81.5 ± 11.5 years) were enrolled. Mean energy intake was 669.0 ± 573.9 kcal/day, and mean protein intake was 30.7 ± 25.8 g/day. Over 60% of patients ingested ≤50% of their calculated energy and protein requirements: these patients were older (p = 0.026), had a lower middle-upper arm circumference (p = 0.022) and total arm area (p = 0.038), a higher C-reactive protein/albumin ratio and Instant Nutritional Assessment score (p < 0.01), and experienced longer hospital stays (p ≤ 0.04) and higher in

Variations in isoflavone levels in soy foods and soy protein isolates and issues related to isoflavone databases and food labeling.

PubMed

Setchell, Kenneth D R; Cole, Sidney J

2003-07-02

The reliability of databases on the isoflavone composition of foods designed to estimate dietary intakes is contingent on the assumption that soy foods are consistent in their isoflavone content. To validate this, total and individual isoflavone compositions were determined by HPLC for two different soy protein isolates used in the commercial manufacture of soy foods over a 3-year period (n = 30/isolate) and 85 samples of 40 different brands of soy milks. Total isoflavone concentrations differed markedly between the soy protein isolates, varying by 200-300% over 3 years, whereas the protein content varied by only 3%. Total isoflavone content varied by up to 5-fold among different commercial soy milks and was not consistent between repeat purchases. Whole soybean milks had significantly higher isoflavone levels than those made from soy protein isolates (mean +/- SD, 63.6 +/- 21.9 mg/L, n = 43, vs 30.2 +/- 5.8 mg/L, n = 38, respectively, p < 0.0001), although some isolated soy protein-based milks were similar in content to "whole bean" varieties. The ratio of genistein to daidzein isoflavone forms was higher in isolated soy protein-based versus "whole bean" soy milks (2.72 +/- 0.24 vs 1.62 +/- 0.47, respectively, p < 0.0001), and the greatest variability in isoflavone content was observed among brands of whole bean soy milks. These studies illustrate large variability in the isoflavone content of isolated soy proteins used in food manufacture and in commercial soy milks and reinforce the need to accurately determine the isoflavone content of foods used in dietary intervention studies while exposing the limitations of food databases for estimating daily isoflavone intakes.

Protein Beverage vs. Protein Gel on Appetite Control and Subsequent Food Intake in Healthy Adults

PubMed Central

Zhang, Sha; Leidy, Heather J.; Vardhanabhuti, Bongkosh

2015-01-01

The objective of this study was to compare the effects of food form and physicochemical properties of protein snacks on appetite and subsequent food intake in healthy adults. Twelve healthy subjects received a standardized breakfast and then 2.5 h post-breakfast consumed the following snacks, in randomized order: 0 kcal water (CON) or 96 kcal whey protein snacks as beverages with a pH of either 3.0 (Bev-3.0) or 7.0 (Bev-7.0) or gels as acid (Gel-Acid) or heated (Gel-Heated). In-vitro study showed that Bev-3.0 was more resistant to digestion than Bev-7.0, while Gel-Acid and Gel-Heated had similar digestion pattern. Appetite questionnaires were completed every 20 min until an ad libitum lunch was provided. Post-snack hunger, desire to eat, and prospective food consumption were lower following the beverages and gels vs. CON (all, p < 0.05), and post-snack fullness was greater following the snacks (except for the Bev-3.0) vs. CON (all, p < 0.05). Gel-Heated treatment led to lower prospective food consumption vs. Bev-3.0; however, no other differences were detected. Although all snacks reduced energy intake vs. CON, no differences were observed among treatments. This study suggested that whey protein in either liquid or solid form improves appetite, but the physicochemical property of protein has a minimal effect. PMID:26506378

Early Life Protein Intake: Food Sources, Correlates, and Tracking across the First 5 Years of Life.

PubMed

Campbell, Karen J; Abbott, Gavin; Zheng, Miaobing; McNaughton, Sarah A

2017-08-01

High consumption of protein has been associated with accelerated growth and adiposity in early childhood. To describe intake, food sources, correlates, and tracking of protein in young children. Secondary analysis of Melbourne Infant Feeding Activity and Nutrition Trial (InFANT). Dietary data were collected using three 24-hour dietary recalls at ages 9 and 18 months as well as 3.5 and 5 years. First-time mothers and their child (n=542) participated in an 18-month intervention to prevent childhood obesity and the cohort was followed-up with no intervention when children were aged 3.5 and 5 years. Protein intake, food sources, correlates, and tracking of protein. Child and maternal correlates of protein intake were identified using linear regression and tracking of protein intake was examined using Pearson correlations of residualized protein scores between time points. Mean protein (grams per day) intake was 29.7±11.0, 46.3±11.5, 54.2±13.8, and 60.0±14.8 at 9 and 18 months and 3.5 and 5 years, respectively. Protein intakes at all ages were two to three times greater than age-appropriate Australian recommendations. The primary source of protein at 9 months was breast/formula milk. At later ages, the principal sources were milk/milk products, breads/cereals, and meat/meat products. Earlier breastfeeding cessation, earlier introduction of solids, high dairy milk consumption (≥500 mL), and high maternal education were significant predictors of high protein intake at various times (P<0.05). Slight tracking was found for protein intakes at 9 months, 18 months, and 5 years (r=0.16 to 0.21; P<0.01). This study provides unique insights into food sources and correlates of young children's high protein intakes, and confirms that early protein intakes track slightly up to age 5 years. These finding have potential to inform nutrition interventions and strategies to address high protein intakes and protein-related obesity risk. Copyright © 2017 Academy of Nutrition and

Interaction of Proteins Identified in Human Thyroid Cells

PubMed Central

Pietsch, Jessica; Riwaldt, Stefan; Bauer, Johann; Sickmann, Albert; Weber, Gerhard; Grosse, Jirka; Infanger, Manfred; Eilles, Christoph; Grimm, Daniela

2013-01-01

Influence of gravity forces on the regulation of protein expression by healthy and malignant thyroid cells was studied with the aim to identify protein interactions. Western blot analyses of a limited number of proteins suggested a time-dependent regulation of protein expression by simulated microgravity. After applying free flow isoelectric focusing and mass spectrometry to search for differently expressed proteins by thyroid cells exposed to simulated microgravity for three days, a considerable number of candidates for gravi-sensitive proteins were detected. In order to show how proteins sensitive to microgravity could directly influence other proteins, we investigated all polypeptide chains identified with Mascot scores above 100, looking for groups of interacting proteins. Hence, UniProtKB entry numbers of all detected proteins were entered into the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and processed. The program indicated that we had detected various groups of interacting proteins in each of the three cell lines studied. The major groups of interacting proteins play a role in pathways of carbohydrate and protein metabolism, regulation of cell growth and cell membrane structuring. Analyzing these groups, networks of interaction could be established which show how a punctual influence of simulated microgravity may propagate via various members of interaction chains. PMID:23303277

Development of fish protein powder as an ingredient for food applications: a review.

PubMed

Shaviklo, Amir Reza

2015-02-01

The increasing awareness that dried fish protein can be applied for food fortification and production of value added/functional foods has encouraged the food industry to examine different methods for developing fish protein ingredient from different raw materials. Fish protein powder (FPP) is a dried and stable fish product, intended for human consumption, in which the protein is more concentrated than in the original fish flesh. Quality and acceptability of FPP depend on several factors. The fat content of the FPP is a critical issue because when it is oxidized a strong and often rancid flavour is produced. Protein content of FPP depends on the raw materials, amount of additives and moisture content, but it contains at least 65 % proteins. FPP is used in the food industry for developing re-structured and ready-to-eat food products. The FPP maintains its properties for 6 months at 5 °C but loses them rapidly at 30 °C. Deterioration of the FPP during storage is prevented by lowering the moisture content of the product and eliminating of oxygen from the package. The FPP can be applied as a functional ingredient for developing formulated ready-to-eat products. This article reviews methods for extracting fish proteins, drying methods, characteristics and applications of FPP and factors affecting FPP quality.

Gliadin Detection in Food by Immunoassay

NASA Astrophysics Data System (ADS)

Grant, Gordon; Sporns, Peter; Hsieh, Y.-H. Peggy

Immunoassays are very sensitive and efficient tests that are commonly used to identify a specific protein. Examples of applications in the food industry include identification of proteins expressed in genetically modified foods, allergens, or proteins associated with a disease, including celiac disease. This genetic disease is associated with Europeans and affects about one in every 200 people in North America. These individuals react immunologically to wheat proteins, and consequently their own immune systems attack and damage their intestines. This disease can be managed if wheat proteins, specifically "gliadins," are avoided in foods.

Food-cooking processes modulate allergenic properties of hen's egg white proteins.

PubMed

Liu, Xiaoyu; Feng, Bai-Sui; Kong, Xiaoli; Xu, Hong; Li, Xiumin; Yang, Ping-Chang; Liu, Zhigang

2013-01-01

Reducing the allergenicity of food allergens can suppress the clinical symptoms of food allergy. The objective of the present study was to investigate the effects of processing on the allergenic properties of hen's egg white proteins. Eggs were processed by traditional Chinese cooking, including steaming, water boiling, frying, spicing and tea boiling. The contents of processed egg protein were assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis; the allergenicity was evaluated by Western blotting, enzyme-linked immunosorbent assay and enzyme allergosorbent test inhibition. Circular dichroism spectrum analysis of four major egg allergens from various egg products was performed as well. A mouse model of food allergy was developed to test the allergenicity of processed egg protein in vivo. Protein degradation was significant following tea boiling and spiced-tea boiling. The total allergenic potential of water-boiled egg and fried egg was relatively higher than that of steamed egg, spiced egg and tea-boiled egg. Challenge with proteins from raw egg, water-boiled egg and fried egg induced skewed T-helper 2 pattern responses (Th2 responses) in the intestine of mice sensitized to egg proteins; however, when the mice sensitized to egg proteins were challenged with proteins from steamed egg, spiced egg and tea-boiled egg, respectively, only weak Th2 responses were induced in their intestine. Processing by steaming, spicing, or tea boiling can weaken the allergenicity of egg proteins. Copyright © 2012 S. Karger AG, Basel.

Microbial protein: future sustainable food supply route with low environmental footprint.

PubMed

Matassa, Silvio; Boon, Nico; Pikaar, Ilje; Verstraete, Willy

2016-09-01

Microbial biotechnology has a long history of producing feeds and foods. The key feature of today's market economy is that protein production by conventional agriculture based food supply chains is becoming a major issue in terms of global environmental pollution such as diffuse nutrient and greenhouse gas emissions, land use and water footprint. Time has come to re-assess the current potentials of producing protein-rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass, producible with a lower environmental footprint compared with other plant or animal-based alternatives. A major driver is the need to no longer disintegrate but rather upgrade a variety of low-value organic and inorganic side streams in our current non-cyclic economy. In this context, microbial bioconversions of such valuable matters to nutritive microbial cells and cell components are a powerful asset. The worldwide market of animal protein is of the order of several hundred million tons per year, that of plant protein several billion tons of protein per year; hence, the expansion of the production of microbial protein does not pose disruptive challenges towards the process of the latter. Besides protein as nutritive compounds, also other cellular components such as lipids (single cell oil), polyhydroxybuthyrate, exopolymeric saccharides, carotenoids, ectorines, (pro)vitamins and essential amino acids can be of value for the growing domain of novel nutrition. In order for microbial protein as feed or food to become a major and sustainable alternative, addressing the challenges of creating awareness and achieving public and broader regulatory acceptance are real and need to be addressed with care and expedience. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

A lanthipeptide library used to identify a protein-protein interaction inhibitor.

PubMed

Yang, Xiao; Lennard, Katherine R; He, Chang; Walker, Mark C; Ball, Andrew T; Doigneaux, Cyrielle; Tavassoli, Ali; van der Donk, Wilfred A

2018-04-01

In this article we describe the production and screening of a genetically encoded library of 10 6 lanthipeptides in Escherichia coli using the substrate-tolerant lanthipeptide synthetase ProcM. This plasmid-encoded library was combined with a bacterial reverse two-hybrid system for the interaction of the HIV p6 protein with the UEV domain of the human TSG101 protein, which is a critical protein-protein interaction for HIV budding from infected cells. Using this approach, we identified an inhibitor of this interaction from the lanthipeptide library, whose activity was verified in vitro and in cell-based virus-like particle-budding assays. Given the variety of lanthipeptide backbone scaffolds that may be produced with ProcM, this method may be used for the generation of genetically encoded libraries of natural product-like lanthipeptides containing substantial structural diversity. Such libraries may be combined with any cell-based assay to identify lanthipeptides with new biological activities.

Production and supply of high-quality food protein for human consumption: sustainability, challenges, and innovations.

PubMed

Wu, Guoyao; Fanzo, Jessica; Miller, Dennis D; Pingali, Prabhu; Post, Mark; Steiner, Jean L; Thalacker-Mercer, Anna E

2014-08-01

The Food and Agriculture Organization of the United Nations estimates that 843 million people worldwide are hungry and a greater number suffer from nutrient deficiencies. Approximately one billion people have inadequate protein intake. The challenge of preventing hunger and malnutrition will become even greater as the global population grows from the current 7.2 billion people to 9.6 billion by 2050. With increases in income, population, and demand for more nutrient-dense foods, global meat production is projected to increase by 206 million tons per year during the next 35 years. These changes in population and dietary practices have led to a tremendous rise in the demand for food protein, especially animal-source protein. Consuming the required amounts of protein is fundamental to human growth and health. Protein needs can be met through intakes of animal and plant-source foods. Increased consumption of food proteins is associated with increased greenhouse gas emissions and overutilization of water. Consequently, concerns exist regarding impacts of agricultural production, processing and distribution of food protein on the environment, ecosystem, and sustainability. To address these challenging issues, the New York Academy of Sciences organized the conference "Frontiers in Agricultural Sustainability: Studying the Protein Supply Chain to Improve Dietary Quality" to explore sustainable innovations in food science and programming aimed at producing the required quality and quantity of protein through improved supply chains worldwide. This report provides an extensive discussion of these issues and summaries of the presentations from the conference. © 2014 New York Academy of Sciences.

Agouti-related protein increases food hoarding more than food intake in Siberian hamsters.

PubMed

Day, Diane E; Bartness, Timothy J

2004-01-01

Agouti-related protein (AgRP), an endogenous melanocortin 3/4 receptor antagonist, appears to play an important role in the control of food intake and energy balance because exogenous administration in rats and overexpression in mice result in hyperphagia and body mass gain. Furthermore, arcuate nucleus AgRP mRNA is increased with fasting in laboratory rats and mice and is decreased with refeeding. In Siberian hamsters, fasting also increases arcuate nucleus AgRP mRNA, but these animals increase food hoarding, rather than food intake with refeeding. Therefore, we tested whether exogenous AgRP increased food hoarding in this species. Hamsters were trained in a hoarding/foraging apparatus to run a programmed number of wheel revolutions to earn food pellets. Four doses of AgRP-(83-132) or vehicle were injected into the third ventricle at the beginning of the dark phase, and food hoarding, food intake, and foraging were measured at various time points subsequently. Overall, food hoarding was stimulated as much as 10 times more than food intake, and both responses occurred as early as 1 h after injection. Food hoarding was increased the greatest at the lowest dose (0.1 nmol), whereas food intake was increased the greatest at the second lowest dose (1 nmol). Food intake and especially food hoarding were increased up to seven days after the AgRP injections. Foraging was increased at all AgRP doses except the highest dose (100 nmol). These results suggest that AgRP triggers the search for food in this species, and once they find it, hoarding predominates over eating.

Vegetable foods: a cheap source of proteins and peptides with antihypertensive, antioxidant, and other less occurrence bioactivities.

PubMed

García, M C; Puchalska, P; Esteve, C; Marina, M L

2013-03-15

Despite less explored than foods from animal origin, plant derived foods also contain biologically active proteins and peptides. Bioactive peptides can be present as an independent entity in the food or, more frequently, can be in a latent state as part of the sequence of a protein. Release from that protein requires protein hydrolysis by enzymatic digestion, fermentation or autolysis. Different methodologies have been used to test proteins and peptides bioactivities. Fractionation, separation, and identification techniques have also been employed for the isolation and identification of bioactive proteins or peptides. In this work, proteins and peptides from plant derived foods exerting antihypertensive, antioxidant, hypocholesterolemic, antithrombotic, and immunostimulating capacities or ability to reduce food intake have been reviewed. Copyright © 2013 Elsevier B.V. All rights reserved.

Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase

USDA-ARS?s Scientific Manuscript database

Rice, the staple food of South and East Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16 kDa, 26 kDa, 33 kDa and 56 kDa have been identified as allergens. Re...

Study of human salivary proline-rich proteins interaction with food tannins.

PubMed

Soares, Susana; García-Estévez, Ignacio; Ferrer-Galego, Raúl; Brás, Natércia F; Brandão, Elsa; Silva, Mafalda; Teixeira, Natércia; Fonseca, Fátima; Sousa, Sérgio F; Ferreira-da-Silva, Frederico; Mateus, Nuno; de Freitas, Victor

2018-03-15

In this work, saturation transfer difference-NMR, isothermal microcalorimetry and molecular dynamics simulations have been used to study the individual interactions between basic, glycosylated and acidic proline-rich proteins (bPRPS, gPRPs, aPRPs) and P-B peptide with some representative food tannins [procyanidin B2, procyanidin B2 3'-O-gallate (B2g) and procyanidin trimer (catechin-4-8-catechin-4-8-catechin)]. Results showed that P-B peptide was in general the salivary protein (SP) with higher affinity whereas aPRPs showed lower affinity to the studied procyanidins. Moreover, B2g was the procyanidin with higher affinity for all SP. Hydrophobic and hydrogen bonds were present in all interactions but the major driving force depended on the procyanidin-SP pair. Furthermore, proline clusters or residues in their vicinity were identified as the probable sites of proteins for interaction with procyanidins. For bPRP and aPRP a significant change to less extended conformations was observed, while P-B peptide did not display any structural rearrangement upon procyanidins binding. Copyright © 2017. Published by Elsevier Ltd.

Natural history of food protein-induced enterocolitis syndrome.

PubMed

Katz, Yitzhak; Goldberg, Michael R

2014-06-01

Because of the paucity of reports and variability in the diagnostic criteria utilized, little is known regarding the natural outcome of patients with food protein-induced enterocolitis syndrome (FPIES). Data extracted from referenced manuscripts, as well as allergists' unpublished observations from across the globe, were used to form a cohesive opinion regarding its natural outcome. All authors concur that there is a generally high rate of recovery for FPIES. The most common foods causing FPIES are milk and soy. Depending upon which study is analyzed, by the age of 3-5 years, approximately 90% of patients recover from their disease. Recovery from FPIES to solid foods, occurs at a later age, but may reflect a later stage of introduction of the food into the diet. An important clinical outcome, although not common, is a shift from FPIES food hypersensitivity to an IgE-mediated food allergy. This necessitates a change in the oral food challenge protocol, if IgE-mediated sensitization is detected. Over the past several years, there has been an increasing awareness of FPIES. This knowledge should lead to a more timely diagnosis and should reassure parents and practitioners alike regarding its favorable course.

Identifying Food Safety Concerns when Communication Barriers Exist

ERIC Educational Resources Information Center

Neal, Jack A.; Dawson, Mary; Madera, Juan M.

2011-01-01

Abstract: Students must be prepared to lead a diverse workforce. The objective of this study was to establish a teaching method that helps students identify barriers to food safety while working in a simulated environment with communication barriers. This study employed a perspective taking exercise based upon the principles of social learning…

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

PubMed Central

Ren, Jun; Zhou, Wei; Wang, Jianxin

2014-01-01

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes. PMID:25143945

Impact of surface coating and food-mimicking media on nanosilver-protein interaction

NASA Astrophysics Data System (ADS)

Burcza, Anna; Gräf, Volker; Walz, Elke; Greiner, Ralf

2015-11-01

The application of silver nanoparticles (AgNPs) in food contact materials has recently become a subject of dispute due to the possible migration of silver in nanoform into foods and beverages. Therefore, the analysis of the interaction of AgNPs with food components, especially proteins, is of high importance in order to increase our knowledge of the behavior of nanoparticles in food matrices. AgPURE™ W10 (20 nm), an industrially applied nanomaterial, was compared with AgNPs of similar size frequently investigated for scientific purposes differing in the surface capping agent (spherical AgNP coated with either PVP or citrate). The interactions of the AgNPs with whey proteins (BSA, α-lactalbumin and β-lactoglobulin) at different pH values (4.2, 7 or 7.4) were investigated using surface plasmon resonance, SDS-PAGE, and asymmetric flow field-flow fractionation. The data obtained by the three different methods correlated well. Besides the nature of the protein and the nanoparticle coating, the environment was shown to affect the interaction significantly. The strongest interaction was obtained with BSA and AgNPs in an acidic environment. Neutral and slightly alkaline conditions however, seemed to prevent the AgNP-protein interaction almost completely. Furthermore, the interaction of whey proteins with AgPURE™ W10 was found to be weaker compared to the interaction with the other two AgNPs under all conditions investigated.

Achieving Optimal Post-Exercise Muscle Protein Remodeling in Physically Active Adults through Whole Food Consumption

PubMed Central

van Vliet, Stephan; Beals, Joseph W.; Martinez, Isabel G.; Skinner, Sarah K.; Burd, Nicholas A.

2018-01-01

Dietary protein ingestion is critical to maintaining the quality and quantity of skeletal muscle mass throughout adult life. The performance of acute exercise enhances muscle protein remodeling by stimulating protein synthesis rates for several hours after each bout, which can be optimized by consuming protein during the post-exercise recovery period. To date, the majority of the evidence regarding protein intake to optimize post-exercise muscle protein synthesis rates is limited to isolated protein sources. However, it is more common to ingest whole food sources of protein within a normal eating pattern. Emerging evidence demonstrates a promising role for the ingestion of whole foods as an effective nutritional strategy to support muscle protein remodeling and recovery after exercise. This review aims to evaluate the efficacy of the ingestion of nutrient-rich and protein-dense whole foods to support post-exercise muscle protein remodeling and recovery with pertinence towards physically active people. PMID:29462924

Using Social Media to Identify Sources of Healthy Food in Urban Neighborhoods.

PubMed

Gomez-Lopez, Iris N; Clarke, Philippa; Hill, Alex B; Romero, Daniel M; Goodspeed, Robert; Berrocal, Veronica J; Vinod Vydiswaran, V G; Veinot, Tiffany C

2017-06-01

An established body of research has used secondary data sources (such as proprietary business databases) to demonstrate the importance of the neighborhood food environment for multiple health outcomes. However, documenting food availability using secondary sources in low-income urban neighborhoods can be particularly challenging since small businesses play a crucial role in food availability. These small businesses are typically underrepresented in national databases, which rely on secondary sources to develop data for marketing purposes. Using social media and other crowdsourced data to account for these smaller businesses holds promise, but the quality of these data remains unknown. This paper compares the quality of full-line grocery store information from Yelp, a crowdsourced content service, to a "ground truth" data set (Detroit Food Map) and a commercially-available dataset (Reference USA) for the greater Detroit area. Results suggest that Yelp is more accurate than Reference USA in identifying healthy food stores in urban areas. Researchers investigating the relationship between the nutrition environment and health may consider Yelp as a reliable and valid source for identifying sources of healthy food in urban environments.

ATPS: "Aqueous two-phase System" as the "Answer to Protein Separation" for protein-processing Food Industry.

PubMed

Khan, Bilal Muhammad; Liu, Zhi-Cong; Shi, Fu-Lin; Cheong, Kit-Leong; Liu, Yang

2018-06-08

Every individual needs food for its nutritional value and flavor while the economic growth of a nation depends on a thriving profit-generating industry. The food industry caters to both needs in an efficient manner. Proteins can rightly be considered as the driving force behind the overwhelming success of this industry. However, purification of proteins is not an easy undertaking due to their intricate nature while presently employed procedures for this purpose, regrettably, are both costly, and labor- and time-intensive in addition to being unsettling on proteins structural conformity. ATPS has accumulated a lot of interest from the scientific community due to its mild operating conditions, high recovery yield, ease of scaling it up, and its cost-effective and environment friendly nature. This review tries to amass some accounts concerning the utility of ATPS for the separation and purification of proteins. Some auspicious clues in this regard can be witnessed along with a few loopholes which need to be addressed before this technique can truly demonstrate its potential vis-à-vis industrial protein purification. Overall, a polymer - salt (citrates in particular) ATPS with an added inert supplementary salt can be regarded as a better option for purifying proteins.

Detection of soy proteins in processed foods: literature overview and new experimental work.

PubMed

Koppelman, Stef J; Lakemond, Catriona M M; Vlooswijk, Riek; Hefle, Susan L

2004-01-01

Several tests for the detection of soy proteins in foods have been described in the literature, and some are commercially available. This article gives an overview of these methods and discusses the advantages and disadvantages of each individual method. Based on the conclusions of this inventory, an experimental approach was designed to improve the sensitivity of measuring soy protein in processed foods. The aimed sensitivity is 10 ppm (10 microg soy protein in 1 g solid sample), which is over 100-fold lower than presently available tests. The aimed sensitivity is this low because levels of food allergens at 10 ppm and above may provoke reactions in food allergic persons. Native soybean meal, soy protein isolate, soy protein concentrate, and textured soy flakes were used as test materials. Several extraction procedures were compared and a new method using high pH was selected. Polyclonal antibodies were raised in rabbits and goats, and immunopurified antibodies were used in sandwich and inhibition enzyme-linked immunosorbent assay (ELISA). Extraction at pH 12 resulted in good yields for all tested samples, both quantitatively (Bradford) and qualitatively by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunopurified rabbit antibodies against this extract used in a competition ELISA format resulted in a sensitive test with a detection limit of 0.02 microg/mL, corresponding to 0.4 microg/g (0.4 ppm) in food samples. Cross-reactivity with some main food ingredients was measured and appeared to be negative in all cases. The presently developed test is applicable for soy ingredients and soy-containing foods that are processed in different ways. The limit of quantitation is 1 ppm, which is an enormous improvement over earlier described methods.

Unbiased screen identifies aripiprazole as a modulator of abundance of the polyglutamine disease protein, ataxin-3

PubMed Central

Costa, Maria do Carmo; Ashraf, Naila S.; Fischer, Svetlana; Yang, Yemen; Schapka, Emily; Joshi, Gnanada; McQuade, Thomas J.; Dharia, Rahil M.; Dulchavsky, Mark; Ouyang, Michelle; Cook, David; Sun, Duxin; Larsen, Martha J.; Gestwicki, Jason E.; Todi, Sokol V.; Ivanova, Magdalena I.; Paulson, Henry L.

2016-01-01

No disease-modifying treatment exists for the fatal neurodegenerative polyglutamine disease known both as Machado-Joseph disease and spinocerebellar ataxia type 3. As a potential route to therapy, we identified small molecules that reduce levels of the mutant disease protein, ATXN3. Screens of a small molecule collection, including 1250 Food and Drug Administration-approved drugs, in a novel cell-based assay, followed by secondary screens in brain slice cultures from transgenic mice expressing the human disease gene, identified the atypical antipsychotic aripiprazole as one of the hits. Aripiprazole increased longevity in a Drosophila model of Machado-Joseph disease and effectively reduced aggregated ATXN3 species in flies and in brains of transgenic mice treated for 10 days. The aripiprazole-mediated decrease in ATXN3 abundance may reflect a complex response culminating in the modulation of specific components of cellular protein homeostasis. Aripiprazole represents a potentially promising therapeutic drug for Machado-Joseph disease and possibly other neurological proteinopathies. PMID:27645800

A likelihood-based approach to identifying contaminated food products using sales data: performance and challenges.

PubMed

Kaufman, James; Lessler, Justin; Harry, April; Edlund, Stefan; Hu, Kun; Douglas, Judith; Thoens, Christian; Appel, Bernd; Käsbohrer, Annemarie; Filter, Matthias

2014-07-01

Foodborne disease outbreaks of recent years demonstrate that due to increasingly interconnected supply chains these type of crisis situations have the potential to affect thousands of people, leading to significant healthcare costs, loss of revenue for food companies, and--in the worst cases--death. When a disease outbreak is detected, identifying the contaminated food quickly is vital to minimize suffering and limit economic losses. Here we present a likelihood-based approach that has the potential to accelerate the time needed to identify possibly contaminated food products, which is based on exploitation of food products sales data and the distribution of foodborne illness case reports. Using a real world food sales data set and artificially generated outbreak scenarios, we show that this method performs very well for contamination scenarios originating from a single "guilty" food product. As it is neither always possible nor necessary to identify the single offending product, the method has been extended such that it can be used as a binary classifier. With this extension it is possible to generate a set of potentially "guilty" products that contains the real outbreak source with very high accuracy. Furthermore we explore the patterns of food distributions that lead to "hard-to-identify" foods, the possibility of identifying these food groups a priori, and the extent to which the likelihood-based method can be used to quantify uncertainty. We find that high spatial correlation of sales data between products may be a useful indicator for "hard-to-identify" products.

Improvements in the Protein Identifier Cross-Reference service.

PubMed

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis.

PubMed

Hawkes, Corinna

2009-07-01

The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating.

Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis

PubMed Central

Hawkes, Corinna

2009-01-01

The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating. PMID:23144674

Neural responses to visual food stimuli after a normal vs. higher protein breakfast in breakfast-skipping teens: a pilot fMRI study.

PubMed

Leidy, Heather J; Lepping, Rebecca J; Savage, Cary R; Harris, Corey T

2011-10-01

This functional magnetic resonance imaging (fMRI) pilot study identified whether breakfast consumption would alter the neural activity in brain regions associated with food motivation and reward in overweight "breakfast skipping" (BS) adolescent girls and examined whether increased protein at breakfast would lead to additional alterations. Ten girls (Age: 15 ± 1 years; BMI percentile 93 ± 1%; BS 5 ± 1×/week) completed 3 testing days. Following the BS day, the participants were provided with, in randomized order, normal protein (NP; 18 ± 1 g protein) or higher protein (HP; 50 ± 1 g protein) breakfast meals to consume at home for 6 days. On day 7 of each pattern, the participants came to the laboratory to consume their respective breakfast followed by appetite questionnaires and an fMRI brain scan to identify brain activation responses to viewing food vs. nonfood images prior to lunch. Breakfast consumption led to enduring (i.e., 3-h post breakfast) reductions in neural activation in the hippocampus, amygdala, cingulate, and parahippocampus vs. BS. HP led to enduring reductions in insula and middle prefrontal cortex activation vs. NP. Hippocampal, amygdala, cingulate, and insular activations were correlated with appetite and inversely correlated with satiety. In summary, the addition of breakfast led to alterations in brain activation in regions previously associated with food motivation and reward with additional alterations following the higher-protein breakfast. These data suggest that increased dietary protein at breakfast might be a beneficial strategy to reduce reward-driven eating behavior in overweight teen girls. Due to the small sample size, caution is warranted when interpreting these preliminary findings.

Food protein-induced enterocolitis syndrome: a review of the new guidelines.

PubMed

Leonard, Stephanie A; Pecora, Valentina; Fiocchi, Alessandro Giovanni; Nowak-Wegrzyn, Anna

2018-01-01

Food protein-induced enterocolitis syndrome (FPIES) is a non IgE-mediated gastrointestinal food allergy that presents with delayed vomiting after ingestion primarily in infants. While the pathophysiology of FPIES is poorly understood, the clinical presentation of acute FPEIS reactions has been well characterized. The first International Consensus Guidelines for the Diagnosis and Management of Food Protein-induced Enterocolitis Syndrome were published in 2017 and reviewed epidemiology, clinical presentation, and prognosis of acute and chronic FPIES. The workgroup outlined clinical phenotypes, proposed diagnostic criteria, and made recommendations on management. This article summarizes the guidelines and adds recent updates. FPIES is gaining recognition, however there continues to be delays in diagnosis and misdiagnosis due to overlap of symptoms with over conditions, lack of a diagnostic test, and because some of the common trigger foods are not thought of as allergenic. More research into disease mechanisms and factors influencing differences between populations is needed.

Stable Binding of Alternative Protein-enriched Food Matrices with Concentrated Cranberry Bioflavonoids for Functional Food Applications

PubMed Central

Grace, Mary H.; Guzman, Ivette; Roopchand, Diana E.; Moskal, Kristin; Cheng, Diana M.; Pogrebnyak, Natasha; Raskin, Ilya; Howell, Amy; Lila, Mary Ann

2013-01-01

Defatted soy flour (DSF), soy protein isolate (SPI), hemp protein isolate (HPI), medium roast peanut flour (MPF) and pea protein isolate (PPI) stably bind and concentrate cranberry (CB) polyphenols, creating protein/polyphenol-enriched matrices. Proanthocyanidins (PAC) in the enriched matrices ranged from 20.75 mg/g (CB-HPI) to 10.68 mg/g (CB-SPI). Anthocyanins (ANC) ranged from 3.19 mg/g (CB-DSF) to 1.68 mg/g (CB-SPI), while total phenolics (TP) ranged from 37.61 mg/g (CB-HPI) to 21.29 mg/g (CB-SPI). LC-MS indicated that the enriched matrices contained all identifiable ANC, PAC and flavonols present in CB juice. Complexation with SPI stabilized and preserved the integrity of the CB polyphenolic components for at least 15 weeks at 37 °C. PAC isolated from enriched matrices demonstrated comparable anti-adhesion bioactivity to PAC isolated directly from CB juice (MIC 0.4 to 0.16 mg/mL), indicating their potential utility for maintenance of urinary tract health. Approximately 1.0 g of polyphenol-enriched matrix delivered the same amount of PAC available in one cup (300 mL) of commercial CB juice cocktail; which has been shown clinically to be the prophylactic dose for reducing recurring urinary tract infections. CB-SPI inhibited gram- positive and gram-negative bacterial growth. Nutritional and sensory analyses indicated that the targeted CB-matrix combinations have high potential for incorporation in functional food formulations. PMID:23786629

Raw mechanically separated chicken meat and salmon protein hydrolysate as protein sources in extruded dog food: effect on protein and amino acid digestibility.

PubMed

Tjernsbekk, M T; Tauson, A-H; Kraugerud, O F; Ahlstrøm, Ø

2017-10-01

Protein quality was evaluated for mechanically separated chicken meat (MSC) and salmon protein hydrolysate (SPH), and for extruded dog foods where MSC or SPH partially replaced poultry meal (PM). Apparent total tract digestibility (ATTD) of crude protein (CP) and amino acids (AA) in the protein ingredients and extruded foods was determined with mink (Neovison vison). The extruded dog foods included a control diet with protein from PM and grain, and two diets where MSC or SPH provided 25% of the dietary CP. Nutrient composition of the protein ingredients varied, dry matter (DM) was 944.0, 358.0 and 597.4 g/kg, CP was 670.7, 421.2 and 868.9 g/kg DM, crude fat was 141.4, 547.8 and 18.5 g/kg DM and ash was 126.4, 32.1 and 107.0 g/kg DM for PM, MSC and SPH respectively. The content of essential AA (g/100 g CP) was more than 10.0 percentage units lower in SPH than in PM and MSC. The ATTD of CP differed (p < 0.001) between protein ingredients and was 80.9%, 88.2% and 91.3% for PM, MSC and SPH respectively. The ATTD of total AA was lowest (p < 0.001) for PM, and similar (p > 0.05) for MSC and SPH. In the extruded diets, the expected higher ATTD of CP and AA from replacement of PM with MSC or SPH was not observed. The ATTD of CP was determined to be 80.3%, 81.3% and 79.0% for the PM, MSC and SPH extruded foods respectively. Furthermore, the ATTD of several AA was numerically highest for the PM diet. Possibly, extrusion affected ATTD of the diets differently due to different properties and previous processing of the three protein ingredients. Journal of Animal Physiology and Animal Nutrition © 2017 Blackwell Verlag GmbH.

Bioinformatic analysis for allergenicity assessment of Bacillus thuringiensis Cry proteins expressed in insect-resistant food crops.

PubMed

Randhawa, Gurinder Jit; Singh, Monika; Grover, Monendra

2011-02-01

The novel proteins introduced into the genetically modified (GM) crops need to be evaluated for the potential allergenicity before their introduction into the food chain to address the safety concerns of consumers. At present, there is no single definitive test that can be relied upon to predict allergic response in humans to a new protein; hence a composite approach to allergic response prediction is described in this study. The present study reports on the evaluation of the Cry proteins, encoded by cry1Ac, cry1Ab, cry2Ab, cry1Ca, cry1Fa/cry1Ca hybrid, being expressed in Bt food crops that are under field trials in India, for potential allergenic cross-reactivity using bioinformatics search tools. The sequence identity of amino acids was analyzed using FASTA3 of AllergenOnline version 10.0 and BLASTX of NCBI Entrez to identify any potential sequence matches to allergen proteins. As a step further in the detection of allergens, an independent database of domains in the allergens available in the AllergenOnline database was also developed. The results indicated no significant alignment and similarity of Cry proteins at domain level with any of the known allergens revealing that there is no potential risk of allergenic cross-reactivity. Copyright © 2010 Elsevier Ltd. All rights reserved.

InterPred: A pipeline to identify and model protein-protein interactions.

PubMed

Mirabello, Claudio; Wallner, Björn

2017-06-01

Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed. Here we present InterPred, a fully automated pipeline that predicts and model PPIs from sequence using structural modeling combined with massive structural comparisons and molecular docking. A key component of the method is the use of a novel random forest classifier that integrate several structural features to distinguish correct from incorrect protein-protein interaction models. We show that InterPred represents a major improvement in protein-protein interaction detection with a performance comparable or better than experimental high-throughput techniques. We also show that our full-atom protein-protein complex modeling pipeline performs better than state of the art protein docking methods on a standard benchmark set. In addition, InterPred was also one of the top predictors in the latest CAPRI37 experiment. InterPred source code can be downloaded from http://wallnerlab.org/InterPred Proteins 2017; 85:1159-1170. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

An ensemble framework for identifying essential proteins.

PubMed

Zhang, Xue; Xiao, Wangxin; Acencio, Marcio Luis; Lemke, Ney; Wang, Xujing

2016-08-25

Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, and the number of common predicted essential proteins by different methods is very small. In this paper, an ensemble framework is proposed which integrates gene expression data and protein-protein interaction networks (PINs). It aims to improve the prediction accuracy of basic centrality measures. The idea behind this ensemble framework is that different protein-protein interactions (PPIs) may show different contributions to protein essentiality. Five standard centrality measures (degree centrality, betweenness centrality, closeness centrality, eigenvector centrality, and subgraph centrality) are integrated into the ensemble framework respectively. We evaluated the performance of the proposed ensemble framework using yeast PINs and gene expression data. The results show that it can considerably improve the prediction accuracy of the five centrality measures individually. It can also remarkably increase the number of common predicted essential proteins among those predicted by each centrality measure individually and enable each centrality measure to find more low-degree essential proteins. This paper demonstrates that it is valuable to differentiate the contributions of different PPIs for identifying essential proteins based on network topological characteristics. The proposed ensemble framework is a successful paradigm to this end.

Local food in Iceland: identifying behavioral barriers to increased production and consumption

NASA Astrophysics Data System (ADS)

Ósk Halldórsdóttir, Þórhildur; Nicholas, Kimberly A.

2016-11-01

Increased production and consumption of local food may reduce the negative environmental, social, and economic impacts of industrialized and globalized food production. Here we examined potential barriers to increasing production and consumption of food produced in Iceland. First, we developed a new framework to address the behaviors of production and consumption simultaneously, to comprehensively analyze their potential barriers. We examined structural barriers by estimating the food production capacity of Iceland, and cultural and personal barriers through survey data on cultural norms and purchasing behavior from Matís, a research and development company. We found no structural barriers preventing Iceland from increasing production of local cereals, which would compliment current local production of meat and dairy and reduce reliance on imports, currently at 50% of the daily caloric intake. However, if food production became entirely local without changing the current mix of crops grown, there would be a 50% reduction in diversity (from 50 to 25 items in eight out of ten food categories). We did not identify any cultural barriers, as survey results demonstrated that consumers hold generally positive worldviews towards local food, with 88% satisfied with local food they had purchased. More than two-thirds of consumers regarded supporting the local farmer and considerations such as environmentally friendly production, fewer food miles, lower carbon footprint as important. However, they rated the local food they have access to as lower in meeting sustainability criteria, showing that they make justifications for not choosing local food in practice. This is a personal barrier to increased consumption of local food, and implies that marketing strategies and general knowledge connected to local food in Iceland might be improved. Although the results apply to the case of Iceland, the method of identifying behavioral barriers to change is applicable to other countries

Sex differences in snack food reinforcement in response to increasing dietary protein

USDA-ARS?s Scientific Manuscript database

BRACKGROUND: Protein is posited to play a dynamic role in energy balance and reward-driven eating behavior. However, little is known about the effect of increasing protein intake on snack food reinforcement. OBJECTIVE: We sought to determine the extent to which increasing dietary protein changes th...

Most consumed processed foods by patients on hemodialysis: Alert for phosphate-containing additives and the phosphate-to-protein ratio.

PubMed

Watanabe, Marcela T; Araujo, Raphael M; Vogt, Barbara P; Barretti, Pasqual; Caramori, Jacqueline C T

2016-08-01

Hyperphosphatemia is common in patients with chronic kidney disease (CKD) stages IV and V because of decreased phosphorus excretion. Phosphatemia is closely related to dietary intake. Thus, a better understanding of sources of dietary phosphate consumption, absorption and restriction, particularly inorganic phosphate found in food additives, is key to prevent consequences of this complication. Our aims were to investigate the most commonly consumed processed foods by patients with CKD on hemodialysis, to analyze phosphate and protein content of these foods using chemical analysis and to compare these processed foods with fresh foods. We performed a cross-sectional descriptive analytical study using food frequency questionnaires to rank the most consumed industrialized foods and beverages. Total phosphate content was determined by metavanadate colorimetry, and nitrogen content was determined by the Kjeldahl method. Protein amounts were estimated from nitrogen content. The phosphate-to-protein ratio (mg/g) was then calculated. Processed meat protein and phosphate content were compared with the nutritional composition of fresh foods using the Brazilian Food Composition Table. Phosphate measurement results were compared with data from the Food Composition Table - Support for Nutritional Decisions. An α level of 5% was considered significant. Food frequency questionnaires were performed on 100 patients (mean age, 59 ± 14 years; 57% male). Phosphate additives were mentioned on 70% of the product labels analyzed. Proteins with phosphate-containing additives provided approximately twice as much phosphate per gram of protein compared with that of fresh foods (p < 0.0001). Protein and phosphate content of processed foods are higher than those of fresh foods, as well as phosphate-to-protein ratio. A better understanding of phosphate content in foods, particularly processed foods, may contribute to better control of phosphatemia in patients with CKD. Copyright © 2016

Clinical features and resolution of food protein-induced enterocolitis syndrome: 10-year experience.

PubMed

Caubet, Jean Christoph; Ford, Lara Simone; Sickles, Laura; Järvinen, Kirsi M; Sicherer, Scott H; Sampson, Hugh A; Nowak-Węgrzyn, Anna

2014-08-01

Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy. FPIES diagnosis is frequently delayed because of the absence of classic allergic symptoms and lack of biomarkers. We sought to characterize the clinical features and resolution of FPIES in patients evaluated in our practice. Subjects 6 months to 45 years of age with FPIES were prospectively recruited for oral food challenges (OFCs). Medical records were searched to identify the subjects who did not participate in OFCs. Among 160 subjects, 54% were male; median age at diagnosis was 15 months. We performed 180 OFCs to 15 foods in 82 subjects; 30% of the study population had FPIES confirmed based on OFC results. The most common foods were cow's milk (44%), soy (41%), rice (22.5%), and oat (16%). The majority (65%) reacted to 1 food, 26% reacted to 2 foods, and 9% reacted to 3 or more foods. The majority were atopic, and 39% had IgE sensitization to another food. Thirty-nine (24%) subjects had positive specific IgE levels to the food inducing FPIES. Among children with specific IgE to cow's milk, 41% changed from a milk FPIES to an IgE-mediated phenotype over time. The median age when tolerance was established was 4.7 years for rice, 4 years for oat, and 6.7 years for soy. Median age when milk tolerance was established for subjects with undetectable milk-specific IgE levels was 5.1 years, whereas none of the subjects with detectable milk-specific IgE became tolerant to milk during the study (P = .003). FPIES typically resolves by age 5 years. Milk FPIES, especially with detectable food-specific IgE, can have a protracted course and eventually transition to acute reactions. Copyright © 2014. Published by Mosby, Inc.

Benchmark data for identifying multi-functional types of membrane proteins.

PubMed

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2016-09-01

Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. In this article, we provide data that are used for training and testing Mem-ADSVM (Wan et al., 2016. "Mem-ADSVM: a two-layer multi-label predictor for identifying multi-functional types of membrane proteins" [1]), a two-layer multi-label predictor for predicting multi-functional types of membrane proteins.

Identifying Bacterial Immune Evasion Proteins Using Phage Display.

PubMed

Fevre, Cindy; Scheepmaker, Lisette; Haas, Pieter-Jan

2017-01-01

Methods aimed at identification of immune evasion proteins are mainly rely on in silico prediction of sequence, structural homology to known evasion proteins or use a proteomics driven approach. Although proven successful these methods are limited by a low efficiency and or lack of functional identification. Here we describe a high-throughput genomic strategy to functionally identify bacterial immune evasion proteins using phage display technology. Genomic bacterial DNA is randomly fragmented and ligated into a phage display vector that is used to create a phage display library expressing bacterial secreted and membrane bound proteins. This library is used to select displayed bacterial secretome proteins that interact with host immune components.

Action of microbial transglutaminase (MTGase) in the modification of food proteins: a review.

PubMed

Gaspar, Ana Luisa Camolezi; de Góes-Favoni, Silvana Pedroso

2015-03-15

Microbial transglutaminase (MTGase) is an enzyme of the class of transferases widely known to modify protein functional properties in food systems. The main mechanisms of action involved are polymerisations, which result in changes in the molecule's hydrophobicity. Among the functional properties, MTGase affects solubility and hence gelation, emulsification, foaming, viscosity and water-holding capacity, which all depend on protein solubility. Although the enzyme's benefits for protein functionality in a variety of food systems are widely reported in the literature, few studies have focussed on its mechanisms. The purpose of this review is therefore to investigate the mechanisms of action of MTGase and consider its influence on the functional properties with different protein substrates. Understanding these mechanisms is the first step in the development and application, in food production, of new and better functional properties with improved and/or innovative characteristics that can satisfy consumer expectations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Positive effect of protein-supplemented hospital food on protein intake in patients at nutritional risk: a randomised controlled trial.

PubMed

Munk, T; Beck, A M; Holst, M; Rosenbom, E; Rasmussen, H H; Nielsen, M A; Thomsen, T

2014-04-01

New evidence indicates that increased dietary protein ingestion promotes health and recovery from illness, and also maintains functionality in older adults. The present study aimed to investigate whether a novel food service concept with protein-supplementation would increase protein and energy intake in hospitalised patients at nutritional risk. A single-blinded randomised controlled trial was conducted. Eighty-four participants at nutritional risk, recruited from the departments of Oncology, Orthopaedics and Urology, were included. The intervention group (IG) received the protein-supplemented food service concept. The control group (CG) received the standard hospital menu. Primary outcome comprised the number of patients achieving ≥75% of energy and protein requirements. Secondary outcomes comprised mean energy and protein intake, body weight, handgrip strength and length of hospital stay. In IG, 76% versus 70% CG patients reached ≥75% of their energy requirements (P = 0.57); 66% IG versus 30% CG patients reached ≥75% of their protein requirements (P = 0.001). The risk ratio for achieving ≥75% of protein requirements: 2.2 (95% confidence interval = 1.3-3.7); number needed to treat = 3 (95% confidence interval = 2-6). IG had a higher mean intake of energy and protein when adjusted for body weight (CG: 82 kJ kg(-1) versus IG: 103 kJ kg(-1) , P = 0.013; CG: 0.7 g protein kg(-1) versus 0.9 g protein kg(-1) , P = 0.003). Body weight, handgrip strength and length of hospital stay did not differ between groups. The novel food service concept had a significant positive impact on overall protein intake and on weight-adjusted energy intake in hospitalised patients at nutritional risk. © 2014 The British Dietetic Association Ltd.

Wild blueberry polyphenol-protein food ingredients produced by three drying methods: Comparative physico-chemical properties, phytochemical content, and stability during storage.

PubMed

Correia, Roberta; Grace, Mary H; Esposito, Debora; Lila, Mary Ann

2017-11-15

Particulate colloidal aggregate food ingredients were prepared by complexing wheat flour, chickpea flour, coconut flour and soy protein isolate with aqueous wild blueberry pomace extracts, then spray drying, freeze drying, or vacuum oven drying to prepare dry, flour-like matrices. Physico-chemical attributes, phytochemical content and stability during storage were compared. Eighteen anthocyanins peaks were identified for samples. Spray dried matrices produced with soy protein isolate had the highest concentration of polyphenols (156.2mg GAE/g) and anthocyanins (13.4mg/g) and the most potent DPPH scavenging activity (714.1μmolesTE/g). Spray dried blueberry polyphenols complexed with protein were protected from degradation during 16weeks at 4°C and 20°C. Soy protein isolate more efficiently captured and stabilized wild blueberry pomace phytochemicals than other protein sources. Overall, spray drying the blueberry extracts complexed with protein proved to be an environment-friendly strategy to produce stable functional ingredients with multiple applications for the food industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Non-parametric Cutout Index for Robust Evaluation of Identified Proteins*

PubMed Central

Serang, Oliver; Paulo, Joao; Steen, Hanno; Steen, Judith A.

2013-01-01

This paper proposes a novel, automated method for evaluating sets of proteins identified using mass spectrometry. The remaining peptide-spectrum match score distributions of protein sets are compared to an empirical absent peptide-spectrum match score distribution, and a Bayesian non-parametric method reminiscent of the Dirichlet process is presented to accurately perform this comparison. Thus, for a given protein set, the process computes the likelihood that the proteins identified are correctly identified. First, the method is used to evaluate protein sets chosen using different protein-level false discovery rate (FDR) thresholds, assigning each protein set a likelihood. The protein set assigned the highest likelihood is used to choose a non-arbitrary protein-level FDR threshold. Because the method can be used to evaluate any protein identification strategy (and is not limited to mere comparisons of different FDR thresholds), we subsequently use the method to compare and evaluate multiple simple methods for merging peptide evidence over replicate experiments. The general statistical approach can be applied to other types of data (e.g. RNA sequencing) and generalizes to multivariate problems. PMID:23292186

Role of Hypothalamic Melanocortin System in Adaptation of Food Intake to Food Protein Increase in Mice

PubMed Central

Pillot, Bruno; Duraffourd, Céline; Bégeot, Martine; Joly, Aurélie; Luquet, Serge; Houberdon, Isabelle; Naville, Danielle; Vigier, Michèle; Gautier-Stein, Amandine; Magnan, Christophe; Mithieux, Gilles

2011-01-01

The hypothalamic melanocortin system—the melanocortin receptor of type 4 (MC4R) and its ligands: α-melanin-stimulating hormone (α-MSH, agonist, inducing hypophagia), and agouti-related protein (AgRP, antagonist, inducing hyperphagia)—is considered to play a central role in the control of food intake. We tested its implication in the mediation of the hunger-curbing effects of protein-enriched diets (PED) in mice. Whereas there was a 20% decrease in food intake in mice fed on the PED, compared to mice fed on an isocaloric starch-enriched diet, there was a paradoxical decrease in expression of the hypothalamic proopiomelanocortin gene, precursor of α-MSH, and increase in expression of the gene encoding AgRP. The hypophagia effect of PED took place in mice with invalidation of either MC4R or POMC, and was even strengthened in mice with ablation of the AgRP-expressing neurons. These data strongly suggest that the hypothalamic melanocortin system does not mediate the hunger-curbing effects induced by changes in the macronutrient composition of food. Rather, the role of this system might be to defend the body against the variations in food intake generated by the nutritional environment. PMID:21544212

Functional properties of whey protein and its application in nanocomposite materials and functional foods

NASA Astrophysics Data System (ADS)

Walsh, Helen

Whey is a byproduct of cheese making; whey proteins are globular proteins which can be modified and polymerized to add functional benefits, these benefits can be both nutritional and structural in foods. Modified proteins can be used in non-foods, being of particular interest in polymer films and coatings. Food packaging materials, including plastics, can linings, interior coatings of paper containers, and beverage cap sealing materials, are generally made of synthetic petroleum based compounds. These synthetic materials may pose a potential human health risk due to presence of certain chemicals such as Bisphenol A (BPA). They also add to environmental pollution, being difficult to degrade. Protein-based materials do not have the same issues as synthetics and so can be used as alternatives in many packaging types. As proteins are generally hydrophilic they must be modified structurally and their performance enhanced by the addition of waterproofing agents. Polymerization of whey proteins results in a network, adding both strength and flexibility. The most interesting of the food-safe waterproofing agents are the (large aspect ratio) nanoclays. Nanoclays are relatively inexpensive, widely available and have low environmental impact. The clay surface can be modified to make it organophilic and so compatible with organic polymers. The objective of this study is the use of polymerized whey protein (PWP), with reinforcing nanoclays, to produce flexible surface coatings which limit the transfer of contents while maintaining food safety. Four smectite and kaolin type clays, one treated and three natural were assessed for strengthening qualities and the potential waterproofing and plasticizing benefits of other additives were also analyzed. The nutritional benefits of whey proteins can also be used to enhance the protein content of various foodstuffs. Drinkable yogurt is a popular beverage in the US and other countries and is considered a functional food, especially when

Identifying protein kinase target preferences using mass spectrometry

PubMed Central

Douglass, Jacqueline; Gunaratne, Ruwan; Bradford, Davis; Saeed, Fahad; Hoffert, Jason D.; Steinbach, Peter J.; Pisitkun, Trairak

2012-01-01

A general question in molecular physiology is how to identify candidate protein kinases corresponding to a known or hypothetical phosphorylation site in a protein of interest. It is generally recognized that the amino acid sequence surrounding the phosphorylation site provides information that is relevant to identification of the cognate protein kinase. Here, we present a mass spectrometry-based method for profiling the target specificity of a given protein kinase as well as a computational tool for the calculation and visualization of the target preferences. The mass spectrometry-based method identifies sites phosphorylated in response to in vitro incubation of protein mixtures with active recombinant protein kinases followed by standard phosphoproteomic methodologies. The computational tool, called “PhosphoLogo,” uses an information-theoretic algorithm to calculate position-specific amino acid preferences and anti-preferences from the mass-spectrometry data (http://helixweb.nih.gov/PhosphoLogo/). The method was tested using protein kinase A (catalytic subunit α), revealing the well-known preference for basic amino acids in positions −2 and −3 relative to the phosphorylated amino acid. It also provides evidence for a preference for amino acids with a branched aliphatic side chain in position +1, a finding compatible with known crystal structures of protein kinase A. The method was also employed to profile target preferences and anti-preferences for 15 additional protein kinases with potential roles in regulation of epithelial transport: CK2, p38, AKT1, SGK1, PKCδ, CaMK2δ, DAPK1, MAPKAPK2, PKD3, PIM1, OSR1, STK39/SPAK, GSK3β, Wnk1, and Wnk4. PMID:22723110

Identifying 'unhealthy' food advertising on television: a case study applying the UK Nutrient Profile model.

PubMed

Jenkin, Gabrielle; Wilson, Nick; Hermanson, Nicole

2009-05-01

To evaluate the feasibility of the UK Nutrient Profile (NP) model for identifying 'unhealthy' food advertisements using a case study of New Zealand television advertisements. Four weeks of weekday television from 15.30 hours to 18.30 hours was videotaped from a state-owned (free-to-air) television channel popular with children. Food advertisements were identified and their nutritional information collected in accordance with the requirements of the NP model. Nutrient information was obtained from a variety of sources including food labels, company websites and a national nutritional database. From the 60 h sample of weekday afternoon television, there were 1893 advertisements, of which 483 were for food products or retailers. After applying the NP model, 66 % of these were classified as advertising high-fat, high-salt and high-sugar (HFSS) foods; 28 % were classified as advertising non-HFSS foods; and the remaining 2 % were unclassifiable. More than half (53 %) of the HFSS food advertisements were for 'mixed meal' items promoted by major fast-food franchises. The advertising of non-HFSS food was sparse, covering a narrow range of food groups, with no advertisements for fresh fruit or vegetables. Despite the NP model having some design limitations in classifying real-world televised food advertisements, it was easily applied to this sample and could clearly identify HFSS products. Policy makers who do not wish to completely restrict food advertising to children outright should consider using this NP model for regulating food advertising.

[High-sensitive detection of multiple allergenic proteins in infant food with high-resolution mass spectrometry].

PubMed

Wu, Ci; Chen, Xi; Liu, Jianhui; Zhang, Xiaolin; Xue, Weifeng; Liang, Zhen; Liu, Mengyao; Cui, Yan; Huang, Daliang; Zhang, Lihua

2017-10-08

A novel method of the simultaneous detection of multiple kinds of allergenic proteins in infant food with parallel reaction monitoring (PRM) mode using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was established. In this method, unique peptides with good stability and high sensibility were used to quantify the corresponding allergenic proteins. Furthermore, multiple kinds of allergenic proteins are inspected simultaneously with high sensitivity. In addition, such method was successfully used for the detection of multiple allergenic proteins in infant food. As for the sample preparation for infant food, compared with the traditional acetone precipitation strategy, the protein extraction efficiency and capacity of resisting disturbance are both higher with in-situ filter-aided sample pretreatment (i-FASP) method. All allergenic proteins gave a good linear response with the correlation coefficients ( R 2 ) ≥ 0.99, and the largest concentration range of the allergenic proteins could be four orders of magnitude, and the lowest detection limit was 0.028 mg/L, which was better than that reported in references. Finally, the method was conveniently used to detect the allergens from four imported infant food real samples. All the results demonstrate that this novel strategy is of great significance for providing a rapid and reliable analytical technique for allergen proteomics.

ORF phage display to identify cellular proteins with different functions.

PubMed

Li, Wei

2012-09-01

Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages. Copyright © 2012 Elsevier Inc. All rights reserved.

Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan

PubMed Central

Kaplan, Joshua M.

2008-01-01

Cells are organized into distinct compartments to perform specific tasks with spatial precision. In neurons, presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion. Activity-dependent changes in the abundance of presynaptic proteins are thought to endow synapses with different functional states; however, relatively little is known about the rules that govern changes in the composition of presynaptic terminals. We describe a genetic strategy to systematically analyze protein localization at Caenorhabditis elegans presynaptic specializations. Nine presynaptic proteins were GFP-tagged, allowing visualization of multiple presynaptic structures. Changes in the distribution and abundance of these proteins were quantified in 25 mutants that alter different aspects of neurotransmission. Global analysis of these data identified novel relationships between particular presynaptic components and provides a new method to compare gene functions by identifying shared protein localization phenotypes. Using this strategy, we identified several genes that regulate secretion of insulin-like growth factors (IGFs) and influence lifespan in a manner dependent on insulin/IGF signaling. PMID:19043554

Identifying protein complexes based on brainstorming strategy.

PubMed

Shen, Xianjun; Zhou, Jin; Yi, Li; Hu, Xiaohua; He, Tingting; Yang, Jincai

2016-11-01

Protein complexes comprising of interacting proteins in protein-protein interaction network (PPI network) play a central role in driving biological processes within cells. Recently, more and more swarm intelligence based algorithms to detect protein complexes have been emerging, which have become the research hotspot in proteomics field. In this paper, we propose a novel algorithm for identifying protein complexes based on brainstorming strategy (IPC-BSS), which is integrated into the main idea of swarm intelligence optimization and the improved K-means algorithm. Distance between the nodes in PPI network is defined by combining the network topology and gene ontology (GO) information. Inspired by human brainstorming process, IPC-BSS algorithm firstly selects the clustering center nodes, and then they are separately consolidated with the other nodes with short distance to form initial clusters. Finally, we put forward two ways of updating the initial clusters to search optimal results. Experimental results show that our IPC-BSS algorithm outperforms the other classic algorithms on yeast and human PPI networks, and it obtains many predicted protein complexes with biological significance. Copyright © 2016 Elsevier Inc. All rights reserved.

Identifying Floppy and Rigid Regions in Proteins

NASA Astrophysics Data System (ADS)

Jacobs, D. J.; Thorpe, M. F.; Kuhn, L. A.

1998-03-01

In proteins it is possible to separate hard covalent forces involving bond lengths and bond angles from other weak forces. We model the microstructure of the protein as a generic bar-joint truss framework, where the hard covalent forces and strong hydrogen bonds are regarded as rigid bar constraints. We study the mechanical stability of proteins using FIRST (Floppy Inclusions and Rigid Substructure Topography) based on a recently developed combinatorial constraint counting algorithm (the 3D Pebble Game), which is a generalization of the 2D pebble game (D. J. Jacobs and M. F. Thorpe, ``Generic Rigidity: The Pebble Game'', Phys. Rev. Lett.) 75, 4051-4054 (1995) for the special class of bond-bending networks (D. J. Jacobs, "Generic Rigidity in Three Dimensional Bond-bending Networks", Preprint Aug (1997)). This approach is useful in identifying rigid motifs and flexible linkages in proteins, and thereby determines the essential degrees of freedom. We will show some preliminary results from the FIRST analysis on the myohemerythrin and lyozyme proteins.

Emerging Evidence for the Importance of Dietary Protein Source on Glucoregulatory Markers and Type 2 Diabetes: Different Effects of Dairy, Meat, Fish, Egg, and Plant Protein Foods.

PubMed

Comerford, Kevin B; Pasin, Gonca

2016-07-23

Observational studies provide evidence that a higher intake of protein from plant-based foods and certain animal-based foods is associated with a lower risk for type 2 diabetes. However, there are few distinguishable differences between the glucoregulatory qualities of the proteins in plant-based foods, and it is likely their numerous non-protein components (e.g., fibers and phytochemicals) that drive the relationship with type 2 diabetes risk reduction. Conversely, the glucoregulatory qualities of the proteins in animal-based foods are extremely divergent, with a higher intake of certain animal-based protein foods showing negative effects, and others showing neutral or positive effects on type 2 diabetes risk. Among the various types of animal-based protein foods, a higher intake of dairy products (such as milk, yogurt, cheese and whey protein) consistently shows a beneficial relationship with glucose regulation and/or type 2 diabetes risk reduction. Intervention studies provide evidence that dairy proteins have more potent effects on insulin and incretin secretion compared to other commonly consumed animal proteins. In addition to their protein components, such as insulinogenic amino acids and bioactive peptides, dairy products also contain a food matrix rich in calcium, magnesium, potassium, trans-palmitoleic fatty acids, and low-glycemic index sugars-all of which have been shown to have beneficial effects on aspects of glucose control, insulin secretion, insulin sensitivity and/or type 2 diabetes risk. Furthermore, fermentation and fortification of dairy products with probiotics and vitamin D may improve a dairy product's glucoregulatory effects.

Emerging Evidence for the Importance of Dietary Protein Source on Glucoregulatory Markers and Type 2 Diabetes: Different Effects of Dairy, Meat, Fish, Egg, and Plant Protein Foods

PubMed Central

Comerford, Kevin B.; Pasin, Gonca

2016-01-01

Observational studies provide evidence that a higher intake of protein from plant-based foods and certain animal-based foods is associated with a lower risk for type 2 diabetes (T2DM). However, there are few distinguishable differences between the glucoregulatory qualities of the proteins in plant-based foods, and it is likely their numerous non-protein components (e.g., fibers and phytochemicals) that drive the relationship with T2DM risk reduction. Conversely, the glucoregulatory qualities of the proteins in animal-based foods are extremely divergent, with a higher intake of certain animal-based protein foods showing negative effects, and others showing neutral or positive effects on T2DM risk. Among the various types of animal-based protein foods, a higher intake of dairy products (such as milk, yogurt, cheese and whey protein) consistently shows a beneficial relationship with glucose regulation and/or T2DM risk reduction. Intervention studies provide evidence that dairy proteins have more potent effects on insulin and incretin secretion compared to other commonly consumed animal proteins. In addition to their protein components, such as insulinogenic amino acids and bioactive peptides, dairy products also contain a food matrix rich in calcium, magnesium, potassium, trans-palmitoleic fatty acids, and low-glycemic index sugars—all of which have been shown to have beneficial effects on aspects of glucose control, insulin secretion, insulin sensitivity and/or T2DM risk. Furthermore, fermentation and fortification of dairy products with probiotics and vitamin D may improve a dairy product’s glucoregulatory effects. PMID:27455320

Identifying Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

PubMed Central

Li, Min; Chen, Weijie; Wang, Jianxin; Pan, Yi

2014-01-01

Identification of protein complexes from protein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded as core proteins. The protein-complex cores are identified from these always active proteins by detecting dense subgraphs. Final protein complexes are extended from the protein-complex cores by adding attachments based on a topological character of “closeness” and dynamic meaning. The protein complexes produced by our algorithm DPC contain two parts: static core expressed in all the molecular cycle and dynamic attachments short-lived. The proposed algorithm DPC was applied on the data of Saccharomyces cerevisiae and the experimental results show that DPC outperforms CMC, MCL, SPICi, HC-PIN, COACH, and Core-Attachment based on the validation of matching with known complexes and hF-measures. PMID:24963481

Automated Analysis of Fluorescence Microscopy Images to Identify Protein-Protein Interactions

DOE PAGES

Venkatraman, S.; Doktycz, M. J.; Qi, H.; ...

2006-01-01

The identification of protein interactions is important for elucidating biological networks. One obstacle in comprehensive interaction studies is the analyses of large datasets, particularly those containing images. Development of an automated system to analyze an image-based protein interaction dataset is needed. Such an analysis system is described here, to automatically extract features from fluorescence microscopy images obtained from a bacterial protein interaction assay. These features are used to relay quantitative values that aid in the automated scoring of positive interactions. Experimental observations indicate that identifying at least 50% positive cells in an image is sufficient to detect a protein interaction.more » Based on this criterion, the automated system presents 100% accuracy in detecting positive interactions for a dataset of 16 images. Algorithms were implemented using MATLAB and the software developed is available on request from the authors.« less

Dietary Intake of High-Protein Foods and Other Major Foods in Meat-Eaters, Poultry-Eaters, Fish-Eaters, Vegetarians, and Vegans in UK Biobank.

PubMed

Bradbury, Kathryn E; Tong, Tammy Y N; Key, Timothy J

2017-12-02

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.

Dietary Intake of High-Protein Foods and Other Major Foods in Meat-Eaters, Poultry-Eaters, Fish-Eaters, Vegetarians, and Vegans in UK Biobank

PubMed Central

2017-01-01

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. PMID:29207491

Recent Research in Antihypertensive Activity of Food Protein-derived Hydrolyzates and Peptides.

PubMed

Saleh, Ahmed S M; Zhang, Qing; Shen, Qun

2016-01-01

Year to year obesity prevalence, reduced physical activities, bad habits/or stressful lifestyle, and other environmental and physiological impacts lead to increase in diseases such as coronary heart disease, stroke, cancer, diabetes, and hypertension worldwide. Hypertension is considered as one of the most common serious chronic diseases; however, discovery of medications with high efficacy and without side effects for treatment of patients remains a challenge for scientists. Recent trends in functional foods have evidenced that food bioactive proteins play a major role in the concepts of illness and curing; therefore, nutritionists, biomedical scientists, and food scientists are working together to develop improved systems for the discovery of peptides with increased potency and therapeutic benefits. This review presents a recent research carried out to date for the purpose of isolation and identification of bioactive hydrolyzates and peptides with angiotensin I converting enzyme inhibitory activity and antihypertensive effect from animal, marine, microbial, and plant food proteins. Effects of food processing and hydrolyzation conditions as well as some other impacts on formation, activity, and stability of these hydrolyzates and peptides are also presented.

Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks.

PubMed

Wang, Jian; Xie, Dong; Lin, Hongfei; Yang, Zhihao; Zhang, Yijia

2012-06-21

Many biological processes recognize in particular the importance of protein complexes, and various computational approaches have been developed to identify complexes from protein-protein interaction (PPI) networks. However, high false-positive rate of PPIs leads to challenging identification. A protein semantic similarity measure is proposed in this study, based on the ontology structure of Gene Ontology (GO) terms and GO annotations to estimate the reliability of interactions in PPI networks. Interaction pairs with low GO semantic similarity are removed from the network as unreliable interactions. Then, a cluster-expanding algorithm is used to detect complexes with core-attachment structure on filtered network. Our method is applied to three different yeast PPI networks. The effectiveness of our method is examined on two benchmark complex datasets. Experimental results show that our method performed better than other state-of-the-art approaches in most evaluation metrics. The method detects protein complexes from large scale PPI networks by filtering GO semantic similarity. Removing interactions with low GO similarity significantly improves the performance of complex identification. The expanding strategy is also effective to identify attachment proteins of complexes.

Proteomic Analysis of the Soybean Symbiosome Identifies New Symbiotic Proteins*

PubMed Central

Clarke, Victoria C.; Loughlin, Patrick C.; Gavrin, Aleksandr; Chen, Chi; Brear, Ella M.; Day, David A.; Smith, Penelope M.C.

2015-01-01

Legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. This nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. As part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. Fractions containing the symbiosome membrane (SM) and material from the lumen of the symbiosome (peribacteroid space or PBS) were isolated from soybean root nodules and analyzed using nongel proteomic techniques. Bicarbonate stripping and chloroform-methanol extraction of isolated SM were used to reduce complexity of the samples and enrich for hydrophobic integral membrane proteins. One hundred and ninety-seven proteins were identified as components of the SM, with an additional fifteen proteins identified from peripheral membrane and PBS protein fractions. Proteins involved in a range of cellular processes such as metabolism, protein folding and degradation, membrane trafficking, and solute transport were identified. These included a number of proteins previously localized to the SM, such as aquaglyceroporin nodulin 26, sulfate transporters, remorin, and Rab7 homologs. Among the proteome were a number of putative transporters for compounds such as sulfate, calcium, hydrogen ions, peptide/dicarboxylate, and nitrate, as well as transporters for which the substrate is not easy to predict. Analysis of the promoter activity for six genes encoding putative SM proteins showed nodule specific expression, with five showing expression only in infected cells. Localization of two proteins was confirmed using GFP-fusion experiments. The data have been deposited to the ProteomeXchange with identifier PXD001132. This proteome will provide a rich resource for the study of the legume-rhizobium symbiosis. PMID

A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges

PubMed Central

Kaufman, James; Lessler, Justin; Harry, April; Edlund, Stefan; Hu, Kun; Douglas, Judith; Thoens, Christian; Appel, Bernd; Käsbohrer, Annemarie; Filter, Matthias

2014-01-01

Foodborne disease outbreaks of recent years demonstrate that due to increasingly interconnected supply chains these type of crisis situations have the potential to affect thousands of people, leading to significant healthcare costs, loss of revenue for food companies, and—in the worst cases—death. When a disease outbreak is detected, identifying the contaminated food quickly is vital to minimize suffering and limit economic losses. Here we present a likelihood-based approach that has the potential to accelerate the time needed to identify possibly contaminated food products, which is based on exploitation of food products sales data and the distribution of foodborne illness case reports. Using a real world food sales data set and artificially generated outbreak scenarios, we show that this method performs very well for contamination scenarios originating from a single “guilty” food product. As it is neither always possible nor necessary to identify the single offending product, the method has been extended such that it can be used as a binary classifier. With this extension it is possible to generate a set of potentially “guilty” products that contains the real outbreak source with very high accuracy. Furthermore we explore the patterns of food distributions that lead to “hard-to-identify” foods, the possibility of identifying these food groups a priori, and the extent to which the likelihood-based method can be used to quantify uncertainty. We find that high spatial correlation of sales data between products may be a useful indicator for “hard-to-identify” products. PMID:24992565

Protein Hydrolysates and Biopeptides: Production, Biological Activities, and Applications in Foods and Health Benefits. A Review.

PubMed

Nasri, M

In recent years, a great deal of interest has been expressed regarding the production, characterization, and applications of protein hydrolysates and food-derived biopeptides due to their numerous beneficial health effects. In this regard, research is mainly focused on investigating the therapeutic potential of these natural compounds. Based on their amino acids composition, sequences, hydrophobicity, and length, peptides released from food proteins, beyond their nutritional properties, can exhibit various biological activities including antihypertensive, antioxidative, antithrombotic, hypoglycemic, hypocholesterolemic, and antibacterial activities among others. Protein hydrolysates are essentially produced by enzymatic hydrolysis of whole protein sources by appropriate proteolytic enzymes under controlled conditions, followed by posthydrolysis processing to isolate desired and potent bioactive peptides from a complex mixture of active and inactive peptides. Therefore, because of their human health potential and safety profiles, protein hydrolysates and biopeptides may be used as ingredients in functional foods and pharmaceuticals to improve human health and prevent diseases. In this review, we have focused on the major variables influencing the enzymatic process of protein hydrolysates production. The biological properties of protein hydrolysates will be described as well as their applications in foods and health benefits. © 2017 Elsevier Inc. All rights reserved.

Identifying cooperative transcriptional regulations using protein–protein interactions

PubMed Central

Nagamine, Nobuyoshi; Kawada, Yuji; Sakakibara, Yasubumi

2005-01-01

Cooperative transcriptional activations among multiple transcription factors (TFs) are important to understand the mechanisms of complex transcriptional regulations in eukaryotes. Previous studies have attempted to find cooperative TFs based on gene expression data with gene expression profiles as a measure of similarity of gene regulations. In this paper, we use protein–protein interaction data to infer synergistic binding of cooperative TFs. Our fundamental idea is based on the assumption that genes contributing to a similar biological process are regulated under the same control mechanism. First, the protein–protein interaction networks are used to calculate the similarity of biological processes among genes. Second, we integrate this similarity and the chromatin immuno-precipitation data to identify cooperative TFs. Our computational experiments in yeast show that predictions made by our method have successfully identified eight pairs of cooperative TFs that have literature evidences but could not be identified by the previous method. Further, 12 new possible pairs have been inferred and we have examined the biological relevances for them. However, since a typical problem using protein–protein interaction data is that many false-positive data are contained, we propose a method combining various biological data to increase the prediction accuracy. PMID:16126847

Assessing food allergy risks from residual peanut protein in highly refined vegetable oil.

PubMed

Blom, W Marty; Kruizinga, Astrid G; Rubingh, Carina M; Remington, Ben C; Crevel, René W R; Houben, Geert F

2017-08-01

Refined vegetable oils including refined peanut oil are widely used in foods. Due to shared production processes, refined non-peanut vegetable oils can contain residual peanut proteins. We estimated the predicted number of allergic reactions to residual peanut proteins using probabilistic risk assessment applied to several scenarios involving food products made with vegetable oils. Variables considered were: a) the estimated production scale of refined peanut oil, b) estimated cross-contact between refined vegetable oils during production, c) the proportion of fat in representative food products and d) the peanut protein concentration in refined peanut oil. For all products examined the predicted risk of objective allergic reactions in peanut-allergic users of the food products was extremely low. The number of predicted reactions ranged depending on the model from a high of 3 per 1000 eating occasions (Weibull) to no reactions (LogNormal). Significantly, all reactions were predicted for allergen intakes well below the amounts reported for the most sensitive individual described in the clinical literature. We conclude that the health risk from cross-contact between vegetable oils and refined peanut oil is negligible. None of the food products would warrant precautionary labelling for peanut according to the VITAL ® programme of the Allergen Bureau. Copyright © 2017 Elsevier Ltd. All rights reserved.

Food and nutritional security requires adequate protein as well as energy, delivered from whole-year crop production.

PubMed

Coles, Graeme D; Wratten, Stephen D; Porter, John R

2016-01-01

Human food security requires the production of sufficient quantities of both high-quality protein and dietary energy. In a series of case-studies from New Zealand, we show that while production of food ingredients from crops on arable land can meet human dietary energy requirements effectively, requirements for high-quality protein are met more efficiently by animal production from such land. We present a model that can be used to assess dietary energy and quality-corrected protein production from various crop and crop/animal production systems, and demonstrate its utility. We extend our analysis with an accompanying economic analysis of commercially-available, pre-prepared or simply-cooked foods that can be produced from our case-study crop and animal products. We calculate the per-person, per-day cost of both quality-corrected protein and dietary energy as provided in the processed foods. We conclude that mixed dairy/cropping systems provide the greatest quantity of high-quality protein per unit price to the consumer, have the highest food energy production and can support the dietary requirements of the highest number of people, when assessed as all-year-round production systems. Global food and nutritional security will largely be an outcome of national or regional agroeconomies addressing their own food needs. We hope that our model will be used for similar analyses of food production systems in other countries, agroecological zones and economies.

Differential diagnosis of food protein-induced enterocolitis syndrome

PubMed Central

Fiocchi, Alessandro; Claps, Alessia; Dahdah, Lamia; Brindisi, Giulia; Dionisi-Vici, Carlo; Martelli, Alberto

2014-01-01

Purpose of review To assess all the possible differential diagnosis of food protein-induced enterocolitis syndrome (FPIES), both in acute and chronic presentation, reviewing the data reported in published studies. Recent findings There is an increase of reported cases of FPIES in recent years. As the disease presents with nonspecific symptoms, it can be misunderstood in many ways. The differential diagnosis includes, in acute presentations, the following: sepsis, other infectious diseases, acute gastrointestinal episodes, surgical emergencies, food allergies. In its chronic forms, FPIES may mimic malabsorption syndromes, metabolic disorders, primary immunodeficiencies, neurological conditions, coagulation defects, and other types of non-IgE-mediated food allergy. Summary A thorough clinical evaluation, including symptoms, signs, and laboratory findings, is necessary to lead the clinicians toward the diagnosis of FPIES. The major reason for delayed diagnosis appears to be the lack of knowledge of the disease. PMID:24739227

Designing medical foods for inherited metabolic disorders: why intact protein is superior to amino acids.

PubMed

Ney, Denise Marie; Etzel, Mark Raymond

2017-04-01

Phenylketonuria and tyrosinemia are inherited metabolic disorders characterized by high blood levels of phenylalanine (Phe) or tyrosine (Tyr), due to mutations in genes affecting Phe and Tyr metabolism, respectively. The primary management is a lifelong diet restricted in protein from natural foods in combination with medical foods comprised mixtures of synthetic amino acids. Compliance is often poor after childhood leading to neuropsychological sequela. Glycomacropeptide, an intact 64 amino acid glycophosphopeptide isolated from cheese whey, provides a new paradigm for the management of phenylketonuria and tyrosinemia because glycomacropeptide contains no Phe and Tyr in its pure form, and is also a prebiotic. Medical foods made from glycomacropeptide have been used successfully for the management of phenylketonuria and tyrosinemia. Preclinical and clinical studies demonstrate that intact protein from glycomacropeptide provides a more acceptable and physiologic source of defined protein compared to amino acids in medical foods. For example, harmful gut bacteria were reduced, beneficial short chain fatty acids increased, renal workload decreased, protein utilization increased, and bone fragility decreased using intact protein versus amino acids. Advances in biotechnology will propel the transition from synthetic amino acids to intact proteins for the management of inherited metabolic disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploiting genomic data to identify proteins involved in abalone reproduction.

PubMed

Mendoza-Porras, Omar; Botwright, Natasha A; McWilliam, Sean M; Cook, Mathew T; Harris, James O; Wijffels, Gene; Colgrave, Michelle L

2014-08-28

Aside from their critical role in reproduction, abalone gonads serve as an indicator of sexual maturity and energy balance, two key considerations for effective abalone culture. Temperate abalone farmers face issues with tank restocking with highly marketable abalone owing to inefficient spawning induction methods. The identification of key proteins in sexually mature abalone will serve as the foundation for a greater understanding of reproductive biology. Addressing this knowledge gap is the first step towards improving abalone aquaculture methods. Proteomic profiling of female and male gonads of greenlip abalone, Haliotis laevigata, was undertaken using liquid chromatography-mass spectrometry. Owing to the incomplete nature of abalone protein databases, in addition to searching against two publicly available databases, a custom database comprising genomic data was used. Overall, 162 and 110 proteins were identified in females and males respectively with 40 proteins common to both sexes. For proteins involved in sexual maturation, sperm and egg structure, motility, acrosomal reaction and fertilization, 23 were identified only in females, 18 only in males and 6 were common. Gene ontology analysis revealed clear differences between the female and male protein profiles reflecting a higher rate of protein synthesis in the ovary and higher metabolic activity in the testis. A comprehensive mass spectrometry-based analysis was performed to profile the abalone gonad proteome providing the foundation for future studies of reproduction in abalone. Key proteins involved in both reproduction and energy balance were identified. Genomic resources were utilised to build a database of molluscan proteins yielding >60% more protein identifications than in a standard workflow employing public protein databases. Copyright © 2014 Elsevier B.V. All rights reserved.

Food for the Future: A Study of Insects as a Protein Source

NASA Astrophysics Data System (ADS)

Riggs, S.

2017-12-01

This study is designed to gain a sustainable, organic food source containing the proper amino acids, minerals, and protein to sustain the needs of human life on Earth as the current economy and environment will not be able to equip the needs for the future. The hypotheses are if available protein is increased in an insect's diet then their nutritional value will increase to fulfill a human's daily protein requirements in one serving size or less for each species tested and if there is a higher content of protein in the insects, then food created with it will receive higher ratings. Protein supplements were added to an insect's natural diet to increase nutritional value. Protein value in the insects increased to fulfill a human's daily dietary protein requirement in a third of a serving size. Biuret and absorption spectrometry testing demonstrates this correlation. Insects increased protein in their body showing a positive correlation to the hypothesis. Week one, protein values doubled and tripled in some species, unexpectedly. After three weeks, protein still continued increasing. There was high success in increasing the protein value in the different species of insects chosen. Is there a taste difference benefit with a higher content of protein in the insects? Over 55% of participants rated the brownies with more protein higher than the control groups, and overall 88% preferred brownies with insects opposed to without, supporting the second hypothesis.

Single cell protein production of Chlorella sp. using food processing waste as a cultivation medium

NASA Astrophysics Data System (ADS)

Putri, D.; Ulhidayati, A.; Musthofa, I. A.; Wardani, A. K.

2018-03-01

The aim of this study was to investigate the effect of various food processing wastes on the production of single cell protein by Chlorella sp. Three various food processing wastes i.e. tofu waste, tempeh waste and cheese whey waste were used as cultivation medium for Chlorella sp. growth. Sea water was used as a control of cultivation medium. The addition of waste into cultivation medium was 10%, 20%, 30%, 40%, and 50%. The result showed that the highest yield of cell mass and protein content was found in 50% tofu waste cultivation medium was 47.8 × 106 cell/ml with protein content was 52.24%. The 50% tofu waste medium showed improved cell yield as nearly as 30% than tempeh waste medium. The yield of biomass and protein content when 30% tempeh waste was used as cultivation medium was 37.1 × 106 cell/ml and 52%, respectively. Thus, food processing waste especially tofu waste would be a promising candidate for cultivation medium for single cell production from Chlorella sp. Moreover, the utilization of waste can reduce environmental pollution and increase protein supply for food supplement or animal feed.

Newer Approaches to Identify Potential Untoward Effects in Functional Foods.

PubMed

Marone, Palma Ann; Birkenbach, Victoria L; Hayes, A Wallace

2016-01-01

Globalization has greatly accelerated the numbers and variety of food and beverage products available worldwide. The exchange among greater numbers of countries, manufacturers, and products in the United States and worldwide has necessitated enhanced quality measures for nutritional products for larger populations increasingly reliant on functionality. These functional foods, those that provide benefit beyond basic nutrition, are increasingly being used for their potential to alleviate food insufficiency while enhancing quality and longevity of life. In the United States alone, a steady import increase of greater than 15% per year or 24 million shipments, over 70% products of which are food related, is regulated under the Food and Drug Administration (FDA). This unparalleled growth has resulted in the need for faster, cheaper, and better safety and efficacy screening methods in the form of harmonized guidelines and recommendations for product standardization. In an effort to meet this need, the in vitro toxicology testing market has similarly grown with an anticipatory 15% increase between 2010 and 2015 of US$1.3 to US$2.7 billion. Although traditionally occupying a small fraction of the market behind pharmaceuticals and cosmetic/household products, the scope of functional food testing, including additives/supplements, ingredients, residues, contact/processing, and contaminants, is potentially expansive. Similarly, as functional food testing has progressed, so has the need to identify potential adverse factors that threaten the safety and quality of these products. © The Author(s) 2015.

Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts*

PubMed Central

Anderson, Jonathan P.; Hane, James K.; Stoll, Thomas; Pain, Nicholas; Hastie, Marcus L.; Kaur, Parwinder; Hoogland, Christine; Gorman, Jeffrey J.; Singh, Karam B.

2016-01-01

Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806. PMID:26811357

Protein and amino acid bioavailability of extruded dog food with protein meals of different quality using growing mink () as a model.

PubMed

Tjernsbekk, M T; Tauson, A-H; Matthiesen, C F; Ahlstrøm, Ø

2016-09-01

The present study evaluated growing mink () as a model for dietary protein quality assessment of protein meals used in extruded dog foods. Three foods with similar CP content but of different protein quality were produced using different protein meals. The protein meals varied with respect to CP digestibility and AA composition and included lamb meal (LBM), poultry meal (PM), and fish meal (FM) with low, intermediate, and high protein quality, respectively. Nitrogen balance, BW gain, protein efficiency ratio (PER), and apparent total tract digestibility (ATTD) were used as measures of protein and AA bioavailability in growing mink. Standardized ileal digestibility (SID) was used to measure protein and AA bioavailability in adult dogs (). The mink study (3 × 3 Latin square design) included 12 kits aged 8 to 11 wk. The dog study included 12 dogs divided in 3 groups allocated to 1 of the experimental diets. The growing mink responded in accordance with the different AA supply between diets, as determined by the first limiting AA. The LBM diet deviated from the other diets with lower ( < 0.001) values for N retention, BW gain, and PER, and the diets differed ( < 0.001) in ATTD of CP and all AA, except for hydroxyproline. Retention of N was 0.66, 1.04, and 1.18 g·kg·d; BW gain was 8.2, 26.8, and 35.3 g/d; PER was 0.38, 1.39, and 1.71; and ATTD of CP was 66.8, 73.8, and 82.1% for the LBM, PM, and FM diets, respectively. In dogs, SID of CP and AA differed ( ≤ 0.017) between diets and was generally lowest for the LBM diet, intermediate for the PM diet, and greatest for the FM diet. For CP, SID was 71.5, 80.2, and 87.0% for the LBM, PM, and FM diets, respectively. The contents of digestible CP and AA (based on SID) covered the minimal requirement for adult dogs set by the NRC for all diets, except for the content of digestible Met + Cys in the LBM diet. Despite this, dietary content of Met + Cys in the LBM diet agreed with the recommended level set by the NRC and the

ELISA testing for common food antigens in four dry dog foods used in dietary elimination trials.

PubMed

Raditic, D M; Remillard, R L; Tater, K C

2011-02-01

This study evaluated four over the counter venison dry dog foods available from one on-line retail vendor for potential contamination with common known food allergens: soy, poultry or beef. An amplified, double sandwich type enzyme linked immunosorbent assay (ELISA) test of soy, poultry and beef proteins were performed by an independent accredited food laboratory. The ELISA test for poultry protein was found to be unreliable when testing in dry dog foods because false negatives occurred. ELISA testing of control diets for both soy and beef proteins performed as expected and could be useful in antigen testing in dry dog foods. Three of the four over the counter (OTC) venison canine dry foods with no soy products named in the ingredient list were ELISA positive for soy; additionally one OTC diet tested positive for beef protein with no beef products listed as an ingredient list. One OTC venison diet was not found to be positive for soy, poultry or beef proteins. However, none of the four OTC venison diets could be considered suitable for a diagnostic elimination trial as they all contained common pet food proteins, some of which were readily identifiable on the label and some that were only detected by ELISA. Therefore, if the four OTC venison products selected in this study are representative of OTC products in general, then the use of OTC venison dry dog foods should not be used during elimination trials in suspected food allergy patients. © 2010 Blackwell Verlag GmbH.

Can we identify patients at risk of life-threatening allergic reactions to food?

PubMed

Turner, P J; Baumert, J L; Beyer, K; Boyle, R J; Chan, C-H; Clark, A T; Crevel, R W R; DunnGalvin, A; Fernández-Rivas, M; Gowland, M H; Grabenhenrich, L; Hardy, S; Houben, G F; O'B Hourihane, J; Muraro, A; Poulsen, L K; Pyrz, K; Remington, B C; Schnadt, S; van Ree, R; Venter, C; Worm, M; Mills, E N C; Roberts, G; Ballmer-Weber, B K

2016-09-01

Anaphylaxis has been defined as a 'severe, life-threatening generalized or systemic hypersensitivity reaction'. However, data indicate that the vast majority of food-triggered anaphylactic reactions are not life-threatening. Nonetheless, severe life-threatening reactions do occur and are unpredictable. We discuss the concepts surrounding perceptions of severe, life-threatening allergic reactions to food by different stakeholders, with particular reference to the inclusion of clinical severity as a factor in allergy and allergen risk management. We review the evidence regarding factors that might be used to identify those at most risk of severe allergic reactions to food, and the consequences of misinformation in this regard. For example, a significant proportion of food-allergic children also have asthma, yet almost none will experience a fatal food-allergic reaction; asthma is not, in itself, a strong predictor for fatal anaphylaxis. The relationship between dose of allergen exposure and symptom severity is unclear. While dose appears to be a risk factor in at least a subgroup of patients, studies report that individuals with prior anaphylaxis do not have a lower eliciting dose than those reporting previous mild reactions. It is therefore important to consider severity and sensitivity as separate factors, as a highly sensitive individual will not necessarily experience severe symptoms during an allergic reaction. We identify the knowledge gaps that need to be addressed to improve our ability to better identify those most at risk of severe food-induced allergic reactions. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Fish protein hydrolysates: application in deep-fried food and food safety analysis.

PubMed

He, Shan; Franco, Christopher; Zhang, Wei

2015-01-01

Four different processes (enzymatic, microwave-intensified enzymatic, chemical, and microwave-intensified chemical) were used to produce fish protein hydrolysates (FPH) from Yellowtail Kingfish for food applications. In this study, the production yield and oil-binding capacity of FPH produced from different processes were evaluated. Microwave intensification significantly increased the production yields of enzymatic process from 42% to 63%. It also increased the production yields of chemical process from 87% to 98%. The chemical process and microwave-intensified chemical process produced the FPH with low oil-binding capacity (8.66 g oil/g FPH and 6.25 g oil/g FPH), whereas the microwave-intensified enzymatic process produced FPH with the highest oil-binding capacity (16.4 g oil/g FPH). The FPH from the 4 processes were applied in the formulation of deep-fried battered fish and deep-fried fish cakes. The fat uptake of deep-fried battered fish can be reduced significantly from about 7% to about 4.5% by replacing 1% (w/w) batter powder with FPH, and the fat uptake of deep-fried fish cakes can be significantly reduced from about 11% to about 1% by replacing 1% (w/w) fish mince with FPH. Food safety tests of the FPH produced by these processes demonstrated that the maximum proportion of FPH that can be safely used in food formulation is 10%, due to its high content of histamine. This study demonstrates the value of FPH to the food industry and bridges the theoretical studies with the commercial applications of FPH. © 2015 Institute of Food Technologists®

Application of the adverse outcome pathway (AOP) concept to structure the available in vivo and in vitro mechanistic data for allergic sensitization to food proteins.

PubMed

van Bilsen, Jolanda H M; Sienkiewicz-Szłapka, Edyta; Lozano-Ojalvo, Daniel; Willemsen, Linette E M; Antunes, Celia M; Molina, Elena; Smit, Joost J; Wróblewska, Barbara; Wichers, Harry J; Knol, Edward F; Ladics, Gregory S; Pieters, Raymond H H; Denery-Papini, Sandra; Vissers, Yvonne M; Bavaro, Simona L; Larré, Colette; Verhoeckx, Kitty C M; Roggen, Erwin L

2017-01-01

The introduction of whole new foods in a population may lead to sensitization and food allergy. This constitutes a potential public health problem and a challenge to risk assessors and managers as the existing understanding of the pathophysiological processes and the currently available biological tools for prediction of the risk for food allergy development and the severity of the reaction are not sufficient. There is a substantial body of in vivo and in vitro data describing molecular and cellular events potentially involved in food sensitization. However, these events have not been organized in a sequence of related events that is plausible to result in sensitization, and useful to challenge current hypotheses. The aim of this manuscript was to collect and structure the current mechanistic understanding of sensitization induction to food proteins by applying the concept of adverse outcome pathway (AOP). The proposed AOP for food sensitization is based on information on molecular and cellular mechanisms and pathways evidenced to be involved in sensitization by food and food proteins and uses the AOPs for chemical skin sensitization and respiratory sensitization induction as templates. Available mechanistic data on protein respiratory sensitization were included to fill out gaps in the understanding of how proteins may affect cells, cell-cell interactions and tissue homeostasis. Analysis revealed several key events (KE) and biomarkers that may have potential use in testing and assessment of proteins for their sensitizing potential. The application of the AOP concept to structure mechanistic in vivo and in vitro knowledge has made it possible to identify a number of methods, each addressing a specific KE, that provide information about the food allergenic potential of new proteins. When applied in the context of an integrated strategy these methods may reduce, if not replace, current animal testing approaches. The proposed AOP will be shared at the www

Potential utilization of algal protein concentrate as a food ingredient in space habitats

NASA Technical Reports Server (NTRS)

Nakhost, Z.; Karel, M.

1989-01-01

Green alga Scenedesmus obliquus was studied as one of the potential sources of macronutrients in a space habitat. Algal protein concentrate (70.5% protein) was incorporated into a variety of food products such as bran muffins, fettuccine (spinach noodle imitation) and chocolate chip cookies. Food products containing 20 to 40% of incorporated algal proteins were considered. In the sensory analysis the greenish color of the bran muffins and cookies was not found to be objectional. The mild spinachy flavor (algae flavor) was less detectable in chocolate chip cookies than in bran muffins. The color and taste of the algae noodles were found to be pleasant and compared well with commercially available spinach noodles. Commercially available spray-dried Spirulina algae was also incorporated so the products can be compared with those containing Scenedesmus obliquus concentrate. Food products containing commercial algae had a dark green color and a "burnt after taste" and were less acceptable to the panelists.

A novel approach for the detection of potentially hazardous pepsin stable hazelnut proteins as contaminants in chocolate-based food.

PubMed

Akkerdaas, Jaap H; Wensing, Marjolein; Knulst, André C; Stephan, Oliver; Hefle, Susan L; Aalberse, Rob C; van Ree, Ronald

2004-12-15

Contamination of food products with pepsin resistant allergens is generally believed to be a serious threat to patients with severe food allergy. A sandwich type enzyme-linked immunosorbent assay (ELISA) was developed to measure pepsin resistant hazelnut protein in food products. Capturing and detecting rabbit antibodies were raised against pepsin-digested hazelnut and untreated hazelnut protein, respectively. The assay showed a detection limit of 0.7 ng/mL hazelnut protein or <1 microg hazelnut in 1 g food matrix and a maximum of 0.034% cross-reactivity (peanut). Chocolate samples spiked with 0.5-100 microg hazelnut/g chocolate showed a mean recovery of 97.3%. In 9/12 food products labeled "may contain nuts", hazelnut was detected between 1.2 and 417 microg hazelnut/g food. It can be concluded that the application of antibodies directed to pepsin-digested food extracts in ELISA can facilitate specific detection of stable proteins that have the highest potential of inducing severe food anaphylaxis.

Plant food allergies: a suggested approach to allergen-resolved diagnosis in the clinical practice by identifying easily available sensitization markers.

PubMed

Asero, Riccardo

2005-09-01

Molecular biology techniques have led to the identification of a number of allergens in vegetable foods, but due to the lack of purified food proteins for routine diagnostic use, the detection of sensitizing allergens remains a nearly impossible task in most clinical settings. The allergen-resolved diagnosis of food allergy is essential because each plant-derived food may contain a number of different allergens showing different physical/chemical characteristics that strongly influence the clinical expression of allergy; moreover, many allergens may cross-react with homologue proteins present in botanically unrelated vegetable foods. Through a review of the available literature, this study aimed to detect "markers" of sensitization to specific plant food allergens that are easily accessible in the clinical practice. There are several "markers" of sensitization to different allergenic proteins in vegetable foods that can be helpful in the clinical practice. Specific algorithms for patients allergic to Rosaceae and to tree nuts were built. Clinical allergologists lacking the assistance of an advanced molecular biology lab may take advantage of some specific clinical data as well as of some "markers" in the difficult task of correctly diagnosing patients with plant food allergy and to provide them the best preventive advice. Copyright (c) 2005 S. Karger AG, Basel.

Food Protein-Induced Enterocolitis Instead of Necrotizing Enterocolitis? A Neonatal Intensive Care Unit Case Series.

PubMed

Lenfestey, Mary W; de la Cruz, Diomel; Neu, Josef

2018-05-23

Necrotizing enterocolitis is an important disease in infants born premature. However, other disease entities present with similar signs and symptoms. This series reviews 5 atypical cases initially diagnosed as necrotizing enterocolitis that may be more consistent with food protein-induced enterocolitis. Food protein-induced enterocolitis may be underdiagnosed in this population. Copyright © 2018 Elsevier Inc. All rights reserved.

Gene Unprediction with Spurio: A tool to identify spurious protein sequences.

PubMed

Höps, Wolfram; Jeffryes, Matt; Bateman, Alex

2018-01-01

We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation.  Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases.  We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes.  Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins. However, transposon proteins are prone to be predicted as spurious because of the frequency of degraded homologs found in the DNA sequence databases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the AntiFam resource. The Spurio software and source code is available under an MIT license at the following URL: https://bitbucket.org/bateman-group/spurio.

Risks of allergic reactions to biotech proteins in foods: perception and reality.

PubMed

Lehrer, S B; Bannon, G A

2005-05-01

In recent years, significant attention has been paid to the use of biotechnology to improve the quality and quantity of the food supply due in part to the projected growth in the world population, plus limited options available for increasing the amount of land under cultivation. Alterations in the food supply induced by classical breeding and selection methods typically involve the movement of large portions of genomic DNA between different plant varieties to obtain the desired trait. This is in contrast to techniques of genetic engineering which allows the selection and transfers specific genes from one species to another. The primary allergy risk to consumers from genetically modified crops may be placed into one of three categories. The first represents the highest risk to the allergic consumer is the transfer of known allergen or cross-reacting allergen into a food crop. The second category, representing an intermediate risk to the consumer, is the potential for replacing the endogenous allergenicity of a genetically-modified crop. The last category involves expression of novel proteins that may become allergens in man and generally represents a relatively low risk to the consumer, although this possibility has received attention of late. In order to mitigate the three categories of potential allergy risk associated with biotech crops, all genes introduced into food crops undergo a series of tests designed to determine if the biotech protein exhibits properties of known food allergens. The result of this risk assessment process to date is that no biotech proteins in foods have been documented to cause allergic reactions. These results indicate that the current assessment process is robust, although as science of allergy and allergens evolves, new information and new technology should help further the assessment process for potential allergenicity.

Extracellular vesicle-derived protein from Bifidobacterium longum alleviates food allergy through mast cell suppression.

PubMed

Kim, Jung-Hwan; Jeun, Eun-Ji; Hong, Chun-Pyo; Kim, Seong-Hoon; Jang, Min Seong; Lee, Eun-Jung; Moon, Sook Jin; Yun, Chang Ho; Im, Sin-Hyeog; Jeong, Seok-Geun; Park, Beom-Young; Kim, Kyong-Tai; Seoh, Ju-Young; Kim, Yoon-Keun; Oh, Sung-Jong; Ham, Jun-Sang; Yang, Bo-Gie; Jang, Myoung Ho

2016-02-01

The incidence of food allergies has increased dramatically during the last decade. Recently, probiotics have been studied for the prevention and treatment of allergic disease. We examined whether Bifidobacterium longum KACC 91563 and Enterococcus faecalis KACC 91532 have the capacity to suppress food allergies. B longum KACC 91563 and E faecalis KACC 91532 were administered to BALB/c wild-type mice, in which food allergy was induced by using ovalbumin and alum. Food allergy symptoms and various immune responses were assessed. B longum KACC 91563, but not E faecalis KACC 91532, alleviated food allergy symptoms. Extracellular vesicles of B longum KACC 91563 bound specifically to mast cells and induced apoptosis without affecting T-cell immune responses. Furthermore, injection of family 5 extracellular solute-binding protein, a main component of extracellular vesicles, into mice markedly reduced the occurrence of diarrhea in a mouse food allergy model. B longum KACC 91563 induces apoptosis of mast cells specifically and alleviates food allergy symptoms. Accordingly, B longum KACC 91563 and family 5 extracellular solute-binding protein exhibit potential as therapeutic approaches for food allergies. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Novel royal jelly proteins identified by gel-based and gel-free proteomics.

PubMed

Han, Bin; Li, Chenxi; Zhang, Lan; Fang, Yu; Feng, Mao; Li, Jianke

2011-09-28

Royal jelly (RJ) plays an important role in caste determination of the honeybee; the genetically same female egg develops into either a queen or worker bee depending on the time and amount of RJ fed to the larvae. RJ also has numerous health-promoting properties for humans. Gel-based and gel-free proteomics approaches and high-performance liquid chromatography-chip quadruple time-of-flight tandem mass spectrometry were applied to comprehensively investigate the protein components of RJ. Overall, 37 and 22 nonredundant proteins were identified by one-dimensional gel electrophoresis and gel-free analysis, respectively, and 19 new proteins were found by these two proteomics approaches. Major royal jelly proteins (MRJPs) were identified as the principal protein components of RJ, and proteins related to carbohydrate metabolism such as glucose oxidase, α-glucosidase precursor, and glucose dehydrogenase were also successfully identified. Importantly, the 19 newly identified proteins were mainly classified into three functional categories: oxidation-reduction (ergic53 CG6822-PA isoform A isoform 1, Sec61 CG9539-PA, and ADP/ATP translocase), protein binding (regucalcin and translationally controlled tumor protein CG4800-PA isoform 1), and lipid transport (apolipophorin-III-like protein). These new findings not only significantly increase the RJ proteome coverage but also help to provide new knowledge of RJ for honeybee biology and potential use for human health promotion.

The Meat and Protein Group. The Food Guide Pyramid.

ERIC Educational Resources Information Center

Frost, Helen

This booklet for young children is part of a series that supports national science standards related to physical health and nutrition, describing and illustrating the importance of using the Food Guide Pyramid and eating from the meat and protein group. Colorful photographs support early readers in understanding the text. The repetition of words…

Semantic integration to identify overlapping functional modules in protein interaction networks

PubMed Central

Cho, Young-Rae; Hwang, Woochang; Ramanathan, Murali; Zhang, Aidong

2007-01-01

Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification. PMID:17650343

Food Allergy - Basic Mechanisms and Applications to Identifying Risks Associated with Plant Incorporated Pesticides and Other Genetically Modified Crops

EPA Science Inventory

Food allergy is a relatively new concern for toxicologists as a result of the incorporation of novel proteins into food crops in order to promote resistance to pests and other stresses, improve nutrition, or otherwise modify the phenotype. Food allergy can manifest as inflammatio...

A coevolution analysis for identifying protein-protein interactions by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI).

A coevolution analysis for identifying protein-protein interactions by Fourier transform

PubMed Central

Yin, Changchuan; Yau, Stephen S. -T.

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI). PMID:28430779

New proteins identified in epididymal fluid from the platypus (Ornithorhynchus anatinus).

PubMed

Dacheux, Jean-Louis; Dacheux, Francoise; Labas, Valerie; Ecroyd, Heath; Nixon, Brett; Jones, Russell C

2009-01-01

The platypus epididymal proteome is being studied because epididymal proteins are essential for male fertility in mammals and it is considered that knowledge of the epididymal proteome in an early mammal would be informative in assessing the convergence and divergence of proteins that are important in the function of the mammalian epididymis. Few of the epididymal proteins that have been identified in eutherian mammals were found in platypus caudal epididymal fluid, and the major epididymal proteins in the platypus (PXN-FBPL, SPARC and E-OR20) have never been identified in the epididymis of any other mammal.

School Foodservice Personnel's Struggle with Using Labels to Identify Whole-Grain Foods

ERIC Educational Resources Information Center

Chu, Yen Li; Orsted, Mary; Marquart, Len; Reicks, Marla

2012-01-01

Objective: To describe how school foodservice personnel use current labeling methods to identify whole-grain products and the influence on purchasing for school meals. Methods: Focus groups explored labeling methods to identify whole-grain products and barriers to incorporating whole-grain foods in school meals. Qualitative analysis procedures and…

Mutagens from the cooking of food. II. Survey by Ames/Salmonella test of mutagen formation in the major protein-rich foods of the American diet.

PubMed

Bjeldanes, L F; Morris, M M; Felton, J S; Healy, S; Stuermer, D; Berry, P; Timourian, H; Hatch, F T

1982-08-01

The formation of mutagens in the major cooked protein-rich foods in the US diet was studied in the Ames Salmonella typhimurium test. The nine protein-rich foods most commonly eaten in the USA--ground beef, beef steak, eggs, pork chops, fried chicken, pot-roasted beef, ham, roast beef and bacon--were examined for their mutagenicity towards S. typhimurium TA1538 after normal 'household' cooking (deep frying, griddle/pan frying, baking/roasting, broiling, stewing, braising or boiling of 100-475 degrees C). Well-done fried ground beef, beef steak, ham pork chops and bacon showed significant mutagen formation. For chicken and beef steak high-temperature broiling produced the most mutagenicity, followed by baking/roasting and frying. Stewing, braising and deep frying produced little mutagen. Eggs and egg products produced mutagens only after cooking at high temperatures (the yolk to a greater extent than the white). Commercially cooked hamburgers showed a wide range of mutagenic activity. We conclude that mutagen formation following cooking of protein-containing foods is a complex function of food type, cooking time and cooking temperature. It seems clear that all the major protein-rich foods if cooked to a well-done state on the griddle (eggs only at temperatures above 225 degrees C) or by broiling will contain mutagens detectable by the Ames/Salmonella assay. This survey is a step towards determining whether any human health hazard results from cooking protein-rich foods. Further testing in both short- and long-term genotoxicity bioassays and carcinogenesis assays are needed before any human risk extrapolations can be made.

Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease

NASA Astrophysics Data System (ADS)

Keane, Harriet; Ryan, Brent J.; Jackson, Brendan; Whitmore, Alan; Wade-Martins, Richard

2015-11-01

Neurodegenerative diseases are complex multifactorial disorders characterised by the interplay of many dysregulated physiological processes. As an exemplar, Parkinson’s disease (PD) involves multiple perturbed cellular functions, including mitochondrial dysfunction and autophagic dysregulation in preferentially-sensitive dopamine neurons, a selective pathophysiology recapitulated in vitro using the neurotoxin MPP+. Here we explore a network science approach for the selection of therapeutic protein targets in the cellular MPP+ model. We hypothesised that analysis of protein-protein interaction networks modelling MPP+ toxicity could identify proteins critical for mediating MPP+ toxicity. Analysis of protein-protein interaction networks constructed to model the interplay of mitochondrial dysfunction and autophagic dysregulation (key aspects of MPP+ toxicity) enabled us to identify four proteins predicted to be key for MPP+ toxicity (P62, GABARAP, GBRL1 and GBRL2). Combined, but not individual, knockdown of these proteins increased cellular susceptibility to MPP+ toxicity. Conversely, combined, but not individual, over-expression of the network targets provided rescue of MPP+ toxicity associated with the formation of autophagosome-like structures. We also found that modulation of two distinct proteins in the protein-protein interaction network was necessary and sufficient to mitigate neurotoxicity. Together, these findings validate our network science approach to multi-target identification in complex neurological diseases.

Protein extraction method for the proteomic study of a Mexican traditional fermented starchy food.

PubMed

Cárdenas, C; Barkla, B J; Wacher, C; Delgado-Olivares, L; Rodríguez-Sanoja, R

2014-12-05

Pozol is a traditional fermented maize dough prepared in southeastern Mexico. Wide varieties of microorganisms have already been isolated from this spontaneously fermented product; and include fungi, yeasts, and lactic- and non-lactic acid bacteria. Pozol presents physicochemical features different from that of other food fermentation products, such as a high starch content, in addition to a low protein content. It is these qualities that make it intractable for protein recovery and characterization. The aim of this study was to develop a methodology to optimize the recovery of proteins from the pozol dough following fermentation, by reducing the complexity of the mixture prior to 2D-PAGE analysis and sequencing, to allow the characterization of the metaproteome of the dough. The proteome of 15day fermented maize dough was characterized; proteins were separated and analyzed by mass spectrometry (LC-MS/MS). Subsequent sequence homology database searching, identified numerous bacterial and fungi proteins; with a predominance of lactic acid bacterial proteins, mainly from the Lactobacillus genus. Fungi are mainly represented by Aspergillus. For dominant genera, the most prevalent proteins belong to carbohydrate metabolism and energy production, which suggest that at 15days of fermentation not only fungi but also bacteria are metabolically active. Several methodologies have been employed to study pozol, with a specific focus toward the identification of the microbiota of this fermented maize dough, using both traditional cultivation techniques and culture independent molecular techniques. However to date, the dynamics of this complex fermentation is not well understood. With the purpose to gain further insight into the nature of the fermentation, we used proteomic technologies to identify the origin of proteins and enzymes that facilitate substrate utilization and ultimately the development of the microbiota and fermentation. In this paper we overcome the first general

Four infants presenting with severe vomiting in solid food protein-induced enterocolitis syndrome: a case series.

PubMed

Bansal, Amolak S; Bhaskaran, Sree; Bansal, Rhea A

2012-06-26

Several different foods have been implicated in inducing the delayed and very significant vomiting and sometimes diarrhea that occurs in food protein-induced enterocolitis syndrome. While immunoglobulin E is not involved, the mechanism(s) that result in the food-induced gastrointestinal symptoms are unclear, although T cell activation has been considered. We report four cases of food protein-induced enterocolitis syndrome caused by different solid foods and without concomitant immunoglobulin E sensitization to milk and soya. Clinical and laboratory evidence of type I immunoglobulin E mediated food reactivity and food-induced T cell activation was absent in each case. Case 1 concerned a 20-month-old South Asian boy who had experienced four episodes of severe vomiting with flaccidity since four months of age and two hours after consuming rice.Case 2 involved a nine-month-old Caucasian boy who had suffered three episodes of severe vomiting with flaccidity since six months of age and three hours after consuming wheat.The child in Case 3 was a 16-month-old Caucasian boy who had suffered three episodes of severe vomiting with flaccidity since nine months of age and two hours after consuming cod.Case 4 involved a 15-month-old South Asian boy who had suffered three episodes of severe vomiting since eight months of age and two hours after consuming chicken. In children with recurrent marked delayed vomiting after the ingestion of specific foods and in whom bronchospasm, skin rash and angioedema are absent, food protein-induced enterocolitis syndrome should be considered. Skin prick testing and specific immunoglobulin E antibodies are negative and the mechanism of the vomiting is unclear. We speculate whether food protein-induced oligoclonal T cell activation may be present. This has similarities to various animal models and improvement may involve deletion of these T cells.

Food hypersensitivity reactions in Soft Coated Wheaten Terriers with protein-losing enteropathy or protein-losing nephropathy or both: gastroscopic food sensitivity testing, dietary provocation, and fecal immunoglobulin E.

PubMed

Vaden, S L; Hammerberg, B; Davenport, D J; Orton, S M; Trogdon, M M; Melgarejo, L T; VanCamp, S D; Williams, D A

2000-01-01

The purpose of this study was to evaluate Soft Coated Wheaten Terriers (SCWTs) affected with protein-losing enteropathy (PLE) or protein-losing nephropathy (PLN) or both for allergy to food. We performed gastroscopic food-sensitivity testing, a provocative dietary trial, and measurement of fecal immunoglobulin E (IgE) in 6 SCWTs affected with PLE or PLN or both. Positive gastroscopic food-sensitivity test reactions were noted in 5 of 6 dogs. Positive reactions were found to milk in 4 dogs, to lamb in 2 dogs, and to wheat and chicken each in 1 dog. Adverse reactions to food (diarrhea, vomiting, or pruritus) were detected in all 6 dogs during the provocative dietary trial. Adverse reactions were found to corn in 5 dogs, to tofu in 3 dogs, to cottage cheese in 2 dogs, to milk in 2 dogs, to farina cream of wheat in 2 dogs, and to lamb in 2 dogs. Serum albumin concentrations significantly decreased and fecal alpha1-protease inhibitor concentration significantly increased 4 days after the provocative trial when compared with baseline values. Antigen-specific fecal IgE varied throughout the provocative trial, with peak levels following ingestion of test meals. We conclude that food hypersensitivities are present in SCWTs affected with the syndrome of PLE/PLN. Mild inflammatory bowel disease was already established in the 6 SCWTs of this report at the time of study, making it impossible to determine if food allergies were the cause or result of the enteric disease.

Production of single cell protein (SCP) from food and agricultural waste by using Saccharomyces cerevisiae.

PubMed

Gervasi, Teresa; Pellizzeri, Vito; Calabrese, Giorgio; Di Bella, Giuseppa; Cicero, Nicola; Dugo, Giacomo

2018-03-01

Food waste is the single-largest component of the waste stream, in order to protect and safeguard the public health, useful and innovative recycling methods are investigated. The conversion of food wastes in value-added products is becoming a more economically viable and interesting practice. Food waste, collected in the distribution sector and citrus industries, was characterised for its potential as a raw material to use in fermentation processes. In this study, the production of single-cell protein (SCP) using food waste as a substrate was investigated. The purpose of this study has been to produce SCP from mixtures of food waste using Saccharomyces cerevisiae. The main fermentation test was carried out using a 25 l bioreactor. The utilisation of food waste can allow us to not only to reduce environmental pollution, but also to obtain value-added products such as protein supply for animal feed.

Food safety assessment of Cry8Ka5 mutant protein using Cry1Ac as a control Bt protein.

PubMed

Farias, Davi Felipe; Viana, Martônio Ponte; Oliveira, Gustavo Ramos; Santos, Vanessa Olinto; Pinto, Clidia Eduarda Moreira; Viana, Daniel Araújo; Vasconcelos, Ilka Maria; Grossi-de-Sa, Maria Fátima; Carvalho, Ana Fontenele Urano

2015-07-01

Cry8Ka5 is a mutant protein from Bacillus thuringiensis (Bt) that has been proposed for developing transgenic plants due to promising activity against coleopterans, like Anthonomus grandis (the major pest of Brazilian cotton culture). Thus, an early food safety assessment of Cry8Ka5 protein could provide valuable information to support its use as a harmless biotechnological tool. This study aimed to evaluate the food safety of Cry8Ka5 protein following the two-tiered approach, based on weights of evidence, proposed by ILSI. Cry1Ac protein was used as a control Bt protein. The history of safe use revealed no convincing hazard reports for Bt pesticides and three-domain Cry proteins. The bioinformatics analysis with the primary amino acids sequence of Cry8Ka5 showed no similarity to any known toxic, antinutritional or allergenic proteins. The mode of action of Cry proteins is well understood and their fine specificity is restricted to insects. Cry8Ka5 and Cry1Ac proteins were rapidly degraded in simulated gastric fluid, but were resistant to simulated intestinal fluid and heat treatment. The LD50 for Cry8Ka5 and Cry1Ac was >5000 mg/kg body weight when administered by gavage in mice. Thus, no expected relevant risks are associated with the consumption of Cry8Ka5 protein. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of casein and egg white proteins on the structure of wheat gluten-based protein-rich food.

PubMed

Wouters, Arno G B; Rombouts, Ine; Lagrain, Bert; Delcour, Jan A

2016-02-01

There is a growing interest in texturally and nutritionally satisfying vegetable alternatives to meat. Wheat gluten proteins have unique functional properties but a poor nutritional value in comparison to animal proteins. This study investigated the potential of egg white and bovine milk casein with well-balanced amino acid composition to increase the quality of wheat gluten-based protein-rich foods. Heating a wheat gluten (51.4 g)-water (100.0 mL) blend for 120 min at 100 °C increased its firmness less than heating a wheat gluten (33.0 g)-freeze-dried egg white (16.8 g)-water (100.0 mL) blend. In contrast, the addition of casein to the gluten-water blend negatively impacted firmness after heating. Firmness was correlated with loss of protein extractability in sodium dodecyl sulfate containing medium during heating, which was higher with egg white than with casein. Even more, heat-induced polymerization of the gluten-water blend with egg white but not with casein was greater than expected from the losses in extractability of gluten and egg white on their own. Structure formation was favored by mixing gluten with egg white but not with casein. These observations were linked to the intrinsic polymerization behavior of egg white and casein, but also to their interaction with gluten. Thus not all nutritionally suitable proteins can be used for enrichment of gluten-based protein-rich foods. © 2015 Society of Chemical Industry.

Proteomics-based approach identified differentially expressed proteins with potential roles in endometrial carcinoma.

PubMed

Li, Zhengyu; Min, Wenjiao; Huang, Canhua; Bai, Shujun; Tang, Minghai; Zhao, Xia

2010-01-01

We used proteomic approaches to identify altered expressed proteins in endometrial carcinoma, with the aim of discovering potential biomarkers or therapeutic targets for endometrial carcinoma. The global proteins extracted from endometrial carcinoma and normal endometrial tissues were separated by 2-dimensional electrophoresis and analyzed with PDQuest (Bio-Rad, Hercules, Calif) software. The differentially expressed spots were identified by mass spectrometry and searched against NCBInr protein database. Those proteins with potential roles were confirmed by Western blotting and immunohistochemical assays. Ninety-nine proteins were identified by mass spectrometry, and a cluster diagram analysis indicated that these proteins were involved in metabolism, cell transformation, protein folding, translation and modification, proliferation and apoptosis, signal transduction, cytoskeleton, and so on. In confirmatory immunoblotting and immunohistochemical analyses, overexpressions of epidermal fatty acid-binding protein, calcyphosine, and cyclophilin A were also observed in endometrial carcinoma tissues, which were consistent with the proteomic results. Our results suggested that these identified proteins, including epidermal fatty acid-binding protein, calcyphosine, and cyclophilin A, might be of potential values in the studies of endometrial carcinogenesis or investigations of diagnostic biomarkers or treatment targets for endometrial carcinoma.

The self-assembly, aggregation and phase transitions of food protein systems in one, two and three dimensions

NASA Astrophysics Data System (ADS)

Mezzenga, Raffaele; Fischer, Peter

2013-04-01

The aggregation of proteins is of fundamental relevance in a number of daily phenomena, as important and diverse as blood coagulation, medical diseases, or cooking an egg in the kitchen. Colloidal food systems, in particular, are examples that have great significance for protein aggregation, not only for their importance and implications, which touches on everyday life, but also because they allow the limits of the colloidal science analogy to be tested in a much broader window of conditions, such as pH, ionic strength, concentration and temperature. Thus, studying the aggregation and self-assembly of proteins in foods challenges our understanding of these complex systems from both the molecular and statistical physics perspectives. Last but not least, food offers a unique playground to study the aggregation of proteins in three, two and one dimensions, that is to say, in the bulk, at air/water and oil/water interfaces and in protein fibrillation phenomena. In this review we will tackle this very ambitious task in order to discuss the current understanding of protein aggregation in the framework of foods, which is possibly one of the broadest contexts, yet is of tremendous daily relevance.

Food protein-stabilized nanoemulsions as potential delivery systems for poorly water-soluble drugs: preparation, in vitro characterization, and pharmacokinetics in rats

PubMed Central

He, Wei; Tan, Yanan; Tian, Zhiqiang; Chen, Lingyun; Hu, Fuqiang; Wu, Wei

2011-01-01

Nanoemulsions stabilized by traditional emulsifiers raise toxicological concerns for long-term treatment. The present work investigates the potential of food proteins as safer stabilizers for nanoemulsions to deliver hydrophobic drugs. Nanoemulsions stabilized by food proteins (soybean protein isolate, whey protein isolate, β-lactoglobulin) were prepared by high-pressure homogenization. The toxicity of the nanoemulsions was tested in Caco-2 cells using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide viability assay. In vivo absorption in rats was also evaluated. Food protein-stabilized nanoemulsions, with small particle size and good size distribution, exhibited better stability and biocompatibility compared with nanoemulsions stabilized by traditional emulsifiers. Moreover, β-lactoglobulin had a better emulsifying capacity and biocompatibility than the other two food proteins. The pancreatic degradation of the proteins accelerated drug release. It is concluded that an oil/water nanoemulsion system with good biocompatibility can be prepared by using food proteins as emulsifiers, allowing better and more rapid absorption of lipophilic drugs. PMID:21468355

Food protein-stabilized nanoemulsions as potential delivery systems for poorly water-soluble drugs: preparation, in vitro characterization, and pharmacokinetics in rats.

PubMed

He, Wei; Tan, Yanan; Tian, Zhiqiang; Chen, Lingyun; Hu, Fuqiang; Wu, Wei

2011-01-01

Nanoemulsions stabilized by traditional emulsifiers raise toxicological concerns for long-term treatment. The present work investigates the potential of food proteins as safer stabilizers for nanoemulsions to deliver hydrophobic drugs. Nanoemulsions stabilized by food proteins (soybean protein isolate, whey protein isolate, β-lactoglobulin) were prepared by high-pressure homogenization. The toxicity of the nanoemulsions was tested in Caco-2 cells using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide viability assay. In vivo absorption in rats was also evaluated. Food protein-stabilized nanoemulsions, with small particle size and good size distribution, exhibited better stability and biocompatibility compared with nanoemulsions stabilized by traditional emulsifiers. Moreover, β-lactoglobulin had a better emulsifying capacity and biocompatibility than the other two food proteins. The pancreatic degradation of the proteins accelerated drug release. It is concluded that an oil/water nanoemulsion system with good biocompatibility can be prepared by using food proteins as emulsifiers, allowing better and more rapid absorption of lipophilic drugs.

Characteristics of children with food protein-induced enterocolitis and allergic proctocolitis.

PubMed

Arik Yilmaz, Ebru; Soyer, Ozge; Cavkaytar, Ozlem; Karaatmaca, Betul; Buyuktiryaki, Betul; Sahiner, Umit M; Sekerel, Bulent E; Sackesen, Cansin

2017-01-01

The aim of this study was to determine and compare the clinical and laboratory features of food protein-induced enterocolitis syndrome (FPIES) and food protein-induced allergic proctocolitis (FPIAP), and to provide information about the short-term prognoses. Children diagnosed with FPIES or FPIAP between 2010 and 2015 were enrolled in this study. Overall, 64 infants (37 FPIAP, 27 FPIES) were evaluated, with the average age at the onset of symptoms being significantly lower in the patients with FPIAP than in the patients with FPIES (2 months [1-3 months] versus 4 months [1.5-6 months]; p = 0.043). Fifteen of the patients with FPIAP (40.5%) and six of the patients with FPIES (22.2%) were exclusively breast-fed at the time of the onset of symptoms. Cow's milk was the most frequent trigger (100% FPIAP, 74% FPIES); solid foods caused FPIES more frequently. Forty-eight of the 64 patients were followed up until at least 2 years of age, with the resolution rates being 91.3% for FPIAP and 60% for FPIES. The solid food-induced cases of FPIES (27.3%) had a significantly lower rate of resolution than the liquid food-induced FPIES (83.3%) (p = 0.003). Cow's milk is the most common trigger of both FPIAP and FPIES. The symptom onset age seemed to be earlier in FPIAP. The resolution age was similar, however, the recovery in FPIES may be later if the trigger food is solid. To our knowledge, this was the first clinical study to compare the clinical and laboratory characteristics of patients with FPIAP and FPIES.

Using Twitter to Identify and Respond to Food Poisoning: The Food Safety STL Project.

PubMed

Harris, Jenine K; Hawkins, Jared B; Nguyen, Leila; Nsoesie, Elaine O; Tuli, Gaurav; Mansour, Raed; Brownstein, John S

Foodborne illness affects 1 in 4 US residents each year. Few of those sickened seek medical care or report the illness to public health authorities, complicating prevention efforts. Citizens who report illness identify food establishments with more serious and critical violations than found by regular inspections. New media sources, including online restaurant reviews and social media postings, have the potential to improve reporting. We implemented a Web-based Dashboard (HealthMap Foodborne Dashboard) to identify and respond to tweets about food poisoning from St Louis City residents. This report examines the performance of the Dashboard in its first 7 months after implementation in the City of St Louis Department of Health. We examined the number of relevant tweets captured and replied to, the number of foodborne illness reports received as a result of the new process, and the results of restaurant inspections following each report. In its first 7 months (October 2015-May 2016), the Dashboard captured 193 relevant tweets. Our replies to relevant tweets resulted in more filed reports than several previously existing foodborne illness reporting mechanisms in St Louis during the same time frame. The proportion of restaurants with food safety violations was not statistically different (P = .60) in restaurants inspected after reports from the Dashboard compared with those inspected following reports through other mechanisms. The Dashboard differs from other citizen engagement mechanisms in its use of current data, allowing direct interaction with constituents on issues when relevant to the constituent to provide time-sensitive education and mobilizing information. In doing so, the Dashboard technology has potential for improving foodborne illness reporting and can be implemented in other areas to improve response to public health issues such as suicidality, spread of Zika virus infection, and hospital quality.

Using Twitter to Identify and Respond to Food Poisoning: The Food Safety STL Project

PubMed Central

Hawkins, Jared B.; Nguyen, Leila; Nsoesie, Elaine O.; Tuli, Gaurav; Mansour, Raed; Brownstein, John S.

2017-01-01

Context: Foodborne illness affects 1 in 4 US residents each year. Few of those sickened seek medical care or report the illness to public health authorities, complicating prevention efforts. Citizens who report illness identify food establishments with more serious and critical violations than found by regular inspections. New media sources, including online restaurant reviews and social media postings, have the potential to improve reporting. Objective: We implemented a Web-based Dashboard (HealthMap Foodborne Dashboard) to identify and respond to tweets about food poisoning from St Louis City residents. Design and Setting: This report examines the performance of the Dashboard in its first 7 months after implementation in the City of St Louis Department of Health. Main Outcome Measures: We examined the number of relevant tweets captured and replied to, the number of foodborne illness reports received as a result of the new process, and the results of restaurant inspections following each report. Results: In its first 7 months (October 2015-May 2016), the Dashboard captured 193 relevant tweets. Our replies to relevant tweets resulted in more filed reports than several previously existing foodborne illness reporting mechanisms in St Louis during the same time frame. The proportion of restaurants with food safety violations was not statistically different (P = .60) in restaurants inspected after reports from the Dashboard compared with those inspected following reports through other mechanisms. Conclusion: The Dashboard differs from other citizen engagement mechanisms in its use of current data, allowing direct interaction with constituents on issues when relevant to the constituent to provide time-sensitive education and mobilizing information. In doing so, the Dashboard technology has potential for improving foodborne illness reporting and can be implemented in other areas to improve response to public health issues such as suicidality, spread of Zika virus

Diet Modeling in Older Americans: The Impact of Increasing Plant-Based Foods or Dairy Products on Protein Intake.

PubMed

Houchins, J A; Cifelli, C J; Demmer, E; Fulgoni, V L

2017-01-01

To determine the effects of increasing plant-based foods or dairy products on protein intake in older Americans by performing diet modeling. Data from What We Eat in America (WWEIA), the dietary component of the National Health and Nutrition Examination Survey (NHANES), 2007-2010 for Americans aged 51 years and older (n=5,389), divided as 51-70 years (n=3,513) and 71 years and older (n=1,876) were used. Usual protein intake was compared among three dietary models that increased intakes by 100%: (1) plant-based foods; (2) higher protein plant-based foods (i.e., legumes, nuts, seeds, soy); and (3) dairy products (milk, cheese, and yogurt). Models (1) and (2) had commensurate reductions in animal-based protein intake. Doubling intake of plant-based foods (as currently consumed) resulted in a drop of protein intake by approximately 22% for males and females aged 51+ years. For older males and females, aged 71+ years, doubling intake of plant-based foods (as currently consumed) resulted in an estimated usual intake of 0.83±0.02 g/kg ideal body weight (iBW))/day and 0.78±0.01 g/kg iBW/day, respectively. In this model, 33% of females aged 71+ years did not meet the estimated average requirement for protein. Doubling dairy product consumption achieved current protein intake recommendations. These data illustrate that increasing plant-based foods and reducing animal-based products could have unintended consequences on protein intake of older Americans. Doubling dairy product intake can help older adults get to an intake level of approximately 1.2 g/kg iBW/day, consistent with the growing consensus that older adults need to consume higher levels of protein for health.

Identifying protein domains by global analysis of soluble fragment data.

PubMed

Bulloch, Esther M M; Kingston, Richard L

2014-11-15

The production and analysis of individual structural domains is a common strategy for studying large or complex proteins, which may be experimentally intractable in their full-length form. However, identifying domain boundaries is challenging if there is little structural information concerning the protein target. One experimental procedure for mapping domains is to screen a library of random protein fragments for solubility, since truncation of a domain will typically expose hydrophobic groups, leading to poor fragment solubility. We have coupled fragment solubility screening with global data analysis to develop an effective method for identifying structural domains within a protein. A gene fragment library is generated using mechanical shearing, or by uracil doping of the gene and a uracil-specific enzymatic digest. A split green fluorescent protein (GFP) assay is used to screen the corresponding protein fragments for solubility when expressed in Escherichia coli. The soluble fragment data are then analyzed using two complementary approaches. Fragmentation "hotspots" indicate possible interdomain regions. Clustering algorithms are used to group related fragments, and concomitantly predict domain location. The effectiveness of this Domain Seeking procedure is demonstrated by application to the well-characterized human protein p85α. Copyright © 2014 Elsevier Inc. All rights reserved.

Assessment of Recovery of Milk Protein Allergens from Processed Food for Mass Spectrometry Quantification.

PubMed

Groves, Kate; Cryar, Adam; Walker, Michael; Quaglia, Milena

2018-01-01

Assessing the recovery of food allergens from solid processed matrixes is one of the most difficult steps that needs to be overcome to enable the accurate quantification of protein allergens by immunoassay and MS. A feasibility study is described herein applying International System of Units (SI)-traceably quantified milk protein solutions to assess recovery by an improved extraction method. Untargeted MS analysis suggests that this novel extraction method can be further developed to provide high recoveries for a broad range of food allergens. A solution of α-casein was traceably quantified to the SI for the content of α-S1 casein. Cookie dough was prepared by spiking a known amount of the SI-traceable quantified solution into a mixture of flour, sugar, and soya spread, followed by baking. A novel method for the extraction of protein food allergens from solid matrixes based on proteolytic digestion was developed, and its performance was compared with the performance of methods reported in the literature.

Protein source and quality in therapeutic foods affect the immune response and outcome in severe acute malnutrition

USDA-ARS?s Scientific Manuscript database

Protein is a vital component of therapeutic foods designed to treat severe acute malnutrition (SAM) in children; however there are still unknowns about the quality and quantity of the proteins to use in these foods. This review examines two recent studies investigating several different qualities an...

Does flavor impact function? Potential consequences of polyphenol-protein interactions in delivery and bioactivity of flavan-3-ols from foods.

PubMed

Ferruzzi, Mario G; Bordenave, Nicolas; Hamaker, Bruce R

2012-11-05

Astringency is a component of the overall flavor experienced when consuming polyphenol rich foods and beverages such as tea, wine, cocoa and select fruits. Following consumption, the astringent sensation results from the well documented ability of polyphenols to bind to salivary proline rich proteins (PRP) and facilitate their precipitation in the oral cavity. In a similar fashion, polyphenols are also known to non-specifically bind food and other biological proteins. While much is known regarding the polyphenol-protein interactions leading to astringency, significantly less information is available regarding the impact of these polyphenol-protein interactions with food or other biological proteins on relevant physiological outcomes. This paper focuses on the interactions between flavan-3-ols, one of the most abundant dietary polyphenol forms, with proteins in food, salivary PRP and other physiological proteins. The physiological implications of these interactions in food and through the gut will be discussed in relation to manipulation of flavan-3-ol bioavailability, metabolism and biological activities including inhibition of digestive enzymes in the gut. Copyright © 2012 Elsevier Inc. All rights reserved.

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites

NASA Astrophysics Data System (ADS)

Lu, Cheng-Tsung; Chen, Shu-An; Bretaña, Neil Arvin; Cheng, Tzu-Hsiu; Lee, Tzong-Yi

2011-10-01

In proteins, glutamate (Glu) residues are transformed into γ-carboxyglutamate (Gla) residues in a process called carboxylation. The process of protein carboxylation catalyzed by γ-glutamyl carboxylase is deemed to be important due to its involvement in biological processes such as blood clotting cascade and bone growth. There is an increasing interest within the scientific community to identify protein carboxylation sites. However, experimental identification of carboxylation sites via mass spectrometry-based methods is observed to be expensive, time-consuming, and labor-intensive. Thus, we were motivated to design a computational method for identifying protein carboxylation sites. This work aims to investigate the protein carboxylation by considering the composition of amino acids that surround modification sites. With the implication of a modified residue prefers to be accessible on the surface of a protein, the solvent-accessible surface area (ASA) around carboxylation sites is also investigated. Radial basis function network is then employed to build a predictive model using various features for identifying carboxylation sites. Based on a five-fold cross-validation evaluation, a predictive model trained using the combined features of amino acid sequence (AA20D), amino acid composition, and ASA, yields the highest accuracy at 0.874. Furthermore, an independent test done involving data not included in the cross-validation process indicates that in silico identification is a feasible means of preliminary analysis. Additionally, the predictive method presented in this work is implemented as Carboxylator (http://csb.cse.yzu.edu.tw/Carboxylator/), a web-based tool for identifying carboxylated proteins with modification sites in order to help users in investigating γ-glutamyl carboxylation.

Traffic to the malaria parasite food vacuole: a novel pathway involving a phosphatidylinositol 3-phosphate-binding protein.

PubMed

McIntosh, Michael T; Vaid, Ankush; Hosgood, H Dean; Vijay, Justin; Bhattacharya, Anindita; Sahani, Mayurbhai H; Baevova, Pavlina; Joiner, Keith A; Sharma, Pushkar

2007-04-13

Phosphatidylinositol 3-phosphate (PI3P) is a key ligand for recruitment of endosomal regulatory proteins in higher eukaryotes. Subsets of these endosomal proteins possess a highly selective PI3P binding zinc finger motif belonging to the FYVE domain family. We have identified a single FYVE domain-containing protein in Plasmodium falciparum which we term FCP. Expression and mutagenesis studies demonstrate that key residues are involved in specific binding to PI3P. In contrast to FYVE proteins in other organisms, endogenous FCP localizes to a lysosomal compartment, the malaria parasite food vacuole (FV), rather than to cytoplasmic endocytic organelles. Transfections of deletion mutants further indicate that FCP is essential for trophozoite and FV maturation and that it traffics to the FV via a novel constitutive cytoplasmic to vacuole targeting pathway. This newly discovered pathway excludes the secretory pathway and is directed by a C-terminal 44-amino acid peptide domain. We conclude that an FYVE protein that might be expected to participate in vesicle targeting in the parasite cytosol instead has a vital and functional role in the malaria parasite FV.

Identifying the Community Structure of the Food-Trade International Multi-Network

NASA Technical Reports Server (NTRS)

Torreggiani, S.; Mangioni, G.

2018-01-01

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of international food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the multi-network's community structure. Here we find that the individual crop-specific layers of the multi-network have densely connected trading groups, a consistent characteristic over the period 2001-2011. Further, the multi-network is characterized by low variability over this period but with substantial heterogeneity across layers in each year. In particular, the layers are mostly assortative: more-intensively connected countries tend to import from and export to countries that are themselves more connected. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors-such as geographical proximity and trade-agreement co-membership-than on country economic size and/or income. These community-structure findings of the multi-network are especially valuable for efforts to understand past and emerging dynamics in the global food system, especially those that examine potential 'shocks' to global food trade.

Identifying the community structure of the food-trade international multi-network

NASA Astrophysics Data System (ADS)

Torreggiani, S.; Mangioni, G.; Puma, M. J.; Fagiolo, G.

2018-05-01

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of international food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the multi-network’s community structure. Here we find that the individual crop-specific layers of the multi-network have densely connected trading groups, a consistent characteristic over the period 2001–2011. Further, the multi-network is characterized by low variability over this period but with substantial heterogeneity across layers in each year. In particular, the layers are mostly assortative: more-intensively connected countries tend to import from and export to countries that are themselves more connected. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors—such as geographical proximity and trade-agreement co-membership—than on country economic size and/or income. These community-structure findings of the multi-network are especially valuable for efforts to understand past and emerging dynamics in the global food system, especially those that examine potential ‘shocks’ to global food trade.

Yellow Mealworm Protein for Food Purposes - Extraction and Functional Properties

PubMed Central

Zhao, Xue; Vázquez-Gutiérrez, José Luis; Johansson, Daniel P.; Landberg, Rikard; Langton, Maud

2016-01-01

A protocol for extraction of yellow mealworm larvae proteins was established, conditions were evaluated and the resulting protein extract was characterised. The freeze-dried yellow mealworm larvae contained around 33% fat, 51% crude protein and 43% true protein on a dry matter basis. The true protein content of the protein extract was about 75%, with an extraction rate of 70% under optimised extraction conditions using 0.25 M NaOH, a NaOH solution:ethanol defatted worm ratio of 15:1 mL/g, 40°C for 1 h and extraction twice. The protein extract was a good source of essential amino acids. The lowest protein solubility in distilled water solution was found between pH 4 and 5, and increased with either increasing or decreasing pH. Lower solubility was observed in 0.5 M NaCl solution compared with distilled water. The rheological tests indicated that temperature, sample concentration, addition of salt and enzyme, incubation time and pH alterations influenced the elastic modulus of yellow mealworm protein extract (YMPE). These results demonstrate that the functional properties of YMPE can be modified for different food applications. PMID:26840533

Crystal structure of cocosin, a potential food allergen from coconut (Cocos nucifera) (abstract)

USDA-ARS?s Scientific Manuscript database

RATIONALE: Coconut allergy cases have been reported, but only one coconut allergen has been identified. The 11S seed storage proteins belong to one of a few protein families that contain known food allergens in many food of plant sources. Cocosin, the 11S protein from cocosin remains to be character...

Guaifenesin stone matrix proteomics: a protocol for identifying proteins critical to stone formation.

PubMed

Kolbach-Mandel, A M; Mandel, N S; Cohen, S R; Kleinman, J G; Ahmed, F; Mandel, I C; Wesson, J A

2017-04-01

Drug-related kidney stones are a diagnostic problem, since they contain a large matrix (protein) fraction and are frequently incorrectly identified as matrix stones. A urine proteomics study patient produced a guaifenesin stone during her participation, allowing us to both correctly diagnose her disease and identify proteins critical to this drug stone-forming process. The patient provided three random midday urine samples for proteomics studies; one of which contained stone-like sediment with two distinct fractions. These solids were characterized with optical microscopy and Fourier transform infrared spectroscopy. Immunoblotting and quantitative mass spectrometry were used to quantitatively identify the proteins in urine and stone matrix. Infrared spectroscopy showed that the sediment was 60 % protein and 40 % guaifenesin and its metabolite guaiacol. Of the 156 distinct proteins identified in the proteomic studies, 49 were identified in the two stone-components with approximately 50 % of those proteins also found in this patient's urine. Many proteins observed in this drug-related stone have also been reported in proteomic matrix studies of uric acid and calcium containing stones. More importantly, nine proteins were highly enriched and highly abundant in the stone matrix and 8 were reciprocally depleted in urine, suggesting a critical role for these proteins in guaifenesin stone formation. Accurate stone analysis is critical to proper diagnosis and treatment of kidney stones. Many matrix proteins were common to all stone types, but likely not related to disease mechanism. This protocol defined a small set of proteins that were likely critical to guaifenesin stone formation based on their high enrichment and high abundance in stone matrix, and it should be applied to all stone types.

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

PubMed

Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

2012-01-01

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

The Research on the High-Protein Low-Calorie Food Recipe for Teenager Gymnastics Athletes.

PubMed

Wei, Cong

2015-01-01

In order to prevent teenager gymnastics athletes getting fat deposition, weight gain, they should supply a rational food. This paper considers the normal growth and development of athletes, body fat deposition proteins and hunger feel, configured high-protein low-calorie food recipe. Then analysis the composition and the essential amino acids of the recipe. In the final choiced 18 adolescent gymnastics athletes as subjects, to verify the validity of the formula. And analysis the experimental results. The experimental results analysis shows that this recipe basically meets the design requirements.

Optimization of the nutrient content and protein quality of cereal-legume blends for use as complementary foods in Ghana.

PubMed

Suri, Devika J; Tano-Debrah, Kwaku; Ghosh, Shibani A

2014-09-01

Nutritionally adequate complementary foods made from locally available ingredients are of high priority in developing countries, including Ghana. The majority of complementary foods in these countries are cereal-based and are unable to meet the nutrient intakes recommended by the World Health Organization. To evaluate the nutrient content and protein quality of local cereal-legume blends for complementary foods against recommendations and to determine the quantities of additional ingredients required to meet needs by using linear programming. Nine cereal-legume combinations (maize, sorghum, or millet combined with cowpea, peanut, or soybean) and koko (a traditional Ghanaian maize-based complementary food) were evaluated based on the macronutrient targets for a daily ration of complementary food for the age group 12 to 24 months: 264 kcal, 6.5 g of protein, and 8.2 to 11.7 g of fat. Protein quality was assessed by the Protein Digestibility Corrected Amino Acid Score (PDCAAS). Linear programming was then used to determine the amounts of additional oil, sugar, and lysine needed to meet macronutrient requirements. No traditional cereal-legume food met all complementary food macronutrient requirements on its own. Cereal-legume blends made with peanut or cowpeas were low in quality protein, while those with soybean were low in fat. Lysine was the limiting amino acid (PDCAAS 0.50 to 0.82) in all blends. Adding lysine increased utilizable protein by 1% to 10% in soybean blends, 35% to 40% in peanut blends, and 14% to 24% in cowpea blends. Peanut-maize, peanut-millet, and all soybean-cereal blends were able to meet macronutrient targets; most micronutrients remained below recommended levels. Traditional cereal-legume blends made from locally available ingredients do not meet energy, quality protein, and fat recommendations for complementary foods; however, such complementary food blends may be optimized to meet nutrient requirements by using linear programming as a tool to

Identifying Unstable Regions of Proteins Involved in Misfolding Diseases

NASA Astrophysics Data System (ADS)

Guest, Will; Cashman, Neil; Plotkin, Steven

2009-05-01

Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G=o model, changes in solvent-accessible surface area, and all-atoms molecular dynamics. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents.

Genomes2Drugs: Identifies Target Proteins and Lead Drugs from Proteome Data

PubMed Central

Toomey, David; Hoppe, Heinrich C.; Brennan, Marian P.; Nolan, Kevin B.; Chubb, Anthony J.

2009-01-01

Background Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. Methodology/Principal Findings To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i) homologous to previously crystallized proteins or (ii) targets of known drugs, but are (iii) not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. Conclusions/Significance Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines. This free online resource helps in the identification of potential drug targets. Importantly, the program further highlights proteins that are likely to be inhibited by FDA-approved drugs. These drugs can then be rapidly moved into Phase IV clinical studies under ‘change-of-application’ patents. PMID:19593435

Impact of antinutritional factors in food proteins on the digestibility of protein and the bioavailability of amino acids and on protein quality.

PubMed

Sarwar Gilani, G; Wu Xiao, Chao; Cockell, Kevin A

2012-08-01

Dietary antinutritional factors have been reported to adversely affect the digestibility of protein, bioavailability of amino acids and protein quality of foods. Published data on these negative effects of major dietary antinutritional factors are summarized in this manuscript. Digestibility and the quality of mixed diets in developing countries are considerably lower than of those in developed regions. For example, the digestibility of protein in traditional diets from developing countries such as India, Guatemala and Brazil is considerably lower compared to that of protein in typical North American diets (54-78 versus 88-94 %). Poor digestibility of protein in the diets of developing countries, which are based on less refined cereals and grain legumes as major sources of protein, is due to the presence of less digestible protein fractions, high levels of insoluble fibre, and/or high concentrations of antinutritional factors present endogenously or formed during processing. Examples of naturally occurring antinutritional factors include glucosinolates in mustard and canola protein products, trypsin inhibitors and haemagglutinins in legumes, tannins in legumes and cereals, gossypol in cottonseed protein products, and uricogenic nucleobases in yeast protein products. Heat/alkaline treatments of protein products may yield Maillard reaction compounds, oxidized forms of sulphur amino acids, D-amino acids and lysinoalanine (LAL, an unnatural nephrotoxic amino acid derivative). Among common food and feed protein products, soyabeans are the most concentrated source of trypsin inhibitors. The presence of high levels of dietary trypsin inhibitors from soyabeans, kidney beans or other grain legumes have been reported to cause substantial reductions in protein and amino acid digestibility (up to 50 %) and protein quality (up to 100 %) in rats and/or pigs. Similarly, the presence of high levels of tannins in sorghum and other cereals, fababean and other grain legumes can cause

Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy.

PubMed

Marenholz, Ingo; Grosche, Sarah; Kalb, Birgit; Rüschendorf, Franz; Blümchen, Katharina; Schlags, Rupert; Harandi, Neda; Price, Mareike; Hansen, Gesine; Seidenberg, Jürgen; Röblitz, Holger; Yürek, Songül; Tschirner, Sebastian; Hong, Xiumei; Wang, Xiaobin; Homuth, Georg; Schmidt, Carsten O; Nöthen, Markus M; Hübner, Norbert; Niggemann, Bodo; Beyer, Kirsten; Lee, Young-Ae

2017-10-20

Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region. Stratifying the results for the causative food demonstrates that association of the HLA locus is peanut allergy-specific whereas the other four loci increase the risk for any food allergy. Variants in the SERPINB gene cluster are associated with SERPINB10 expression in leukocytes. Moreover, SERPINB genes are highly expressed in the esophagus. All identified loci are involved in immunological regulation or epithelial barrier function, emphasizing the role of both mechanisms in food allergy.

Nutrition. Michigan School Food Service Training Manual.

ERIC Educational Resources Information Center

Michigan State Univ., East Lansing. Cooperative Extension Service.

Definitions, advantages, and functions of nutrition are the starting point for this food service training manual, which includes lessons on proteins, carbohydrates, minerals, and water- and fat-soluble vitamins. Energy foods for child nutrition programs are also identified, as are balanced diets and meal pattern guidelines. Class activities,…

Food protein-induced enterocolitis syndrome by fish: Not necessarily a restricted diet.

PubMed

Infante, S; Marco-Martín, G; Sánchez-Domínguez, M; Rodríguez-Fernández, A; Fuentes-Aparicio, V; Alvarez-Perea, A; Cabrera-Freitag, P; Morales-Cabeza, C; Zubeldia, J M; Zapatero, L

2018-03-01

Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated gastrointestinal food hypersensitivity usually due to cow's milk or soy. Recent researches show that fish is 1 of the most important triggers of FPIES in the Mediterranean countries. Due to the risk of multiple-food FPIES, avoiding foods in the same category or that often occur together may be reasonable. The aim of this study was to evaluate the evolution and follow-up of FPIES related to fish over a period of 20 years. We describe the clinical features of our population, discuss different approaches to oral food challenges, and analyze the possibility of introducing the culprit fish or other nonrelated fish to avoid unnecessary restricted diets. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems

PubMed Central

MacPherson, Jamie I.; Dickerson, Jonathan E.; Pinney, John W.; Robertson, David L.

2010-01-01

Human immunodeficiency virus type 1 (HIV-1) exploits a diverse array of host cell functions in order to replicate. This is mediated through a network of virus-host interactions. A variety of recent studies have catalogued this information. In particular the HIV-1, Human Protein Interaction Database (HHPID) has provided a unique depth of protein interaction detail. However, as a map of HIV-1 infection, the HHPID is problematic, as it contains curation error and redundancy; in addition, it is based on a heterogeneous set of experimental methods. Based on identifying shared patterns of HIV-host interaction, we have developed a novel methodology to delimit the core set of host-cellular functions and their associated perturbation from the HHPID. Initially, using biclustering, we identify 279 significant sets of host proteins that undergo the same types of interaction. The functional cohesiveness of these protein sets was validated using a human protein-protein interaction network, gene ontology annotation and sequence similarity. Next, using a distance measure, we group host protein sets and identify 37 distinct higher-level subsystems. We further demonstrate the biological significance of these subsystems by cross-referencing with global siRNA screens that have been used to detect host factors necessary for HIV-1 replication, and investigate the seemingly small intersect between these data sets. Our results highlight significant host-cell subsystems that are perturbed during the course of HIV-1 infection. Moreover, we characterise the patterns of interaction that contribute to these perturbations. Thus, our work disentangles the complex set of HIV-1-host protein interactions in the HHPID, reconciles these with siRNA screens and provides an accessible and interpretable map of infection. PMID:20686668

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

PubMed Central

Shanahan, Hugh P.; Garcia, Mario A.; Jones, Susan; Thornton, Janet M.

2004-01-01

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix–turn-helix (HTH), helix–hairpin–helix (HhH) and helix–loop–helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif. PMID:15356290

Unique secreted–surface protein complex of Lactobacillus rhamnosus, identified by phage display

PubMed Central

Gagic, Dragana; Wen, Wesley; Collett, Michael A; Rakonjac, Jasna

2013-01-01

Proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. Genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. Here, we used phage display to identify a pair of interacting extracellular proteins in the probiotic bacterium Lactobacillus rhamnosus HN001. A secreted protein, SpcA, containing two bacterial immunoglobulin-like domains type 3 (Big-3) and a domain distantly related to plant pathogen response domain 1 (PR-1-like) was identified by screening of an L. rhamnosus HN001 library using HN001 cells as bait. The SpcA-“docking” protein, SpcB, was in turn detected by another phage display library screening, using purified SpcA as bait. SpcB is a 3275-residue cell-surface protein that contains general features of large glycosylated Serine-rich adhesins/fibrils from gram-positive bacteria, including the hallmark signal sequence motif KxYKxGKxW. Both proteins are encoded by genes within a L. rhamnosus-unique gene cluster that distinguishes this species from other lactobacilli. To our knowledge, this is the first example of a secreted-docking protein pair identified in lactobacilli. PMID:23233310

Identifying sustainable foods: the relationship between environmental impact, nutritional quality, and prices of foods representative of the French diet.

PubMed

Masset, Gabriel; Soler, Louis-Georges; Vieux, Florent; Darmon, Nicole

2014-06-01

Sustainable diets, as defined by the Food and Agriculture Organization, need to combine environment, nutrition, and affordability dimensions. However, it is unknown whether these dimensions are compatible, and no guidance is available in the official recommendations. To identify foods with compatible sustainability dimensions. For 363 of the most commonly consumed foods in the Second French Individual and National Study on Food Consumption, environmental impact indicators (ie, greenhouse gas [GHG] emissions, acidification, and eutrophication), and prices were collected. The nutritional quality of the foods was assessed by calculating the score for the nutritional adequacy of individual foods (SAIN) to score for disqualifying nutrients (LIM) ratio. A sustainability score based on the median GHG emissions, price, and SAIN:LIM was calculated for each food; the foods with the best values for all three variables received the highest score. The environmental indicators were strongly and positively correlated. Meat, fish, and eggs and dairy products had the strongest influence on the environment; starchy foods, legumes, and fruits and vegetables had the least influence. GHG emissions were inversely correlated with SAIN:LIM (r=-0.37) and positively correlated with price per kilogram (r=0.59); the correlation with price per kilocalorie was null. This showed that foods with a heavy environmental impact tend to have lower nutritional quality and a higher price per kilogram but not a lower price per kilocalorie. Using price per kilogram, 94 foods had a maximum sustainability score, including most plant-based foods and excluding all foods with animal ingredients except milk, yogurt, and soups. Using price per kilocalorie restricted the list to 42 foods, including 52% of all starchy foods and legumes but only 11% of fruits and vegetables (mainly 100% fruit juices). Overall, the sustainability dimensions seemed to be compatible when considering price per kilogram of food. However

Sorghum Proteins: The Concentration, Isolation, Modification and Food Applications of Kafirins

USDA-ARS?s Scientific Manuscript database

Celiac disease is a serious condition affecting millions of individuals. Those afflicted with these illnesses are resigned to a lifelong avoidance of products containing gluten, the storage protein found in cereal grains wheat, rye and barley. Since many food products contain gluten, these individ...

Insect (food) allergy and allergens.

PubMed

de Gier, Steffie; Verhoeckx, Kitty

2018-05-03

Insects represent an alternative for meat and fish in satisfying the increasing demand for sustainable sources of nutrition. Approximately two billion people globally consume insects. They are particularly popular in Asia, Latin America, and Africa. Most research on insect allergy has focussed on occupational or inhalation allergy. Research on insect food safety, including allergenicity, is therefore of great importance. The objective of this review is to provide an overview of cases reporting allergy following insect ingestion, studies on food allergy to insects, proteins involved in insect allergy including cross-reactive proteins, and the possibility to alter the allergenic potential of insects by food processing and digestion. Food allergy to insects has been described for silkworm, mealworm, caterpillars, Bruchus lentis, sago worm, locust, grasshopper, cicada, bee, Clanis bilineata, and the food additive carmine, which is derived from female Dactylopius coccus insects. For cockroaches, which are also edible insects, only studies on inhalation allergy have been described. Various insect allergens have been identified including tropomyosin and arginine kinase, which are both pan-allergens known for their cross-reactivity with homologous proteins in crustaceans and house dust mite. Cross-reactivity and/or co-sensitization of insect tropomyosin and arginine kinase has been demonstrated in house dust mite and seafood (e.g. prawn, shrimp) allergic patients. In addition, many other (allergenic) species (various non-edible insects, arachnids, mites, seafoods, mammals, nematoda, trematoda, plants, and fungi) have been identified with sequence alignment analysis to show potential cross-reactivity with allergens of edible insects. It was also shown that thermal processing and digestion did not eliminate insect protein allergenicity. Although purified natural allergens are scarce and yields are low, recombinant allergens from cockroach, silkworm, and Indian mealmoth are

Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

PubMed Central

Antrobus, Robin; Hirst, Jennifer; Bhumbra, Gary S.; Kozik, Patrycja; Jackson, Lauren P.; Sahlender, Daniela A.

2012-01-01

Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions. PMID:22472443

Development of satiating and palatable high-protein meat products by using experimental design in food technology

PubMed Central

Sivertsen, Hanne Kristine; Ueland, Øydis; Westad, Frank

2010-01-01

Background and objectives Foods high in protein are known to satiate more fully than foods high in other constituents. One challenge with these types of food is the degree of palatability. This study was aimed at developing the frankfurter style of sausages that would regulate food intake as well as being the preferred food choice of the consumer. Design and measures 16 sausage varieties with commercial (PE% 20) or higher amount of protein (PE% 40), being modified with vegetable fat (3% of rapeseed oil), and smoked or not, underwent a sensory descriptive analysis, in which the information was used to choose a subsample of four sausages for a satiety test. Twenty-seven subjects were recruited based on liking and frequency of sausage consumption. The participants ranged in age from 20 to 28, and in body mass index (BMI) between 19.6 and 30.9. The students were served a sausage meal for five consecutive days and then filled out a questionnaire to describe their feelings of hunger, satiety, fullness, desire to eat an their prospective consumption on a visual analogue scale (VAS) starting from right before, right after the meal, every half hour for 4 h until the next meal was served, and right after the second meal. Results and conclusion The higher protein sausages were less juicy, oily, fatty, adhesive, but harder and more granular than with lower amount of protein. The high-protein sausages were perceived as more satiating the first 90 min after the first meal. Some indication of satiety effect of added oil versus meat fat. No significant differences in liking among the four sausage varieties. PMID:21116345

Development of a novel scoring system for identifying emerging chemical risks in the food chain.

PubMed

Oltmanns, J; Licht, O; Bitsch, A; Bohlen, M-L; Escher, S E; Silano, V; MacLeod, M; Serafimova, R; Kass, G E N; Merten, C

2018-02-21

The European Food Safety Authority (EFSA) is responsible for risk assessment of all aspects of food safety, including the establishment of procedures aimed at the identification of emerging risks to food safety. Here, a scoring system was developed for identifying chemicals registered under the European REACH Regulation that could be of potential concern in the food chain using the following parameters: (i) environmental release based on maximum aggregated tonnages and environmental release categories; (ii) biodegradation in the environment; (iii) bioaccumulation and in vivo and in vitro toxicity. The screening approach was tested on 100 data-rich chemicals registered under the REACH Regulation at aggregated volumes of at least 1000 tonnes per annum. The results show that substance-specific data generated under the REACH Regulation can be used to identify potential emerging risks in the food chain. After application of the screening procedure, priority chemicals can be identified as potentially emerging risk chemicals through the integration of exposure, environmental fate and toxicity. The default approach is to generate a single total score for each substance using a predefined weighting scenario. However, it is also possible to use a pivot table approach to combine the individual scores in different ways that reflect user-defined priorities, which enables a very flexible, iterative definition of screening criteria. Possible applications of the approaches are discussed using illustrative examples. Either approach can then be followed by in-depth evaluation of priority substances to ensure the identification of substances that present a real emerging chemical risk in the food chain.

Melatonin identified in meats and other food stuffs: potentially nutritional impact.

PubMed

Tan, Dun-Xian; Zanghi, Brian M; Manchester, Lucien C; Reiter, Russel J

2014-09-01

Melatonin has been identified in primitive photosynthetic bacteria, fungi, plants, and animals including humans. Vegetables, fruits, cereals, wine, and beers all contain melatonin. However, the melatonin content in meats has not been reported previously. Here, for the first time, we report melatonin in meats, eggs, colostrum, and in other edible food products. The levels of melatonin measured by HPLC, in lamb, beef, pork, chicken, and fish, are comparable to other food stuffs (in the range of ng/g). These levels are significantly higher than melatonin concentrations in the blood of vertebrates. As melatonin is a potent antioxidant, its presence in the meat could contribute to shelf life duration as well as preserve their quality and taste. In addition, the consumption of these foods by humans or animals could have health benefits considering the important functions of melatonin as a potent free radical scavenger and antioxidant. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Proteomic analysis identifies insulin-like growth factor-binding protein-related protein-1 as a podocyte product.

PubMed

Matsumoto, Takayuki; Hess, Sonja; Kajiyama, Hiroshi; Sakairi, Toru; Saleem, Moin A; Mathieson, Peter W; Nojima, Yoshihisa; Kopp, Jeffrey B

2010-10-01

The podocyte secretory proteome may influence the phenotype of adjacent podocytes, endothelial cells, parietal epithelial cells, and tubular epithelial cells but has not been systematically characterized. We have initiated studies to characterize this proteome, with the goal of further understanding the podocyte cell biology. We cultured differentiated conditionally immortalized human podocytes and subjected the proteins in conditioned medium to mass spectrometry. At a false discovery rate of <3%, we identified 111 candidates from conditioned medium, including 44 proteins that have signal peptides or are described as secreted proteins in the UniProt database. As validation, we confirmed that one of these proteins, insulin-like growth factor-binding protein-related protein-1 (IGFBP-rP1), was expressed in mRNA and protein of cultured podocytes. In addition, transforming growth factor-β1 stimulation increased IGFBP-rP1 in conditioned medium. We analyzed IGFBP-rP1 glomerular expression in a mouse model of human immunodeficiency virus-associated nephropathy. IGFBP-rP1 was absent from podocytes of normal mice and was expressed in podocytes and pseudocrescents of transgenic mice, where it was coexpressed with desmin, a podocyte injury marker. We conclude that IGFBP-rP1 may be a product of injured podocytes. Further analysis of the podocyte secretory proteome may identify biomarkers of podocyte injury.

Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mudenda, Lwiindi; Aguilar Pierle, Sebastian; Turse, Joshua E.

2014-08-07

Dermacentor andersoni, known as the Rocky Mountain wood tick, is found in the western United States and transmits pathogens that cause diseases of veterinary and public health importance including Rocky Mountain spotted fever, tularemia, Colorado tick fever and bovine anaplasmosis. Tick saliva is known to modulate both innate and acquired immune responses, enabling ticks to feed for several days without detection. During feeding ticks subvert host defences such as hemostasis and inflammation, which would otherwise result in coagulation, wound repair and rejection of the tick. Molecular characterization of the proteins and pharmacological molecules secreted in tick saliva offers an opportunitymore » to develop tick vaccines as an alternative to the use of acaricides, as well as new anti-inflammatory drugs. We performed proteomics informed by transcriptomics to identify D. andersoni saliva proteins that are secreted during feeding. The transcript data generated a database of 21,797 consensus sequences, which we used to identify 677 proteins secreted in the saliva of D. andersoni ticks fed for 2 and 5 days, following proteomic investigations of whole saliva using mass spectrometry. Salivary gland transcript levels of unfed ticks were compared with 2 and 5 day fed ticks to identify genes upregulated early during tick feeding. We cross-referenced the proteomic data with the transcriptomic data to identify 157 proteins of interest for immunomodulation and blood feeding. Proteins of unknown function as well as known immunomodulators were identified.« less

Anabolic sensitivity of postprandial muscle protein synthesis to the ingestion of a protein-dense food is reduced in overweight and obese young adults.

PubMed

Beals, Joseph W; Sukiennik, Richard A; Nallabelli, Julian; Emmons, Russell S; van Vliet, Stephan; Young, Justin R; Ulanov, Alexander V; Li, Zhong; Paluska, Scott A; De Lisio, Michael; Burd, Nicholas A

2016-10-01

Excess body fat diminishes muscle protein synthesis rates in response to hyperinsulinemic-hyperaminoacidemic clamps. However, muscle protein synthetic responses after the ingestion of a protein-dense food source across a range of body mass indexes (BMIs) have not been compared. We compared the myofibrillar protein synthetic response and underlying nutrient-sensing mechanisms after the ingestion of lean pork between obese, overweight, and healthy-weight adults. Ten healthy-weight [HW; BMI (in kg/m 2 ): 22.7 ± 0.4], 10 overweight (OW; BMI: 27.1 ± 0.5), and 10 obese (OB; BMI: 35.9 ± 1.3) adults received primed continuous l-[ring- 13 C 6 ]phenylalanine infusions. Blood and muscle biopsy samples were collected before and after the ingestion of 170 g pork (36 g protein and 3 g fat) to assess skeletal muscle anabolic signaling, amino acid transporters [large neutral and small neutral amino acid transporters (LAT1, SNAT2) and CD98], and myofibrillar protein synthesis. At baseline, OW and OB groups showed greater relative amounts of mammalian target of rapamycin complex 1 (mTORC1) protein than the HW group. Pork ingestion increased mTORC1 phosphorylation only in the HW group (P = 0.001). LAT1 and SNAT2 protein content increased during the postprandial period in all groups (time effect, P < 0.05). Basal myofibrillar protein synthetic responses were similar between groups (P = 0.43). However, myofibrillar protein synthetic responses (0-300 min) were greater in the HW group (1.6-fold; P = 0.005) after pork ingestion than in the OW and OB groups. There is a diminished myofibrillar protein synthetic response to the ingestion of protein-dense food in overweight and obese adults compared with healthy-weight controls. These data indicate that impaired postprandial myofibrillar protein synthetic response may be an early defect with increasing fat mass, potentially dependent on altered anabolic signals, that reduces muscle sensitivity to food ingestion. This trial was registered

Use of mass spectrometry fingerprinting to identify urinary metabolites after consumption of specific foods.

PubMed

Lloyd, Amanda J; Favé, Gaëlle; Beckmann, Manfred; Lin, Wanchang; Tailliart, Kathleen; Xie, Long; Mathers, John C; Draper, John

2011-10-01

The lack of robust biological markers of dietary exposure hinders the quantitative understanding of causal relations between diet and health. We aimed to develop an efficient procedure to discover metabolites in urine that may have future potential as biomarkers of acute exposure to foods of high public health importance. Twenty-four participants were provided with a test breakfast in which the cereal component of a standardized breakfast was replaced by 1 of 4 foods of high public health importance; 1.5-, 3-, and 4.5-h postprandial urine samples were collected. Flow infusion electrospray-ionization mass spectrometry followed by supervised multivariate data analysis was used to discover signals resulting from consumption of each test food. Fasted-state urine samples provided a universal comparator for food biomarker lead discovery in postprandial urine. The filtering of data features associated with consumption of the common components of the standardized breakfast improved discrimination models and readily identified metabolites that showed consumption of specific test foods. A combination of trimethylamine-N-oxide and 1-methylhistidine was associated with salmon consumption. Novel ascorbate derivatives were discovered in urine after consumption of either broccoli or raspberries. Sulphonated caffeic acid and sulphonated methyl-epicatechin concentrations increased dramatically after consumption of raspberries. This biomarker lead discovery strategy can identify urinary metabolites associated with acute exposure to individual foods. Future studies are required to validate the specificity and utility of potential biomarkers in an epidemiologic context.

Intraduodenal Administration of Intact Pea Protein Effectively Reduces Food Intake in Both Lean and Obese Male Subjects

PubMed Central

Geraedts, Maartje C. P.; Troost, Freddy J.; Munsters, Marjet J. M.; Stegen, Jos H. C. H.; de Ridder, Rogier J.; Conchillo, Jose M.; Kruimel, Joanna W.; Masclee, Ad A. M.; Saris, Wim H. M.

2011-01-01

Background Human duodenal mucosa secretes increased levels of satiety signals upon exposure to intact protein. However, after oral protein ingestion, gastric digestion leaves little intact proteins to enter the duodenum. This study investigated whether bypassing the stomach, through intraduodenal administration, affects hormone release and food-intake to a larger extent than orally administered protein in both lean and obese subjects. Methods Ten lean (BMI:23.0±0.7 kg/m2) and ten obese (BMI:33.4±1.4 kg/m2) healthy male subjects were included. All subjects randomly received either pea protein solutions (250 mg/kg bodyweight in 0.4 ml/kg bodyweight of water) or placebo (0.4 ml/kg bodyweight of water), either orally or intraduodenally via a naso-duodenal tube. Appetite-profile, plasma GLP-1, CCK, and PYY concentrations were determined over a 2 h period. After 2 h, subjects received an ad-libitum meal and food-intake was recorded. Results CCK levels were increased at 10(p<0.02) and 20(p<0.01) minutes after intraduodenal protein administration (IPA), in obese subjects, compared to lean subjects, but also compared to oral protein administration (OPA)(p<0.04). GLP-1 levels increased after IPA in obese subjects after 90(p<0.02) to 120(p<0.01) minutes, compared to OPA. Food-intake was reduced after IPA both in lean and obese subjects (-168.9±40 kcal (p<0.01) and −298.2±44 kcal (p<0.01), respectively), compared to placebo. Also, in obese subjects, food-intake was decreased after IPA (−132.6±42 kcal; p<0.01), compared to OPA. Conclusions Prevention of gastric proteolysis through bypassing the stomach effectively reduces food intake, and seems to affect obese subjects to a greater extent than lean subjects. Enteric coating of intact protein supplements may provide an effective dietary strategy in the prevention/treatment of obesity. PMID:21931864

Protein expression profiling identifies molecular targets of quercetin as a major dietary flavonoid in human colon cancer cells.

PubMed

Wenzel, Uwe; Herzog, Angelika; Kuntz, Sabine; Daniel, Hannelore

2004-07-01

A high dietary intake of plant foods is thought to contribute to the prevention of colorectal cancers in humans and flavonoids as part of such a diet are considered to contribute to those protective effects. Quercetin is a major dietary flavonoid consumed with a diet rich in onions, tea, and apples. We used HT-29 human colon cancer cells and investigated the effects of quercetin on proliferation, apoptosis, and differentiation as processes shown to be disregulated during cancer development. To identify the cellular targets of quercetin action, two-dimensional gel electrophoresis was performed and proteins altered in expression level after quercetin exposure of cells were identified by mass spectrometry of peptide fragments generated by tryptic digestion. Quercetin inhibited the proliferation of HT-29 cells with an IC(50)-value of 81.2 +/- 6.6 microM. Cell differentiation based on surface expression of alkaline phosphatase was enhanced 4-fold and the activity of the pro-apoptotic effector caspase-3 increased 3-fold. Those effects were associated with the regulation of heat-shock proteins and annexins shown to both play a crucial role in the process of apoptosis. Cytoskeletal caspase substrates were found as regulated as well and various proteins involved in intermediary metabolism and in gene regulation showed altered steady-state expression levels upon quercetin treatment of cells. In conclusion, quercetin alters the levels of a variety of proteins involved in growth, differentiation, and apoptosis of colon cancer cells. Their identification as molecular targets of quercetin may explain the anti-cancer activities of this flavonoid.

Juvenile hormone-binding proteins of Melanoplus bivittatus identified by EFDA photoaffinity labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winder, B.S.

1988-01-01

Proteins that bind juvenile hormone in the hemolymph and fat body of the grasshopper, Melanoplus bivittatus were identified by photoaffinity labeling with radiolabeled epoxyfarnesyl diazoacetate ({sup 3}H-EFDA), and were characterized by electrophoretic analysis. A protocol was developed which allowed detection of {sup 3}H-EFDA that was covalently linked to proteins upon exposure to ultraviolet light at 254 nm. Quantification of protein-linked {sup 3}H-EFDA by liquid scintillation spectrometry took advantage of the differential solubility of unlinked {sup 3}H-EFDA in toluene alone, and of the protein-linked {sup 3}H-EFDA in toluene plus the detergent, Triton X-100. Competition between EFDA and juvenile hormone (JH) formore » binding to JH-specific binding sites was measured by hydroxyapatite protein binding assays in the presence of radiolabeled JH or EFDA and competing non-radiolabeled hormone. The protein-linked EFDA was detected on fluorograms of SDS or nondenaturing polyacrylamide gels (PAGE), and by liquid scintillation spectrometry of membranes to which the proteins had been electrophoretically transferred. Proteins which specifically bound JH were identified by photolabeling proteins in the presence and absence of nonlabeled JH-III.« less

Relative validity of a food frequency questionnaire to identify dietary patterns in an adult Mexican population.

PubMed

Denova-Gutiérrez, Edgar; Tucker, Katherine L; Salmerón, Jorge; Flores, Mario; Barquera, Simón

2016-01-01

To examine the validity of a semi-quantitative food frequency questionnaire (SFFQ) to identify dietary patterns in an adult Mexican population. A 140-item SFFQ and two 24-hour dietary recalls (24DRs) were administered. Foods were categorized into 29 food groups used to derive dietary patterns via factor analysis. Pearson and intraclass correlations coefficients between dietary pattern scores identified from the SFFQ and 24DRs were assessed. Pattern 1 was high in snacks, fast food, soft drinks, processed meats and refined grains; pattern 2 was high in fresh vegetables, fresh fruits, and dairy products; and pattern 3 was high in legumes, eggs, sweetened foods and sugars. Pearson correlation coefficients between the SFFQ and the 24DRs for these patterns were 0.66 (P<0.001), 0.41 (P<0.001) and 0.29 (P=0.193) respectively. Our data indicate reasonable validity of the SFFQ, using factor analysis, to derive major dietary patterns in comparison with two 24DR.

A novel approach to identify genes that determine grain protein deviation in cereals.

PubMed

Mosleth, Ellen F; Wan, Yongfang; Lysenko, Artem; Chope, Gemma A; Penson, Simon P; Shewry, Peter R; Hawkesford, Malcolm J

2015-06-01

Grain yield and protein content were determined for six wheat cultivars grown over 3 years at multiple sites and at multiple nitrogen (N) fertilizer inputs. Although grain protein content was negatively correlated with yield, some grain samples had higher protein contents than expected based on their yields, a trait referred to as grain protein deviation (GPD). We used novel statistical approaches to identify gene transcripts significantly related to GPD across environments. The yield and protein content were initially adjusted for nitrogen fertilizer inputs and then adjusted for yield (to remove the negative correlation with protein content), resulting in a parameter termed corrected GPD. Significant genetic variation in corrected GPD was observed for six cultivars grown over a range of environmental conditions (a total of 584 samples). Gene transcript profiles were determined in a subset of 161 samples of developing grain to identify transcripts contributing to GPD. Principal component analysis (PCA), analysis of variance (ANOVA) and means of scores regression (MSR) were used to identify individual principal components (PCs) correlating with GPD alone. Scores of the selected PCs, which were significantly related to GPD and protein content but not to the yield and significantly affected by cultivar, were identified as reflecting a multivariate pattern of gene expression related to genetic variation in GPD. Transcripts with consistent variation along the selected PCs were identified by an approach hereby called one-block means of scores regression (one-block MSR). © 2014 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks.

PubMed

Le, Duc-Hau

2015-01-01

Protein complexes formed by non-covalent interaction among proteins play important roles in cellular functions. Computational and purification methods have been used to identify many protein complexes and their cellular functions. However, their roles in terms of causing disease have not been well discovered yet. There exist only a few studies for the identification of disease-associated protein complexes. However, they mostly utilize complicated heterogeneous networks which are constructed based on an out-of-date database of phenotype similarity network collected from literature. In addition, they only apply for diseases for which tissue-specific data exist. In this study, we propose a method to identify novel disease-protein complex associations. First, we introduce a framework to construct functional similarity protein complex networks where two protein complexes are functionally connected by either shared protein elements, shared annotating GO terms or based on protein interactions between elements in each protein complex. Second, we propose a simple but effective neighborhood-based algorithm, which yields a local similarity measure, to rank disease candidate protein complexes. Comparing the predictive performance of our proposed algorithm with that of two state-of-the-art network propagation algorithms including one we used in our previous study, we found that it performed statistically significantly better than that of these two algorithms for all the constructed functional similarity protein complex networks. In addition, it ran about 32 times faster than these two algorithms. Moreover, our proposed method always achieved high performance in terms of AUC values irrespective of the ways to construct the functional similarity protein complex networks and the used algorithms. The performance of our method was also higher than that reported in some existing methods which were based on complicated heterogeneous networks. Finally, we also tested our method with

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2011 CFR

2011-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2013 CFR

2013-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2014 CFR

2014-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2012 CFR

2012-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2010 CFR

2010-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

Using a research framework to identify knowledge gaps in research on food marketing to children in Australia.

PubMed

Chapman, Kathy; Kelly, Bridget; King, Lesley

2009-06-01

Research in the field of food marketing to children requires a better understanding of the research gaps in order to inform policy development. The purpose of this paper was to propose a framework for classifying food marketing research, using Australian research on food marketing to children to demonstrate how this framework can be used to determine knowledge gaps. A literature review of research databases and 'grey' material was conducted to identify research from the previous 10 years. Studies were classified according to their research focus, and media type, as either: exposure, including content analyses; effects of exposure, including opinions, attitudes and actions resulting from food marketing exposure; regulations, including the type and level of regulation that applies to food marketing; or breaches of regulations, including instances where marketing regulations have been violated. The majority of Australian research on food marketing to children has focused on television advertising and exposure research. Research has consistently shown that the content of food marketing directed at children is predominately for unhealthy foods. There is a lack of research on the effects of food marketing, which would be valuable to inform policy. The development of a logical framework for food marketing research allows for the identification of research gaps and enables research priorities to be identified.

PCR method of detecting pork in foods for verifying allergen labeling and for identifying hidden pork ingredients in processed foods.

PubMed

Tanabe, Soichi; Miyauchi, Eiji; Muneshige, Akemi; Mio, Kazuhiro; Sato, Chikara; Sato, Masahiko

2007-07-01

A PCR method to detect porcine DNA was developed for verifying the allergen labeling of foods and for identifying hidden pork ingredients in processed foods. The primer pair, F2/R1, was designed to detect the gene encoding porcine cytochrome b for the specific detection of pork with high sensitivity. The amplified DNA fragment (130 bp) was specifically detected from porcine DNA, while no amplification occurred with other species such as cattle, chicken, sheep, and horse. When the developed PCR method was used for investigating commercial food products, porcine DNA was clearly detected in those containing pork in the list of ingredients. In addition, 100 ppb of pork in heated gyoza (pork and vegetable dumpling) could be detected by this method. This method is rapid, specific and sensitive, making it applicable for detecting trace amounts of pork in processed foods.

A method for the detection of protein-bound mutagens in food.

PubMed

Ibe, F I; Blowers, S D; Anderson, D; Massey, R

1994-01-01

To investigate the possible presence of protein-bound mutagens in food an analytical procedure has been devised in which the sample is enzymically hydrolysed, fractionated by HPLC and examined by a modified liquid incubation Ames assay. To validate the method MeIQx was added, as a model compound, to beefburger and a recovery of 82% obtained. The limit of detection for protein-bound mutagens was 1 microgram/kg, expressed as equivalents of MeIQx. No detectable mutagenicity was observed when the procedure was applied to samples of well cooked beefburger, irradiated chicken or mycoprotein.

Latest Insights on Food Protein-Induced Enterocolitis Syndrome: An Emerging Medical Condition.

PubMed

Vila Sexto, L

2018-01-01

Food protein-induced enterocolitis syndrome (FPIES) is a type of non-IgE-mediated gastrointestinal food hypersensitivity characterized by profuse vomiting that is frequently associated with pallor or/and lethargy and appears within 1 to 3 hours after ingestion of the offending food. A less frequent chronic form of FPIES is characterized by protracted vomiting, diarrhea, or both accompanied by poor growth. Although FPIES is considered a rare allergic disorder, increasing reports in recent years point to a real increase in incidence, or at least an increased awareness of this condition by pediatricians. The foods most frequently implicated are cow's milk, soy formula, grains, and fish, depending on the geographic area. Diagnosis is based on clinical manifestations and requires a high index of suspicion, since we still lack a diagnostic laboratory tool. Early recognition of FPIES and removal of the offending food are mandatory. International consensus guidelines on diagnosis and management have been published. Prognosis is usually good, with most children tolerating foods before 6 years of age.

Dissecting protein function: an efficient protocol for identifying separation-of-function mutations that encode structurally stable proteins.

PubMed

Lubin, Johnathan W; Rao, Timsi; Mandell, Edward K; Wuttke, Deborah S; Lundblad, Victoria

2013-03-01

Mutations that confer the loss of a single biochemical property (separation-of-function mutations) can often uncover a previously unknown role for a protein in a particular biological process. However, most mutations are identified based on loss-of-function phenotypes, which cannot differentiate between separation-of-function alleles vs. mutations that encode unstable/unfolded proteins. An alternative approach is to use overexpression dominant-negative (ODN) phenotypes to identify mutant proteins that disrupt function in an otherwise wild-type strain when overexpressed. This is based on the assumption that such mutant proteins retain an overall structure that is comparable to that of the wild-type protein and are able to compete with the endogenous protein (Herskowitz 1987). To test this, the in vivo phenotypes of mutations in the Est3 telomerase subunit from Saccharomyces cerevisiae were compared with the in vitro secondary structure of these mutant proteins as analyzed by circular-dichroism spectroscopy, which demonstrates that ODN is a more sensitive assessment of protein stability than the commonly used method of monitoring protein levels from extracts. Reverse mutagenesis of EST3, which targeted different categories of amino acids, also showed that mutating highly conserved charged residues to the oppositely charged amino acid had an increased likelihood of generating a severely defective est3(-) mutation, which nevertheless encoded a structurally stable protein. These results suggest that charge-swap mutagenesis directed at a limited subset of highly conserved charged residues, combined with ODN screening to eliminate partially unfolded proteins, may provide a widely applicable and efficient strategy for generating separation-of-function mutations.

Identify High-Quality Protein Structural Models by Enhanced K-Means.

PubMed

Wu, Hongjie; Li, Haiou; Jiang, Min; Chen, Cheng; Lv, Qiang; Wu, Chuang

2017-01-01

Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K -means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K -means clustering ( SK -means), whereas the other employs squared distance to optimize the initial centroids ( K -means++). Our results showed that SK -means and K -means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K -means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK -means and K -means++ demonstrated substantial improvements relative to results from SPICKER and classical K -means.

Identify High-Quality Protein Structural Models by Enhanced K-Means

PubMed Central

Li, Haiou; Chen, Cheng; Lv, Qiang; Wu, Chuang

2017-01-01

Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K-means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K-means clustering (SK-means), whereas the other employs squared distance to optimize the initial centroids (K-means++). Our results showed that SK-means and K-means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K-means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK-means and K-means++ demonstrated substantial improvements relative to results from SPICKER and classical K-means. PMID:28421198

Use of specific peptide biomarkers for quantitative confirmation of hidden allergenic peanut proteins Ara h 2 and Ara h 3/4 for food control by liquid chromatography-tandem mass spectrometry.

PubMed

Careri, M; Costa, A; Elviri, L; Lagos, J-B; Mangia, A; Terenghi, M; Cereti, A; Garoffo, L Perono

2007-11-01

A liquid chromatography-electrospray-tandem mass spectrometry (LC-ESI-MS-MS) method based on the detection of biomarker peptides from allergenic proteins was devised for confirming and quantifying peanut allergens in foods. Peptides obtained from tryptic digestion of Ara h 2 and Ara h 3/4 proteins were identified and characterized by LC-MS and LC-MS-MS with a quadrupole-time of flight mass analyzer. Four peptides were chosen and investigated as biomarkers taking into account their selectivity, the absence of missed cleavages, the uniform distribution in the Ara h 2 and Ara h 3/4 protein isoforms together with their spectral features under ESI-MS-MS conditions, and good repeatability of LC retention time. Because of the different expression levels, the selection of two different allergenic proteins was proved to be useful in the identification and univocal confirmation of the presence of peanuts in foodstuffs. Using rice crisp and chocolate-based snacks as model food matrix, an LC-MS-MS method with triple quadrupole mass analyzer allowed good detection limits to be obtained for Ara h 2 (5 microg protein g(-1) matrix) and Ara h 3/4 (1 microg protein g(-1) matrix). Linearity of the method was established in the 10-200 microg g(-1) range of peanut proteins in the food matrix investigated. Method selectivity was demonstrated by analyzing tree nuts (almonds, pecan nuts, hazelnuts, walnuts) and food ingredients such as milk, soy beans, chocolate, cornflakes, and rice crisp.

Amino acid composition, score and in vitro protein digestibility of foods commonly consumed in northwest Mexico.

PubMed

Caire-Juvera, Graciela; Vázquez-Ortiz, Francisco A; Grijalva-Haro, Maria I

2013-01-01

A better knowledge of the amino acid composition of foods commonly consumed in different regions is essential to calculate their scores and, therefore, to predict their protein quality. This paper presents the amino acid composition, amino acid score and in vitro protein digestibility of fifteen foods that are commonly consumed in Northwest Mexico. The foods were prepared by the traditional methods and were analyzed by reverse-phase HPLC. The chemical score for each food was determined using the recommendations for children of 1-2 years of age, and the digestibility was evaluated using a multienzyme technique. Lysine was the limiting amino acid in cereal-based products (scores 15 to 54), and methionine and cysteine were limiting in legume products (scores 41 to 47), boiled beef (score = 75) and hamburger (score = 82). The method of preparation had an effect on the content of certain amino acids, some of them increased and others decreased their content. Meat products and regional cheese provided a high amino acid score (scores 67 to 91) and digestibility (80.7 to 87.8%). Bologna, a processed meat product, had a lower digestibility (75.4%). Data on the amino acid composition of foods commonly consumed in Mexico can be used to provide valuable information on food analysis and protein quality, and to contribute to nutrition and health research and health programs. Copyright © AULA MEDICA EDICIONES 2013. Published by AULA MEDICA. All rights reserved.

Identifying and Measuring Food Deserts in Rural Ohio

ERIC Educational Resources Information Center

Mulangu, Francis; Clark, Jill

2012-01-01

The purpose of our article is twofold. First, we introduce a framework for U.S. Extension educators to measure the extent of food access at any scale when information about food carried by retailers is limited. Second, we create a baseline for the Ohio Food Policy Council so that work to increase food access in rural areas will have a benchmark to…

Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools.

PubMed

Felgueiras, Juliana; Silva, Joana Vieira; Fardilha, Margarida

2018-01-16

"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases. Therefore, numerous opportunities have emerged for PPINs as tools for clinical management of diseases: network-based disease classification systems, discovery of biomarkers and identification of therapeutic targets. Despite the great advantages of PPINs, their use is still unrecognised by several researchers who generate high-throughput data to generally characterize interactions in a certain model or to select an interaction to study in detail. We strongly believe that both approaches are not exclusive and that we can use PPINs as a complementary methodology and rich-source of information to the initial study proposal. Here, we suggest a pipeline to deal with Y2H results using bioinformatics tools freely available for academics. Yeast two-hybrid is widely-used to identify protein-protein interactions. Conventionally, the positive clones that result from a yeast two-hybrid screening are sequenced to identify the interactors of the protein of interest (also known as bait protein), and few interactions, thought as potentially relevant for the model in study, are selected for further validation using biochemical methods (e.g. co-immunoprecipitation and co-localization). The huge amount of data that is potentially lost during this conservative approach motivated us to write this tutorial-like review, so that researchers feel encouraged to take advantage of

Hydrolyzed whey protein prevents the development of food allergy to β-lactoglobulin in sensitized mice.

PubMed

Gomes-Santos, Ana Cristina; Fonseca, Roberta Cristelli; Lemos, Luisa; Reis, Daniela Silva; Moreira, Thaís Garcias; Souza, Adna Luciana; Silva, Mauro Ramalho; Silvestre, Marialice Pinto Coelho; Cara, Denise Carmona; Faria, Ana Maria Caetano

2015-01-01

Food allergy is an adverse immune response to dietary proteins. Hydrolysates are frequently used for children with milk allergy. However, hydrolysates effects afterwards are poorly studied. The aim of this study was to investigate the immunological consequences of hydrolyzed whey protein in allergic mice. For that, we developed a novel model of food allergy in BALB/c mice sensitized with alum-adsorbed β-lactoglobulin. These mice were orally challenged with either whey protein or whey hydrolysate. Whey-challenged mice had elevated levels of specific IgE and lost weight. They also presented gut inflammation, enhanced levels of SIgA and IL-5 as well as decreased production of IL-4 and IL-10 in the intestinal mucosa. Conversely, mice challenged with hydrolyzate maintained normal levels of IgE, IL-4 and IL-5 and showed no sign of gut inflammation probably due to increased IL-12 production in the gut. Thus, consumption of hydrolysate prevented the development of clinical signs of food allergy in mice. Copyright © 2015 Elsevier Inc. All rights reserved.

Affinity resins as new tools for identifying target proteins of ascorbic acid.

PubMed

Iwaoka, Yuji; Nishino, Kohei; Ishikawa, Takahiro; Ito, Hideyuki; Sawa, Yoshihiro; Tai, Akihiro

2018-02-12

l-Ascorbic acid (AA) has diverse physiological functions, but little is known about the functional mechanisms of AA. In this study, we synthesized two types of affinity resin on which AA is immobilized in a stable form to identify new AA-targeted proteins, which can provide important clues for elucidating unknown functional mechanisms of AA. To our knowledge, an affinity resin on which AA as a ligand is immobilized has not been prepared, because AA is very unstable and rapidly degraded in an aqueous solution. By using the affinity resins, cytochrome c (cyt c) was identified as an AA-targeted protein, and we showed that oxidized cyt c exhibits specific affinity for AA. These results suggest that two kinds of AA-affinity resin can be powerful tools to identify new target proteins of AA.

Identifying protein biomarkers in predicting disease severity of dengue virus infection using immune-related protein microarray.

PubMed

Soe, Hui Jen; Yong, Yean K; Al-Obaidi, Mazen M Jamil; Raju, Chandramathi Samudi; Gudimella, Ranganath; Manikam, Rishya; Sekaran, Shamala Devi

2018-02-01

Dengue virus is one of the most widespread flaviviruses that re-emerged throughout recent decades. The progression from mild dengue to severe dengue (SD) with the complications such as vascular leakage and hemorrhage increases the fatality rate of dengue. The pathophysiology of SD is not entirely clear. To investigate potential biomarkers that are suggestive of pathogenesis of SD, a small panel of serum samples selected from 1 healthy individual, 2 dengue patients without warning signs (DWS-), 2 dengue patients with warning signs (DWS+), and 5 patients with SD were subjected to a pilot analysis using Sengenics Immunome protein array. The overall fold changes of protein expressions and clustering heat map revealed that PFKFB4, TPM1, PDCL3, and PTPN20A were elevated among patients with SD. Differential expression analysis identified that 29 proteins were differentially elevated greater than 2-fold in SD groups than DWS- and DWS+. From the 29 candidate proteins, pathways enrichment analysis also identified insulin signaling and cytoskeleton pathways were involved in SD, suggesting that the insulin pathway may play a pivotal role in the pathogenesis of SD.

Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food.

PubMed

Agyei, Dominic; Acquah, Caleb; Tan, Kei Xian; Hii, Hieng Kok; Rajendran, Subin R C K; Udenigwe, Chibuike C; Danquah, Michael K

2018-01-01

Food-derived bioactive proteins and peptides have gained acceptance among researchers, food manufacturers and consumers as health-enhancing functional food components that also serve as natural alternatives for disease prevention and/or management. Bioactivity in food proteins and peptides is determined by their conformations and binding characteristics, which in turn depend on their primary and secondary structures. To maintain their bioactivities, the molecular integrity of bioactive peptides must remain intact, and this warrants the study of peptide form and structure, ideally with robust, highly specific and sensitive techniques. Short single-stranded nucleic acids (i.e. aptamers) are known to have high affinity for cognate targets such as proteins and peptides. Aptamers can be produced cost-effectively and chemically derivatized to increase their stability and shelf life. Their improved binding characteristics and minimal modification of the target molecular signature suggests their suitability for real-time detection of conformational changes in both proteins and peptides. This review discusses the developmental progress of systematic evolution of ligands by exponential enrichment (SELEX), an iterative technology for generating cost-effective aptamers with low dissociation constants (K d ) for monitoring the form and structure of bioactive proteins and peptides. The review also presents case studies of this technique in monitoring the structural stability of bioactive peptide formulations to encourage applications in functional foods. The challenges and potential of aptamers in this research field are also discussed. Graphical abstract Advancing bioactive proteins and peptide functionality via aptameric ligands.

Salmonella infections in food workers identified through routine Public Health Surveillance in Minnesota: impact on outbreak recognition.

PubMed

Medus, Carlota; Smith, Kirk E; Bender, Jeffrey B; Leano, Fe; Hedberg, Craig W

2010-11-01

The frequency of Salmonella-infected food workers identified through routine surveillance from 1997 to 2004 in Minnesota was determined in order to evaluate the impact of surveillance on the detection of outbreaks in restaurants and to quantify the duration of Salmonella shedding in stool. Of 4,976 culture-confirmed Salmonella cases reported to the Minnesota Department of Health, 110 (2.2%) were identified as food workers; this was less than one-half the number expected based on the incidence of Salmonella in the general population. Twenty food workers (18%) were associated with outbreaks. Twelve were involved in nine independent outbreaks at the restaurants where they worked. The identification of the index food worker in six of these outbreaks was critical to the initiation of outbreak investigations that revealed much larger problems. Among food workers who submitted specimens until at least one negative result was obtained (n = 69), the median duration of shedding was 22 days (range, 1 to 359 days). Among the four most common serotypes (Enteritidis, Typhimurium, Heidelberg, and Newport) the median duration of shedding was significantly longer for Salmonella Newport (80 days; P = 0.02) and for Salmonella Enteritidis (32 days; P = 0.04) than for Salmonella Heidelberg (8 days). Food workers should be considered an important source of Salmonella transmission, and those identified through surveillance should raise a high index of suspicion of a possible outbreak at their place of work. Food service managers need to be alert to Salmonella-like illnesses among food workers to facilitate prevention and control efforts, including exclusion of infected food workers or restriction of their duties.

Method for early detection of infectious mononucleosis by identifying inmono proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willard, K. E.

1984-10-02

Early detection of infectious mononucleosis is carried out using a sample of human blood by isolating and identifying the presence of Inmono proteins in the sample from a two-dimensional protein map with the proteins being characterized by having isoelectric banding as measured in urea of about -16 to -17 with respect to certain isoelectric point standards and molecular mass of about 70 to 75 K daltons as measured in the presence of sodium dodecylsulfate containing polyacrylamide gels, the presence of the Inmono proteins being correlated with the existence of infectious mononucleosis.

Method for early detection of infectious mononucleosis by identifying Inmono proteins

DOEpatents

Willard, Karen E.

1984-01-01

Early detection of infectious mononucleosis is carried out using a sample of human blood by isolating and identifying the presence of Inmono proteins in the sample from a two-dimensional protein map with the proteins being characterized by having isoelectric banding as measured in urea of about -16 to -17 with respect to certain isoelectric point standards and molecular mass of about 70 to 75 K daltons as measured in the presence of sodium dodecylsulfate containing polyacrylamide gels, the presence of the Inmono proteins being correlated with the existence of infectious mononucleosis.

Effect of a protein preload on food intake and satiety feelings in response to duodenal fat perfusions in healthy male subjects.

PubMed

Oesch, Sibylle; Degen, Lukas; Beglinger, Christoph

2005-10-01

The control of food intake and satiety requires a coordinated interplay. Oral protein and duodenal fat inhibit food intake and induce satiety, but their interactive potential is unclear. Our aim was therefore to investigate the interactions between an oral protein preload and intraduodenal (ID) fat on food intake and satiety feelings. Twenty healthy male volunteers were studied in a randomized, double-blind, four-period crossover design. On each study day, subjects underwent one of the following treatments: 1) water preload plus ID saline perfusion, 2) water preload plus ID fat perfusion, 3) protein preload plus ID saline perfusion, or 4) protein preload plus ID fat perfusion. Subjects were free to eat and drink as much as they wished. An oral protein preload significantly reduced caloric intake (19%, P < 0.01). Simultaneous administration of an oral protein preload and ID fat did not result in a positive synergistic effect with respect to caloric consumption, rejecting the initial hypothesis that the two nutrients exert a positive synergistic effect on food intake. An oral protein preload but not ID fat altered the feelings of hunger and fullness. These data indicate that the satiety effect of an oral protein preload is not amplified by ID fat; indeed, the effect of a protein preload does not seem to be mediated by cholecystokinin, glucagon-like peptide-1, or peptide YY. Much more information is necessary to understand the basic physiological mechanisms that control food intake and satiety.

Metabolic rate and rates of protein turnover in food-deprived cuttlefish, Sepia officinalis (Linnaeus 1758)

PubMed Central

MacCormack, Tyson J.; Sykes, Antonio V.; Hall, Jennifer R.; Speers-Roesch, Ben; Callaghan, Neal I.; Driedzic, William R.

2016-01-01

To determine the metabolic response to food deprivation, cuttlefish (Sepia officinalis) juveniles were either fed, fasted (3 to 5 days food deprivation), or starved (12 days food deprivation). Fasting resulted in a decrease in triglyceride levels in the digestive gland, and after 12 days, these lipid reserves were essentially depleted. Oxygen consumption was decreased to 53% and NH4 excretion to 36% of the fed group following 3–5 days of food deprivation. Oxygen consumption remained low in the starved group, but NH4 excretion returned to the level recorded for fed animals during starvation. The fractional rate of protein synthesis of fasting animals decreased to 25% in both mantle and gill compared with fed animals and remained low in the mantle with the onset of starvation. In gill, however, protein synthesis rate increased to a level that was 45% of the fed group during starvation. In mantle, starvation led to an increase in cathepsin A-, B-, H-, and L-like enzyme activity and a 2.3-fold increase in polyubiquitin mRNA that suggested an increase in ubiquitin-proteasome activity. In gill, there was a transient increase in the polyubiquitin transcript levels in the transition from fed through fasted to the starved state and cathepsin A-, B-, H-, and L-like activity was lower in starved compared with fed animals. The response in gill appears more complex, as they better maintain rates of protein synthesis and show no evidence of enhanced protein breakdown through recognized catabolic processes. PMID:27053650

Food Forensics: Using Mass Spectrometry To Detect Foodborne Protein Contaminants, as Exemplified by Shiga Toxin Variants and Prion Strains.

PubMed

Silva, Christopher J

2018-06-13

Food forensicists need a variety of tools to detect the many possible food contaminants. As a result of its analytical flexibility, mass spectrometry is one of those tools. Use of the multiple reaction monitoring (MRM) method expands its use to quantitation as well as detection of infectious proteins (prions) and protein toxins, such as Shiga toxins. The sample processing steps inactivate prions and Shiga toxins; the proteins are digested with proteases to yield peptides suitable for MRM-based analysis. Prions are detected by their distinct physicochemical properties and differential covalent modification. Shiga toxin analysis is based on detecting peptides derived from the five identical binding B subunits comprising the toxin. 15 N-labeled internal standards are prepared from cloned proteins. These examples illustrate the power of MRM, in that the same instrument can be used to safely detect and quantitate protein toxins, prions, and small molecules that might contaminate our food.

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors.

PubMed

Wallqvist, Anders; Memišević, Vesna; Zavaljevski, Nela; Pieper, Rembert; Rajagopala, Seesandra V; Kwon, Keehwan; Yu, Chenggang; Hoover, Timothy A; Reifman, Jaques

2015-12-29

Francisella tularensis is a select bio-threat agent and one of the most virulent intracellular pathogens known, requiring just a few organisms to establish an infection. Although several virulence factors are known, we lack an understanding of virulence factors that act through host-pathogen protein interactions to promote infection. To address these issues in the highly infectious F. tularensis subsp. tularensis Schu S4 strain, we deployed a combined in silico, in vitro, and in vivo analysis to identify virulence factors and their interactions with host proteins to characterize bacterial infection mechanisms. We initially used comparative genomics and literature to identify and select a set of 49 putative and known virulence factors for analysis. Each protein was then subjected to proteome-scale yeast two-hybrid (Y2H) screens with human and murine cDNA libraries to identify potential host-pathogen protein-protein interactions. Based on the bacterial protein interaction profile with both hosts, we selected seven novel putative virulence factors for mutant construction and animal validation experiments. We were able to create five transposon insertion mutants and used them in an intranasal BALB/c mouse challenge model to establish 50 % lethal dose estimates. Three of these, ΔFTT0482c, ΔFTT1538c, and ΔFTT1597, showed attenuation in lethality and can thus be considered novel F. tularensis virulence factors. The analysis of the accompanying Y2H data identified intracellular protein trafficking between the early endosome to the late endosome as an important component in virulence attenuation for these virulence factors. Furthermore, we also used the Y2H data to investigate host protein binding of two known virulence factors, showing that direct protein binding was a component in the modulation of the inflammatory response via activation of mitogen-activated protein kinases and in the oxidative stress response. Direct interactions with specific host proteins and the

Food labeling issues in patients with severe food allergies: solving a hamlet-like doubt.

PubMed

Fierro, Vincenzo; Di Girolamo, Francesco; Marzano, Valeria; Dahdah, Lamia; Mennini, Maurizio

2017-06-01

We review the laws on labeling in the international community, the difficulties they pose to the food manufacturers to prepare the food labels and the methodologies to determine the concentration of potential allergens in foods. European Food Safety Authority and International Life Sciences Institute Europe are evaluating strategies to identify the threshold level of allergen that can trigger a reaction in individuals. The most used techniques to detect the presence of protein in food are Enzyme-linked immunosorbent assay, polymerase chain reaction and real time polymerase chain reaction. Researchers are now trying to apply proteomics to estimate the amount of protein within the food.In order to protect the health of consumers, the Codex Alimentarius Commission updates constantly the list of allergens. In response to these regulations, some industries have also added some precautionary allergen labeling (PAL). It was generally agreed that PAL statements needed to be visible, simple, and safe. It was suggested that PAL be standardized, an action that would occur if the 'Voluntary Incidental Trace Allergen Labelling' process was made mandatory. So far, no laboratory technique is able to reassure the consumers about the composition of foods found on the packaging. International authorities produced increasingly stringent laws, but more is still to do.

Organic food: nutritious food or food for thought? A review of the evidence.

PubMed

Magkos, Faidon; Arvaniti, Fotini; Zampelas, Antonis

2003-09-01

Apparently, one of the primary reasons for purchasing organic food is the perception that it is more nutritious than conventional food. Given the increasing interest towards organic food products, it is imperative to review the existing literature concerning the nutritional value of the produce, and to determine to what extent are consumer expectations met. There are only few well-controlled studies that are capable of making a valid comparison and, therefore, compilation of the results is difficult and generalisation of the conclusions should be made with caution. In spite of these limitations, however, some differences can be identified. Although there is little evidence that organic and conventional foods differ in respect to the concentrations of the various micronutrients (vitamins, minerals and trace elements), there seems to be a slight trend towards higher ascorbic acid content in organically grown leafy vegetables and potatoes. There is also a trend towards lower protein concentration but of higher quality in some organic vegetables and cereal crops. With respect to the rest of the nutrients and the other food groups, existing evidence is inadequate to allow for valid conclusions. Finally, animal feeding experiments indicate that animal health and reproductive performance are slightly improved when they are organically fed. A similar finding has not yet been identified in humans. Several important directions can be highlighted for future research; it seems, however, that despite any differences, a well-balanced diet can equally improve health regardless of its organic or conventional origin.

Ultra-processed foods, protein leverage and energy intake in the USA.

PubMed

Martínez Steele, Euridice; Raubenheimer, David; Simpson, Stephen J; Baraldi, Larissa Galastri; Monteiro, Carlos A

2018-01-01

Experimental studies have shown that human macronutrient regulation minimizes variation in absolute protein intake and consequently energy intake varies passively with dietary protein density ('protein leverage'). According to the 'protein leverage hypothesis' (PLH), protein leverage interacts with a reduction in dietary protein density to drive energy overconsumption and obesity. Worldwide increase in consumption of ultra-processed foods (UPF) has been hypothesized to be an important determinant of dietary protein dilution, and consequently an ecological driving force of energy overconsumption and the obesity pandemic. The present study examined the relationships between dietary contribution of UPF, dietary proportional protein content and the absolute intakes of protein and energy. National representative cross-sectional study. National Health and Nutrition Examination Survey 2009-2010. Participants (n 9042) aged ≥2 years with at least one day of 24 h dietary recall data. We found a strong inverse relationship between consumption of UPF and dietary protein density, with mean protein content dropping from 18·2 to 13·3 % between the lowest and highest quintiles of dietary contribution of UPF. Consistent with the PLH, increase in the dietary contribution of UPF (previously shown to be inversely associated with protein density) was also associated with a rise in total energy intake, while absolute protein intake remained relatively constant. The protein-diluting effect of UPF might be one mechanism accounting for their association with excess energy intake. Reducing UPF contribution in the US diet may be an effective way to increase its dietary protein concentration and prevent excessive energy intake.

Assessment of children's nutritional attitudes before oral food challenges to identify patients at risk of food reintroduction failure: a prospective study.

PubMed

Polloni, L; Ferruzza, E; Ronconi, L; Toniolo, A; Lazzarotto, F; Bonaguro, R; Celegato, N; Muraro, A

2017-05-01

Inappropriate dietary eliminations may impair quality of life, affect children's growth and unnecessarily impact on healthcare costs. Previous retrospective studies reported that around 25% of children continue a food-avoidance diet despite a negative oral food challenge (OFC). A definite pattern has not been found yet for patients not reintroducing the food. This study aimed to examine the role of child's nutritional attitudes and maternal anxiety in reintroducing food after a negative OFC. A prospective study was conducted involving 81 mothers of children with IgE-mediated food allergy. They completed a survey on nutritional behaviour and attitudes and the State-Trait Anxiety Inventory on the day of OFC and 6 months later. In total, 11.1% of children never or rarely ate the food after a negative OFC. Consumption of the reintroduced food is positively correlated to child's interest in tasting new foods before and after OFC and to changes in child's nutritional habits after OFC. It is negatively correlated to monotony of the diet after OFC. No correlations were found with other participants' characteristics or maternal anxiety. State anxiety significantly decreased after the OFC. A correlation was found between trait and state anxiety and the degree of change in nutritional habits after OFC. Evaluating child's approach towards food before the OFC is a promising approach to identify patients at risk of food reintroduction failure. Furthermore, it underlined the importance of reassessing food consumption in all patients after a negative OFC and supporting patients in the reintroduction of food. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cytokine profile after oral food challenge in infants with food protein-induced enterocolitis syndrome.

PubMed

Kimura, Mitsuaki; Ito, Yasunori; Shimomura, Masaki; Morishita, Hideaki; Meguro, Takaaki; Adachi, Yuichi; Seto, Shiro

2017-07-01

Although food protein-induced enterocolitis syndrome (FPIES) is supposed to be caused by inflammation, the role of cytokines has not yet been clarified. To elucidate the role of cytokines in the development of symptoms and abnormal laboratory findings at an oral food challenge (OFC), changes in serum cytokine levels were analyzed for 6 OFCs in 4 patients with FPIES. The result of OFC was judged positive if any gastrointestinal (GI) symptoms (vomiting, diarrhea, or bloody stool) were induced. Among 11 cytokines profiled, serum levels of interleukin (IL)-2, IL-5, and IL-8 were clearly increased in all 4 positive OFCs in which elevations of the serum level of C-reactive protein (CRP) and peripheral blood neutrophilia were also seen. The level of serum IL-10 also rose in 2 positive OFCs. Remarkable increases in the serum level of interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), IL-6, and IL-12 were observed in a positive OFC where the serum level of CRP rose markedly (6.75 mg/dL). The serum levels of IL-5 were also elevated in 2 negative OFCs. No apparent specific correlations were found between cytokines and GI symptoms. These results suggest that IL-2 and IL-8 are involved in the antigen-specific immune responses in most patients with FPIES. Further studies are needed to elucidate the significance of these cytokine in the pathogenesis of FPIES. Copyright © 2016 Japanese Society of Allergology. Production and hosting by Elsevier B.V. All rights reserved.

Identifying Disease Associated miRNAs Based on Protein Domains.

PubMed

Qin, Gui-Min; Li, Rui-Yi; Zhao, Xing-Ming

2016-01-01

MicroRNAs (miRNAs) are a class of small endogenous non-coding genes, acting as regulators in the post-transcriptional processes. Recently, the miRNAs are found to be widely involved in different types of diseases. Therefore, the identification of disease associated miRNAs can help understand the mechanisms that underlie the disease and identify new biomarkers. However, it is not easy to identify the miRNAs related to diseases due to its extensive involvements in various biological processes. In this work, we present a new approach to identify disease associated miRNAs based on domains, the functional and structural blocks of proteins. The results on real datasets demonstrate that our method can effectively identify disease related miRNAs with high precision.

Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development

DTIC Science & Technology

2012-09-01

orientated immobilization of proteins,” Biotechnology Progress, 22(2), 401-405 ( 2006 ). [26] J. M. Kogot, D. A. Sarkes , I. Val-Addo et al...Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development by Joshua M. Kogot, Deborah A. Sarkes ...Peptide-protein Interactions for Smart Reagent Development Joshua M. Kogot, Deborah A. Sarkes , Dimitra N. Stratis-Cullum, and Paul M

Regulatory Monitoring of Fortified Foods: Identifying Barriers and Good Practices

PubMed Central

Rowe, Laura A; Vossenaar, Marieke; Garrett, Greg S

2015-01-01

While fortification of staple foods and condiments has gained enormous global traction, poor performance persists throughout many aspects of implementation, most notably around the critical element of regulatory monitoring, which is essential for ensuring foods meet national fortification standards. Where coverage of fortified foods is high, limited nutritional impact of fortification programs largely exists due to regulatory monitoring that insufficiently identifies and holds producers accountable for underfortified products. Based on quality assurance data from 20 national fortification programs in 12 countries, we estimate that less than half of the samples are adequately fortified against relevant national standards. In this paper, we outline key findings from a literature review, key informant interviews with 11 fortification experts, and semi-quantitative surveys with 39 individuals from regulatory agencies and the food fortification industry in 17 countries on the perceived effectiveness of regulatory monitoring systems and barriers to compliance against national fortification standards. Findings highlight that regulatory agencies and industry disagree on the value that enforcement mechanisms have in ensuring compliance against standards. Perceived political risk of enforcement and poorly resourced inspectorate capacity appear to adversely reinforce each other within an environment of unclear legislation to create a major hurdle for improving overall compliance of fortification programs against national standards. Budget constraints affect the ability of regulatory agencies to create a well-trained inspector cadre and improve the detection and enforcement of non-compliant and underfortified products. Recommendations to improve fortification compliance include improving technical capacity; ensuring sustained leadership, accountability, and funding in both the private and the public sectors; and removing political barriers to ensure consistent detection of

Elimination diet effectively treats eosinophilic esophagitis in adults; food reintroduction identifies causative factors.

PubMed

Gonsalves, Nirmala; Yang, Guang-Yu; Doerfler, Bethany; Ritz, Sally; Ditto, Anne M; Hirano, Ikuo

2012-06-01

Adults with eosinophilic esophagitis (EoE) typically present with dysphagia and food impaction. A 6-food elimination diet (SFED) is effective in children with EoE. We assessed the effects of the SFED followed by food reintroduction on the histologic response, symptoms, and quality of life in adults with EoE. At the start of the study, 50 adults with EoE underwent esophagogastroduodenoscopies (EGDs), biopsies, and skin-prick tests for food and aeroallergens. After 6 weeks of SFED, patients underwent repeat EGD and biopsies. Histologic responders, defined by ≤ 5 eosinophils/high-power field (eos/hpf) (n = 32), underwent systematic reintroduction of foods followed by EGD and biopsies (n = 20). Symptom and quality of life scores were determined before and after SFED. Common symptoms of EoE included dysphagia (96%), food impaction (74%), and heartburn (94%). The mean peak eosinophil counts in the proximal esophagus were 34 eos/hpf and 8 eos/hpf, before and after the SFED, and 44 eos/hpf and 13 eos/hpf in the distal esophagus, respectively (P < .0001). After the SFED, 64% of patients had peak counts ≤ 5 eos/hpf and 70% had peak counts of ≤ 10 eos/hpf. Symptom scores decreased in 94% (P < .0001). After food reintroduction, esophageal eosinophil counts returned to pretreatment values (P < .0001). Based on reintroduction, the foods most frequently associated with EoE were wheat (60% of cases) and milk (50% of cases). Skin-prick testing predicted only 13% of foods associated with EoE. An elimination diet significantly improves symptoms and reduces endoscopic and histopathologic features of EoE in adults. Food reintroduction re-initiated features of EoE in patients, indicating a role for food allergens in its pathogenesis. Foods that activated EoE were identified by systematic reintroduction analysis but not by skin-prick tests. Copyright © 2012 AGA Institute. Published by Elsevier Inc. All rights reserved.

High consumption foods and their influence on energy and protein intake in institutionalized older adults.

PubMed

Mila, R; Abellana, R; Padro, L; Basulto, J; Farran, A

2012-02-01

The elderly, and especially those attending nursing homes, are at great risk from certain nutritional deficiencies. The aim of this study was to determine which food groups present the highest rates of consumption among the institutionalized elderly and study the energy density of each food group and the number of calories and amount of protein in the total diet of each resident. This was a multicentre observational study of a sample of the institutionalized population over the age of 65. The sample of patients was drawn from four Spanish nursing homes (Santa Coloma Gramanet, Barcelona, Madrid and Bilbao). Our final sample comprised a total of 62 individuals, of whom 22 were men and 40 women, aged between 68 and 96 years. Dietary data were collected using the double weight method for each main meal (breakfast, lunch, afternoon snack and dinner), including food type, the quantity of food served and the amount of plate waste for each of the main meals served during 21 days. The characteristics of the study population were compared by Student's t-test and χ2 test. The results are expressed in terms of their median values and the interquartile range. To analyse the overall differences between sites, gender and food groups we used Kruskall-Wallis test combined with the Mann-Whitney U-test with Bonferroni correction for multiple comparisons. The food group that was served most was milk products (376.25 g/day). A large amount of potatoes were also served (109.64 g/day) as were sweets and pastries (62.14 g/day). The daily serving of fruit (138.34 g/day) and vegetables (239.47 g/day) was equivalent to no more than that of a daily ration in each case. Milk was the food group with the highest consumption (311 g/day). Most of the energy was provided by groups with a higher energy density like as fats and sauces, sweets and pastries and bread. The mean protein consumption was 82,6 g/day (Table 5) and no significant differences were recorded in this consumption between men and

Processing traits and digestibility of extruded dog foods with soy protein concentrate.

PubMed

Venturini, K S; Sarcinelli, M F; Baller, M A; Putarov, T C; Malheiros, E B; Carciofi, A C

2018-04-11

Soya bean protein concentrate (SPC) with two particle sizes were evaluated on extrusion parameters, kibble formation, digestibility and palatability of dog foods. Eight diets were extruded: PBM-control diet based on poultry by-product meal (PBM); GM-a diet in which corn gluten meal (GM) replaced 45% of the diet protein; cSPC15%, cSPC30% and cSPC45%-diets in which SPC of coarse particle size (600 μm) replaced 15%, 30% and 45% of the diet protein; and sSPC15%, sSPC30% and sSPC45%-diets in which SPC of small particle size (200 μm) replaced 15%, 30% and 45% of the diet protein. The digestibility of nutrients was evaluated for the PBM, GM, cSPC45% and sSPC45% diets, using six dogs per food. The PBM, GM and cSPC45% diets were compared for palatability. Data were submitted for analysis of variance, and the means were compared by polynomial contrasts or Tukey's test (p < .05). The cSPC increased the specific mechanical energy (SME) application, extrusion temperature and pressure linearly, resulting in lower kibble density and higher expansion and starch gelatinization (SG) (p < .01). When comparing the PBM, GM, cSPC45% and sSPC45% diets, higher SME, extrusion temperature and pressure, SG and kibble expansion were verified for the cSPC45% diet (p < .05). The DM, fat and crude protein digestibility were similar among diets. Faecal pH, ammonia and lactate did not differ, demonstrating that the removal of oligosaccharides and soluble non-starch polysaccharides of SPC produces an ingredient with mostly non-fermentable fibre. Dogs preferred the PBM to the GM diet (p < .05), but consumed the PBM and cSPC45% foods equally. In conclusion, SPC exhibited good extrusion functionality, favouring kibble expansion and SG, with high digestibility, similar to that of PBM. The removal of soluble compounds from soya beans resulted in an ingredient with low fermentable fibre content, which did not alter faecal formation or characteristics. © 2018 Blackwell Verlag GmbH.

Use of Phage Display to Identify Novel Mineralocorticoid Receptor-Interacting Proteins

PubMed Central

Yang, Jun; Fuller, Peter J.; Morgan, James; Shibata, Hirotaka; McDonnell, Donald P.; Clyne, Colin D.

2014-01-01

The mineralocorticoid receptor (MR) plays a central role in salt and water homeostasis via the kidney; however, inappropriate activation of the MR in the heart can lead to heart failure. A selective MR modulator that antagonizes MR signaling in the heart but not the kidney would provide the cardiovascular protection of current MR antagonists but allow for normal electrolyte balance. The development of such a pharmaceutical requires an understanding of coregulators and their tissue-selective interactions with the MR, which is currently limited by the small repertoire of MR coregulators described in the literature. To identify potential novel MR coregulators, we used T7 phage display to screen tissue-selective cDNA libraries for MR-interacting proteins. Thirty MR binding peptides were identified, from which three were chosen for further characterization based on their nuclear localization and their interaction with other MR-interacting proteins or, in the case of x-ray repair cross-complementing protein 6, its known status as an androgen receptor coregulator. Eukaryotic elongation factor 1A1, structure-specific recognition protein 1, and x-ray repair cross-complementing protein 6 modulated MR-mediated transcription in a ligand-, cell- and/or promoter-specific manner and colocalized with the MR upon agonist treatment when imaged using immunofluorescence microscopy. These results highlight the utility of phage display for rapid and sensitive screening of MR binding proteins and suggest that eukaryotic elongation factor 1A1, structure-specific recognition protein 1, and x-ray repair cross-complementing protein 6 may be potential MR coactivators whose activity is dependent on the ligand, cellular context, and target gene promoter. PMID:25000480

Bioactive characteristics and optimization of tamarind seed protein hydrolysate for antioxidant-rich food formulations.

PubMed

Bagul, Mayuri B; Sonawane, Sachin K; Arya, Shalini S

2018-04-01

Tamarind seed has been a source of valuable nutrients such as protein (contains high amount of many essential amino acids), essential fatty acids, and minerals which are recognized as additive to develop perfect balanced functional foods. The objective of present work was to optimize the process parameters for extraction and hydrolysis of protein from tamarind seeds. Papain-derived hydrolysates showed a maximum degree of hydrolysis (39.49%) and radical scavenging activity (42.92 ± 2.83%) at optimized conditions such as enzyme-to-substrate ratio (1:5), hydrolysis time (3 h), hydrolysis temperature (65 °C), and pH 6. From this study, papain hydrolysate can be considered as good source of natural antioxidants in developing food formulations.

Taste-nutrient relationships in commonly consumed foods.

PubMed

van Dongen, Mirre Viskaal; van den Berg, Marjolijn C; Vink, Nicole; Kok, Frans J; de Graaf, Cees

2012-07-14

Taste is expected to represent a food's nutrient content. The objective was to investigate whether taste acts as nutrient-sensor, within the context of the current diet, which is high in processed foods. Intensities of the five basic tastes of fifty commonly consumed foods were rated by nineteen subjects (aged 21·0 (SD 1·7) years, BMI 21·5 (SD 2·0) kg/m(2)). Linear regression was used to test associations between taste and nutrient contents. Food groups based on taste were identified using cluster analysis; nutrient content was compared between food groups, using ANOVA. Sweetness was associated with mono- and disaccharides (R(2) 0·45, P < 0·01). Saltiness and savouriness were correlated, with r 0·92 (P < 0·01) and both were associated with Na (both: R(2) 0·33, P < 0·01) and protein (R(2) 0·27, P < 0·01 and R(2) 0·33, P < 0·01, respectively). Cluster analysis indicated four food groups: neutral, salty and savoury, sweet-sour and sweet foods. Mono- and disaccharide content was highest in sweet foods (P < 0·01). In salty and savoury foods, protein content (P = 0·01 with sweet-sour foods, not significant with neutral or sweet foods) and Na content (P < 0·05) were the highest. Associations were more pronounced in raw and moderately processed foods, than in highly processed foods. The findings suggest that sweetness, saltiness and savouriness signal nutrient content, particularly for simple sugars, protein and Na. In highly processed foods, however, the ability to sense nutrient content based on taste seems limited.

Chronic food protein-induced enterocolitis syndrome caused by cow's milk proteins passed through breast milk.

PubMed

Miceli Sopo, Stefano; Monaco, Serena; Greco, Monica; Scala, Guglielmo

2014-01-01

We describe 2 cases of food protein-induced enterocolitis syndrome (FPIES) caused by cow's milk (CM) passed through breast milk. The onset in both cases was characterized by chronic symptoms (regurgitation, colic, diarrhea, failure to thrive); in one patient, two acute episodes due to the direct consumption of CM formula by the infant were also reported. The diagnosis of FPIES through breast milk can be easily overlooked, especially in milder cases. We also discuss some important issues concerning the general management of the disease. In conclusion, (1) the diagnosis of chronic FPIES should be taken into account even in exclusively breast-fed infants who present suggestive symptoms such as persistent regurgitation, small amounts of vomiting, lethargy, failure to thrive, dehydration, diarrhea (sometimes bloody) and abdominal distention. A 2-week maternal elimination diet should be considered even in apparently mild cases. (2) CM seems to be the most frequently reported culprit food. (3) In those cases in which acute FPIES is elicited by the direct consumption of the culprit food in breast-fed infants, maternal diet may be unrestricted. © 2014 S. Karger AG, Basel.

Proteomic profiling of human plasma exosomes identifies PPAR{gamma} as an exosome-associated protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Looze, Christopher; Yui, David; Leung, Lester

Exosomes are nanovesicles that are released from cells as a mechanism of cell-free intercellular communication. Only a limited number of proteins have been identified from the plasma exosome proteome. Here, we developed a multi-step fractionation scheme incorporating gel exclusion chromatography, rate zonal centrifugation through continuous sucrose gradients, and high-speed centrifugation to purify exosomes from human plasma. Exosome-associated proteins were separated by SDS-PAGE and 66 proteins were identified by LC-MS/MS, which included both cellular and extracellular proteins. Furthermore, we identified and characterized peroxisome proliferator-activated receptor-{gamma} (PPAR{gamma}), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatorymore » cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPAR{gamma} as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.« less

Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome.

PubMed

Choong, Wai-Kok; Lih, Tung-Shing Mamie; Chen, Yu-Ju; Sung, Ting-Yi

2017-12-01

To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass-spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues. Therefore, we conducted a thorough comparative analysis on data sets in PeptideAtlas Tiered Human Integrated Search Proteome (THISP, 2017-03 release), including neXtProt (2017-01 release), to systematically investigate the possibility of unique peptides in missing proteins (PE2-4), unique peptides in dubious proteins, and variant peptides affected by isobaric substitutions, causing doubtful identification results. In this study, we considered 11 isobaric substitutions. From our analysis, we found <5% of the unique peptides of missing proteins and >6% of variant peptides became shared with peptides of PE1 proteins after isobaric substitutions.

Glycosylation Changes in Serum Proteins Identify Patients with Pancreatic Cancer.

PubMed

Drabik, Anna; Bodzon-Kulakowska, Anna; Suder, Piotr; Silberring, Jerzy; Kulig, Jan; Sierzega, Marek

2017-04-07

After more than a decade of biomarker discovery using advanced proteomic and genomic approaches, very few biomarkers have been involved in clinical diagnostics. Most candidate biomarkers are focused on the protein component. Targeting post-translational modifications (PTMs) in combination with protein sequences will provide superior diagnostic information with regards to sensitivity and specificity. Glycosylation is one of the most common and functionally important PTMs. It plays a central role in many biological processes, including protein folding, host-pathogen interactions, immune response, and inflammation. Cancer-associated aberrant glycosylation has been identified in various types of cancer. Expression of cancer-specific glycan epitopes represents an excellent opportunity for diagnostics and potentially specific detection of tumors. Here, we report four proteins (LIFR, CE350, VP13A, HPT) found in sera from pancreatic cancer patients carrying aberrant glycan structures as compared to those of controls.

Immunological Reactivity Using Monoclonal and Polyclonal Antibodies of Autoimmune Thyroid Target Sites with Dietary Proteins

PubMed Central

Herbert, Martha

2017-01-01

Many hypothyroid and autoimmune thyroid patients experience reactions with specific foods. Additionally, food interactions may play a role in a subset of individuals who have difficulty finding a suitable thyroid hormone dosage. Our study was designed to investigate the potential role of dietary protein immune reactivity with thyroid hormones and thyroid axis target sites. We identified immune reactivity between dietary proteins and target sites on the thyroid axis that includes thyroid hormones, thyroid receptors, enzymes, and transport proteins. We also measured immune reactivity of either target specific monoclonal or polyclonal antibodies for thyroid-stimulating hormone (TSH) receptor, 5′deiodinase, thyroid peroxidase, thyroglobulin, thyroxine-binding globulin, thyroxine, and triiodothyronine against 204 purified dietary proteins commonly consumed in cooked and raw forms. Dietary protein determinants included unmodified (raw) and modified (cooked and roasted) foods, herbs, spices, food gums, brewed beverages, and additives. There were no dietary protein immune reactions with TSH receptor, thyroid peroxidase, and thyroxine-binding globulin. However, specific antigen-antibody immune reactivity was identified with several purified food proteins with triiodothyronine, thyroxine, thyroglobulin, and 5′deiodinase. Laboratory analysis of immunological cross-reactivity between thyroid target sites and dietary proteins is the initial step necessary in determining whether dietary proteins may play a potential immunoreactive role in autoimmune thyroid disease. PMID:28894619

Food protein-originating peptides as tastants - Physiological, technological, sensory, and bioinformatic approaches.

PubMed

Iwaniak, Anna; Minkiewicz, Piotr; Darewicz, Małgorzata; Hrynkiewicz, Monika

2016-11-01

Taste is one of the factors based on which the organism makes the selection of what to ingest. It also protects humans from ingesting toxic compounds and is one of the main attributes when thinking about food quality. Five basic taste sensations are recognized by humans: bitter, salty, sour, sweet, and umami. The taste of foods is affected by some molecules of some specific chemical nature. One of them are peptides derived from food proteins. Although they are not the major natural compounds originating from food sources that are responsible for the taste, they are in the area of scientific research due to the specific composition of amino acids which are well-known for their sensory properties. Literature data implicate that sweet, bitter, and umami are the tastes attributable to peptides. Moreover, the bitter peptide tastants are the dominant among the other tastes. Additionally, other biological activities like, e.g., inhibiting enzymes that regulate the body functions and acting as preventive food agents of civilization diseases, are also associated with the taste of peptides. The advance in information technologies has contributed to the elaboration of internet archives (databases) as well as in silico tools for the analysis of biological compounds. It also concerns peptides - namely taste carriers originating from foods. Thus, our paper provides a summary of knowledge about peptides as tastants with special attention paid to the following aspects: a) basis of taste perception, b) taste peptides detected in food protein sequences with special emphasis put on the role of bitter peptides, c) peptides that may enhance/suppress the taste of foods, d) databases as well as bioinformatic approaches suitable to study the taste of peptides, e) taste-taste interactions, f) basis of sensory analysis in the evaluation of the taste of molecules, including peptides, and g) the methodology applied to reduce/eliminate the undesired taste of peptides. The list of taste

Proteins related to the functions of fibroblast-like synoviocytes identified by proteomic analysis.

PubMed

Zhang, Hui; Fan, Lie Ying; Zong, Ming; Sun, Li Shan; Lu, Liu

2012-01-01

It is well known that the fibroblast-like synoviocytes (FLS) play a key role in pathogenesis of rheumatoid arthritis (RA). This study was performed to separate the differentially expressed proteins of FLS from the patients with RA or osteoarthritis (OA) by two-dimensional electrophoresis (2-DE), and found proteins associated with the functions of FLS by mass spectrometry (MS). Total proteins were extracted and quantified from the primary cultured FLS from patients of RA (n=8) or OA (n=6). Proteins were separated by high-resolution 2-DE, and identified the differentially expressed proteins by MS. Western blot analyses was used to validated the expression of candidate proteins. The mRNA of these proteins was detected by semi-quantitative fluorescent PCR. There are 1147 protein spots from RA and 1324 protein spots from OA showed on 2-DE graphs, respectively. We have selected 84 protein spots for MS analysis, and 27 protein spots were successfully identified. We have found that protein isoaspartyl methyltransferase (PIMT) and pirin (iron-binding nuclear protein, PIR) with lower expression in RA, and thioredoxin 1(Trx-1) only expressed in RA may be associated with functions of FLS. Western Blot confirmed the expression of PIMT and pirin lower in RA, and Trx-1 expressed only in RA. The results of semi-quantitative fluorescent PCR are also consistent with 2-DE graphs. PIMT, pirin and Trx-1 affect the functions of FLS in some style and can be the drug targets of RA.

Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses.

PubMed

Eng, Christine L P; Tong, Joo Chuan; Tan, Tin Wee

2016-01-01

Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.

MultiP-Apo: A Multilabel Predictor for Identifying Subcellular Locations of Apoptosis Proteins

PubMed Central

Li, Hui; Wang, Rong; Gan, Yong

2017-01-01

Apoptosis proteins play an important role in the mechanism of programmed cell death. Predicting subcellular localization of apoptosis proteins is an essential step to understand their functions and identify drugs target. Many computational prediction methods have been developed for apoptosis protein subcellular localization. However, these existing works only focus on the proteins that have one location; proteins with multiple locations are either not considered or assumed as not existing when constructing prediction models, so that they cannot completely predict all the locations of the apoptosis proteins with multiple locations. To address this problem, this paper proposes a novel multilabel predictor named MultiP-Apo, which can predict not only apoptosis proteins with single subcellular location but also those with multiple subcellular locations. Specifically, given a query protein, GO-based feature extraction method is used to extract its feature vector. Subsequently, the GO feature vector is classified by a new multilabel classifier based on the label-specific features. It is the first multilabel predictor ever established for identifying subcellular locations of multilocation apoptosis proteins. As an initial study, MultiP-Apo achieves an overall accuracy of 58.49% by jackknife test, which indicates that our proposed predictor may become a very useful high-throughput tool in this area. PMID:28744305

MultiP-Apo: A Multilabel Predictor for Identifying Subcellular Locations of Apoptosis Proteins.

PubMed

Wang, Xiao; Li, Hui; Wang, Rong; Zhang, Qiuwen; Zhang, Weiwei; Gan, Yong

2017-01-01

Apoptosis proteins play an important role in the mechanism of programmed cell death. Predicting subcellular localization of apoptosis proteins is an essential step to understand their functions and identify drugs target. Many computational prediction methods have been developed for apoptosis protein subcellular localization. However, these existing works only focus on the proteins that have one location; proteins with multiple locations are either not considered or assumed as not existing when constructing prediction models, so that they cannot completely predict all the locations of the apoptosis proteins with multiple locations. To address this problem, this paper proposes a novel multilabel predictor named MultiP-Apo, which can predict not only apoptosis proteins with single subcellular location but also those with multiple subcellular locations. Specifically, given a query protein, GO-based feature extraction method is used to extract its feature vector. Subsequently, the GO feature vector is classified by a new multilabel classifier based on the label-specific features. It is the first multilabel predictor ever established for identifying subcellular locations of multilocation apoptosis proteins. As an initial study, MultiP-Apo achieves an overall accuracy of 58.49% by jackknife test, which indicates that our proposed predictor may become a very useful high-throughput tool in this area.

Identifying specific beliefs to target to improve restaurant employees' intentions for performing three important food safety behaviors.

PubMed

Pilling, Valerie K; Brannon, Laura A; Shanklin, Carol W; Howells, Amber D; Roberts, Kevin R

2008-06-01

Current national food safety training programs appear ineffective at improving food safety practices in foodservice operations, given the substantial number of Americans affected by foodborne illnesses after eating in restaurants each year. The Theory of Planned Behavior (TpB) was used to identify important beliefs that may be targeted to improve foodservice employees' intentions for three food safety behaviors that have the most substantial affect on public health: hand washing, using thermometers, and proper handling of food contact surfaces. In a cross-sectional design, foodservice employees (n=190) across three midwestern states completed a survey assessing TpB components and knowledge for the three food safety behaviors. Multiple regression analyses were performed on the TpB components for each behavior. Independent-samples t tests identified TpB beliefs that discriminated between participants who absolutely intend to perform the behaviors and those with lower intention. Employees' attitudes were the one consistent predictor of intentions for performing all three behaviors. However, a unique combination of important predictors existed for each separate behavior. Interventions for improving employees' behavioral intentions for food safety should focus on TpB components that predict intentions for each behavior and should bring all employees' beliefs in line with those of the employees who already intend to perform the food safety behaviors. Registered dietitians; dietetic technicians, registered; and foodservice managers can use these results to enhance training sessions and motivational programs to improve employees' food safety behaviors. Results also assist these professionals in recognizing their responsibility for enforcing and providing adequate resources for proper food safety behaviors.

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.

PubMed

Floyd, Brendan J; Wilkerson, Emily M; Veling, Mike T; Minogue, Catie E; Xia, Chuanwu; Beebe, Emily T; Wrobel, Russell L; Cho, Holly; Kremer, Laura S; Alston, Charlotte L; Gromek, Katarzyna A; Dolan, Brendan K; Ulbrich, Arne; Stefely, Jonathan A; Bohl, Sarah L; Werner, Kelly M; Jochem, Adam; Westphall, Michael S; Rensvold, Jarred W; Taylor, Robert W; Prokisch, Holger; Kim, Jung-Ja P; Coon, Joshua J; Pagliarini, David J

2016-08-18

Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function. Copyright © 2016 Elsevier Inc. All rights reserved.

A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins.

PubMed

Liu, Yu-Cheng; Yang, Meng-Han; Lin, Win-Li; Huang, Chien-Kang; Oyang, Yen-Jen

2009-12-03

Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biological functions, scientists have been designing various types of predictors for identifying structurally flexible regions in proteins. In this respect, there are two major categories of predictors. One category of predictors attempts to identify conformationally flexible regions through analysis of protein tertiary structures. Another category of predictors works completely based on analysis of the polypeptide sequences. As the availability of protein tertiary structures is generally limited, the design of predictors that work completely based on sequence information is crucial for advances of molecular biology research. In this article, we propose a novel approach to design a sequence-based predictor for identifying conformationally ambivalent regions in proteins. The novelty in the design stems from incorporating two classifiers based on two distinctive supervised learning algorithms that provide complementary prediction powers. Experimental results show that the overall performance delivered by the hybrid predictor proposed in this article is superior to the performance delivered by the existing predictors. Furthermore, the case study presented in this article demonstrates that the proposed hybrid predictor is capable of providing the biologists with valuable clues about the functional sites in a protein chain. The proposed hybrid predictor provides the users with two optional modes, namely, the high-sensitivity mode and the high-specificity mode. The experimental results with an independent testing data set show that the proposed hybrid predictor is capable of delivering sensitivity of 0.710 and specificity of 0.608 under the high-sensitivity mode, while delivering sensitivity of 0.451 and specificity of 0.787 under the high-specificity mode. Though

Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases

PubMed Central

Jazurek, Magdalena; Ciesiolka, Adam; Starega-Roslan, Julia; Bilinska, Katarzyna; Krzyzosiak, Wlodzimierz J.

2016-01-01

RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases. PMID:27625393

Identifying the missing proteins in human proteome by biological language model.

PubMed

Dong, Qiwen; Wang, Kai; Liu, Xuan

2016-12-23

With the rapid development of high-throughput sequencing technology, the proteomics research becomes a trendy field in the post genomics era. It is necessary to identify all the native-encoding protein sequences for further function and pathway analysis. Toward that end, the Human Proteome Organization lunched the Human Protein Project in 2011. However many proteins are hard to be detected by experiment methods, which becomes one of the bottleneck in Human Proteome Project. In consideration of the complicatedness of detecting these missing proteins by using wet-experiment approach, here we use bioinformatics method to pre-filter the missing proteins. Since there are analogy between the biological sequences and natural language, the n-gram models from Natural Language Processing field has been used to filter the missing proteins. The dataset used in this study contains 616 missing proteins from the "uncertain" category of the neXtProt database. There are 102 proteins deduced by the n-gram model, which have high probability to be native human proteins. We perform a detail analysis on the predicted structure and function of these missing proteins and also compare the high probability proteins with other mass spectrum datasets. The evaluation shows that the results reported here are in good agreement with those obtained by other well-established databases. The analysis shows that 102 proteins may be native gene-coding proteins and some of the missing proteins are membrane or natively disordered proteins which are hard to be detected by experiment methods.

Food Insecurity Screening in Pediatric Primary Care: Can Offering Referrals Help Identify Families in Need?

PubMed

Bottino, Clement J; Rhodes, Erinn T; Kreatsoulas, Catherine; Cox, Joanne E; Fleegler, Eric W

2017-07-01

To describe a clinical approach for food insecurity screening incorporating a menu offering food-assistance referrals, and to examine relationships between food insecurity and referral selection. Caregivers of 3- to 10-year-old children presenting for well-child care completed a self-administered questionnaire on a laptop computer. Items included the US Household Food Security Survey Module: 6-Item Short Form (food insecurity screen) and a referral menu offering assistance with: 1) finding a food pantry, 2) getting hot meals, 3) applying for Supplemental Nutrition Assistance Program (SNAP), and 4) applying for Special Supplemental Nutrition Program for Women, Infants, and Children (WIC). Referrals were offered independent of food insecurity status or eligibility. We examined associations between food insecurity and referral selection using multiple logistic regression while adjusting for covariates. A total of 340 caregivers participated; 106 (31.2%) reported food insecurity, and 107 (31.5%) selected one or more referrals. Forty-nine caregivers (14.4%) reported food insecurity but selected no referrals; 50 caregivers (14.7%) selected one or more referrals but did not report food insecurity; and 57 caregivers (16.8%) both reported food insecurity and selected one or more referrals. After adjustment, caregivers who selected one or more referrals had greater odds of food insecurity compared to caregivers who selected no referrals (adjusted odds ratio 4.0; 95% confidence interval 2.4-7.0). In this sample, there was incomplete overlap between food insecurity and referral selection. Offering referrals may be a helpful adjunct to standard screening for eliciting family preferences and identifying unmet social needs. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Identifying protein complexes in PPI network using non-cooperative sequential game.

PubMed

Maulik, Ujjwal; Basu, Srinka; Ray, Sumanta

2017-08-21

Identifying protein complexes from protein-protein interaction (PPI) network is an important and challenging task in computational biology as it helps in better understanding of cellular mechanisms in various organisms. In this paper we propose a noncooperative sequential game based model for protein complex detection from PPI network. The key hypothesis is that protein complex formation is driven by mechanism that eventually optimizes the number of interactions within the complex leading to dense subgraph. The hypothesis is drawn from the observed network property named small world. The proposed multi-player game model translates the hypothesis into the game strategies. The Nash equilibrium of the game corresponds to a network partition where each protein either belong to a complex or form a singleton cluster. We further propose an algorithm to find the Nash equilibrium of the sequential game. The exhaustive experiment on synthetic benchmark and real life yeast networks evaluates the structural as well as biological significance of the network partitions.

Manuscript title: antifungal proteins from moulds: analytical tools and potential application to dry-ripened foods.

PubMed

Delgado, Josué; Owens, Rebecca A; Doyle, Sean; Asensio, Miguel A; Núñez, Félix

2016-08-01

Moulds growing on the surface of dry-ripened foods contribute to their sensory qualities, but some of them are able to produce mycotoxins that pose a hazard to consumers. Small cysteine-rich antifungal proteins (AFPs) from moulds are highly stable to pH and proteolysis and exhibit a broad inhibition spectrum against filamentous fungi, providing new chances to control hazardous moulds in fermented foods. The analytical tools for characterizing the cellular targets and affected pathways are reviewed. Strategies currently employed to study these mechanisms of action include 'omics' approaches that have come to the forefront in recent years, developing in tandem with genome sequencing of relevant organisms. These techniques contribute to a better understanding of the response of moulds against AFPs, allowing the design of complementary strategies to maximize or overcome the limitations of using AFPs on foods. AFPs alter chitin biosynthesis, and some fungi react inducing cell wall integrity (CWI) pathway. However, moulds able to increase chitin content at the cell wall by increasing proteins in either CWI or calmodulin-calcineurin signalling pathways will resist AFPs. Similarly, AFPs increase the intracellular levels of reactive oxygen species (ROS), and moulds increasing G-protein complex β subunit CpcB and/or enzymes to efficiently produce glutathione may evade apoptosis. Unknown aspects that need to be addressed include the interaction with mycotoxin production by less sensitive toxigenic moulds. However, significant steps have been taken to encourage the use of AFPs in intermediate-moisture foods, particularly for mould-ripened cheese and meat products.

Identifying different transcribed proteins in the newly described Theraphosidae Pamphobeteus verdolaga.

PubMed

Estrada-Gómez, Sebastian; Vargas-Muñoz, Leidy Johana; Saldarriaga-Córdoba, Mónica; Cifuentes, Yeimy; Perafan, Carlos

2017-04-01

Theraphosidae spider venoms are well known for possess a complex mixture of protein and non-protein compounds in their venom. The objective of this study was to report and identify different proteins translated from the venom gland DNA information of the recently described Theraphosidae spider Pamphobeteus verdolaga. Using a venom gland transcriptomic analysis, we reported a set of the first complete sequences of seven different proteins of the recenlty described Theraphosidae spider P. verdolaga. Protein analysis indicates the presence of different proteins on the venom composition of this new spider, some of them uncommon in the Theraphosidae family. MS/MS analysis of P. verdolaga showed different fragments matching sphingomyelinases (sicaritoxin), barytoxins, hexatoxins, latroinsectotoxins, and linear (zadotoxins) peptides. Only four of the MS/MS fragments showed 100% sequence similarity with one of the transcribed proteins. Transcriptomic analysis showed the presence of different groups of proteins like phospholipases, hyaluronidases, inhibitory cysteine knots (ICK) peptides among others. The three database of protein domains used in this study (Pfam, SMART and CDD) showed congruency in the search of unique conserved protein domain for only four of the translated proteins. Those proteins matched with EF-hand proteins, cysteine rich secretory proteins, jingzhaotoxins, theraphotoxins and hexatoxins, from different Mygalomorphae spiders belonging to the families Theraphosidae, Barychelidae and Hexathelidae. None of the analyzed sequences showed a complete 100% similarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Effects of Different High-Protein Low-Carbohydrates Proprietary Foods on Blood Sugar in Healthy Subjects.

PubMed

Lodi, Alessandra; Karsten, Bettina; Bosco, Gerardo; Gómez-López, Manuel; Brandão, Paula Paraguassú; Bianco, Antonino; Paoli, Antonio

2016-11-01

The aim of this study was to analyze the effects on blood sugar concentrations through the calculation of the glycemic score (GS) of 10 different high-protein low-carbohydrates (CHOs) proprietary foods that are commonly used as meals during very low-CHO ketogenic diets or during low-CHO diets. Fourteen healthy females were tested for their glycemic response curve elicited by 1000 kJ of glucose three times within a 3-week period (one test each week) compared with one of 10 test foods once on separate days twice a week. After determining the GS of each food in each individual, the mean GS of each test food was calculated. All test foods, compared with glucose, produced a significantly lower glycemic response. The GS of all test food resulted in being lower than 25 and the difference between the mean glycemia after the intake of glucose (mean 122 ± 15 mg/dL) and after the intake of the sweet test foods (mean 89 ± 7 mg/dL) was 33 mg/dL (P < .001), whereas the difference between the mean glycemia after the intake of glucose and after the intake of savory test foods (mean 91 ± 8 mg/dL) was of 31 mg/dL (P < .001). The reformulation of ultraprocessed ready-to-consume foods in a low-CHO, high-protein version can produce a significantly lower glycemic response whilst maintaining the valued ready-to-use format and high palatability demanded by consumers. The low impact on postprandial glycemia and the nutritional characteristics of these proprietary foods makes them useful in both weight control management strategies and in the care management of diabetes.

Interactions Between Flavonoid-Rich Extracts and Sodium Caseinate Modulate Protein Functionality and Flavonoid Bioaccessibility in Model Food Systems.

PubMed

Elegbede, Jennifer L; Li, Min; Jones, Owen G; Campanella, Osvaldo H; Ferruzzi, Mario G

2018-05-01

With growing interest in formulating new food products with added protein and flavonoid-rich ingredients for health benefits, direct interactions between these ingredient classes becomes critical in so much as they may impact protein functionality, product quality, and flavonoids bioavailability. In this study, sodium caseinate (SCN)-based model products (foams and emulsions) were formulated with grape seed extract (GSE, rich in galloylated flavonoids) and green tea extract (GTE, rich in nongalloylated flavonoids), respectively, to assess changes in functional properties of SCN and impacts on flavonoid bioaccessibility. Experiments with pure flavonoids suggested that galloylated flavonoids reduced air-water interfacial tension of 0.01% SCN dispersions more significantly than nongalloylated flavonoids at high concentrations (>50 μg/mL). This observation was supported by changes in stability of 5% SCN foam, which showed that foam stability was increased at high levels of GSE (≥50 μg/mL, P < 0.05) but was not affected by GTE. However, flavonoid extracts had modest effects on SCN emulsion. In addition, galloylated flavonoids had higher bioaccessibility in both SCN foam and emulsion. These results suggest that SCN-flavonoid binding interactions can modulate protein functionality leading to difference in performance and flavonoid bioaccessibility of protein-based products. As information on the beneficial health effects of flavonoids expands, it is likely that usage of these ingredients in consumer foods will increase. However, the necessary levels to provide such benefits may exceed those that begin to impact functionality of the macronutrients such as proteins. Flavonoid inclusion within protein matrices may modulate protein functionality in a food system and modify critical consumer traits or delivery of these beneficial plant-derived components. The product matrices utilized in this study offer relevant model systems to evaluate how fortification with flavonoid

Effects of antinutritional factors on protein digestibility and amino acid availability in foods.

PubMed

Gilani, G Sarwar; Cockell, Kevin A; Sepehr, Estatira

2005-01-01

Digestibility of protein in traditional diets from developing countries such as India, Guatemala, and Brazil is considerably lower compared to that of protein in typical North American diets (54-78 versus 88-94%). The presence of less digestible protein fractions, high levels of insoluble fiber, and high concentrations of antinutritional factors in the diets of developing countries, which are based on less refined cereals and grain legumes as major sources of protein, are responsible for poor digestibility of protein. The effects of the presence of some of the important antinutritional factors on protein and amino digestibilities of food and feed products are reviewed in this chapter. Food and feed products may contain a number of antinutritional factors that may adversely affect protein digestibility and amino acid availability. Antinutritional factors may occur naturally, such as glucosinolates in mustard and rapeseed protein products, trypsin inhibitors and hemagglutinins in legumes, tannins in legumes and cereals, phytates in cereals and oilseeds, and gossypol in cottonseed protein products. Antinutritional factors may also be formed during heat/alkaline processing of protein products, yielding Maillard compounds, oxidized forms of sulfur amino acids, D-amino acids, and lysinoalanine (LAL, an unnatural amino acid derivative). The presence of high levels of dietary trypsin inhibitors from soybeans, kidney beans, or other grain legumes can cause substantial reductions in protein and amino acid digestibilities (up to 50%) in rats and pigs. Similarly, the presence of high levels of tannins in cereals, such as sorghum, and grain legumes, such as fababean (Vicia faba L.), can result in significantly reduced protein and amino acid digestibilities (up to 23%) in rats, poultry, and pigs. Studies involving phytase supplementation of production rations for swine or poultry have provided indirect evidence that normally encountered levels of phytates in cereals and legumes

Antacid medication inhibits digestion of dietary proteins and causes food allergy: a fish allergy model in BALB/c mice.

PubMed

Untersmayr, Eva; Schöll, Isabella; Swoboda, Ines; Beil, Waltraud J; Förster-Waldl, Elisabeth; Walter, Franziska; Riemer, Angelika; Kraml, Georg; Kinaciyan, Tamar; Spitzauer, Susanne; Boltz-Nitulescu, George; Scheiner, Otto; Jensen-Jarolim, Erika

2003-09-01

Digestible proteins were supposed to be irrelevant for oral sensitization and induction of food allergy. Approximately 10% of the adult population uses antacids for the treatment of dyspeptic disorders, drugs that hinder peptic digestion. In these patients, proteins that are normally degradable might act as food allergens. We aimed to study the influence of antacid intake on the allergenicity of dietary proteins, taking sturgeon caviar and parvalbumin, the major fish allergen, as examples. Caviar proteins and recombinant parvalbumin from carp, rCyp c 1, were applied for intragastric feedings with or without the antacids sucralfate, ranitidine or omeprazole, using a Balb/c mouse model. Both caviar proteins and parvalbumin were rapidly degraded in an in vitro digestion assay at pH 2.0, but not at pH 5.0, imitating the effect of antacids. The groups fed with caviar in combination with ranitidine hydrochloride intramuscularly or sucralfate orally had significant levels of caviar-specific IgE antibodies (P <.01), T-cell reactivity, and elevated counts of gastrointestinal eosinophils and mast cells. Food allergy in these groups was further evidenced by oral provocation tests and positive immediate-type skin reactivity. In contrast, feedings with caviar alone led to antigen-specific T-cell tolerance. None of the groups showed immune reactivity against the daily mouse diet. As a proof of the principle, feeding mice with parvalbumin in combination with ranitidine or omeprazole intramuscularly induced allergen-specific IgE antibodies (P <.05). When antacid medication impairs the gastric digestion, IgE synthesis toward novel dietary proteins is promoted, leading to food allergy.

An Appetite for Modernizing the Regulatory Framework for Protein Content Claims in Canada

PubMed Central

Marinangeli, Christopher P. F.; Foisy, Samara; Shoveller, Anna K.; Porter, Cara; Musa-Veloso, Kathy; Sievenpiper, John L.; Jenkins, David J. A.

2017-01-01

The need for protein-rich plant-based foods continues as dietary guidelines emphasize their contribution to healthy dietary patterns that prevent chronic disease and promote environmental sustainability. However, the Canadian Food and Drug Regulations provide a regulatory framework that can prevent Canadian consumers from identifying protein-rich plant-based foods. In Canada, protein nutrient content claims are based on the protein efficiency ratio (PER) and protein rating method, which is based on a rat growth bioassay. PERs are not additive, and the protein rating of a food is underpinned by its Reasonable Daily Intake. The restrictive nature of Canada’s requirements for supporting protein claims therefore presents challenges for Canadian consumers to adapt to a rapidly changing food environment. This commentary will present two options for modernizing the regulatory framework for protein content claims in Canada. The first and preferred option advocates that protein quality not be considered in the determination of the eligibility of a food for protein content claims. The second and less preferred option, an interim solution, is a framework for adopting the protein digestibility corrected amino acid score as the official method for supporting protein content and quality claims and harmonizes Canada’s regulatory framework with that of the USA. PMID:28832556

An Appetite for Modernizing the Regulatory Framework for Protein Content Claims in Canada.

PubMed

Marinangeli, Christopher P F; Foisy, Samara; Shoveller, Anna K; Porter, Cara; Musa-Veloso, Kathy; Sievenpiper, John L; Jenkins, David J A

2017-08-23

The need for protein-rich plant-based foods continues as dietary guidelines emphasize their contribution to healthy dietary patterns that prevent chronic disease and promote environmental sustainability. However, the Canadian Food and Drug Regulations provide a regulatory framework that can prevent Canadian consumers from identifying protein-rich plant-based foods. In Canada, protein nutrient content claims are based on the protein efficiency ratio (PER) and protein rating method, which is based on a rat growth bioassay. PERs are not additive, and the protein rating of a food is underpinned by its Reasonable Daily Intake. The restrictive nature of Canada's requirements for supporting protein claims therefore presents challenges for Canadian consumers to adapt to a rapidly changing food environment. This commentary will present two options for modernizing the regulatory framework for protein content claims in Canada. The first and preferred option advocates that protein quality not be considered in the determination of the eligibility of a food for protein content claims. The second and less preferred option, an interim solution, is a framework for adopting the protein digestibility corrected amino acid score as the official method for supporting protein content and quality claims and harmonizes Canada's regulatory framework with that of the USA.

Characterization and production of multifunctional cationic peptides derived from rice proteins.

PubMed

Taniguchi, Masayuki; Ochiai, Akihito

2017-04-01

Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions.

Physicochemical Changes and Glycation Reaction in Intermediate-Moisture Protein-Sugar Foods with and without Addition of Resveratrol during Storage.

PubMed

Sheng, Zhanwu; Gu, Mantun; Hao, Wangjun; Shen, Yixiao; Zhang, Weimin; Zheng, Lili; Ai, Binling; Zheng, Xiaoyan; Xu, Zhimin

2016-06-22

An intermediate-moisture food (IMF) model consisting of whey protein isolate and glucose and an IMF model fortified with resveratrol were used to study the effect of resveratrol on physicochemical changes and glycation of protein-sugar-rich foods during storage. The water activity (aw) of the storage was controlled at 0.75 or 0.56. The browning rate or hardness of fortified IMFs was significantly lower than that of IMFs after 45-day storage. The rate of Maillard reaction in the samples stored at aw 0.56 was higher than that of samples stored at aw 0.75. The fortified IMFs had lower levels of AGEs (advanced glycation end products), CML (N(ε)-(carboxymethyl)-l-lysine), and insoluble protein during storage. The inhibition capability of resveratrol against glycation was also confirmed by using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), liquid chromatography mass spectrometry (LC-MS), and Fourier transform infrared spectroscopy (FTIR) analysis to monitor glycated proteins and protein aggregation in the samples. The results of this study suggested that resveratrol could be used as an inhibitor to reduce the formation of undesirable AGEs and other Maillard reaction products in foods during storage.

Potential Use of Food Protein-Derived Peptides in the Treatment of Inflammatory Diseases.

PubMed

Santiago-Lopez, Lourdes; Gonzalez-Cordova, Aaron F; Hernandez-Mendoza, Adrian; Vallejo-Cordoba, Belinda

2017-01-01

In recent years, major developments in the field of inflammatory pathophysiology have clearly shown that arthritis, diabetes, intestinal bowel diseases, and obesity, which affect many people around the world, are essentially inflammatory in nature. Different anti-inflammatory drugs have been used to treat these conditions. Some people are able to take these drugs without difficulty, yet others experience negative side effects. Hence, the search for new, natural anti-inflammatory alternatives has rapidly increased in recent years. Evidence has shown that food protein-derived peptides may be one alternative for treating inflammatory diseases. Peptides are encrypted in food proteins, can be released under hydrolysis conditions, and do not cause adverse effects. Despite limited information on the mechanism of action of peptides, in vitro and animal model studies have demonstrated their potential anti-inflammatory activity. Several in vitro studies have demonstrated that peptides can inhibit different pathways of inflammation processes such as that of the nuclear factor kappalight- chain of activated B cells (NF-κB). They can also induce the production of nitric oxide synthase (iNOs) and c-Jun N-terminal kinases (JNK) as well as influence PepT1 and CaRS, the transporters of peptides to the gastrointestinal tract that are responsible for the absorption of dietary peptides in the intestine. However, contradictory evidence has been reported in clinical assays. Hence, in this review, we present the latest research on the anti-inflammatory activity of food protein-derived peptides and provide future perspectives on the use of peptides as potential natural sources of therapeutic treatments. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Tackling Bet v 1 and associated food allergies with a single hybrid protein.

PubMed

Hofer, Heidi; Asam, Claudia; Hauser, Michael; Nagl, Birgit; Laimer, Josef; Himly, Martin; Briza, Peter; Ebner, Christof; Lang, Roland; Hawranek, Thomas; Bohle, Barbara; Lackner, Peter; Ferreira, Fátima; Wallner, Michael

2017-08-01

Allergy vaccines should be easily applicable, safe, and efficacious. For Bet v 1-mediated birch pollen and associated food allergies, a single wild-type allergen does not provide a complete solution. We aimed to combine immunologically relevant epitopes of Bet v 1 and the 2 clinically most important related food allergens from apple and hazelnut to a single hybrid protein, termed MBC4. After identification of T cell epitope-containing parts on each of the 3 parental allergens, the hybrid molecule was designed to cover relevant epitopes and evaluated in silico. Thereby a mutation was introduced into the hybrid sequence, which should alter the secondary structure without compromising the immunogenic properties of the molecule. MBC4 and the parental allergens were purified to homogeneity. Analyses of secondary structure elements revealed substantial changes rendering the hybrid de facto nonreactive with patients' serum IgE. Nevertheless, the protein was monomeric in solution. MBC4 was able to activate T-cell lines from donors with birch pollen allergy and from mice immunized with the parental allergens. Moreover, on immunization of mice and rabbits, MBC4 induced cross-reactive IgG antibodies, which were able to block the binding of human serum IgE. Directed epitope rearrangements combined with a knowledge-based structural modification resulted in a protein unable to bind IgE from allergic patients. Still, properties to activate specific T cells or induce blocking antibodies were conserved. This suggests that MBC4 is a suitable vaccine candidate for the simultaneous treatment of Bet v 1 and associated food allergies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Geospatial techniques to Identify the Location of Farmers Markets and Community Gardens within Food Deserts in Virginia

NASA Astrophysics Data System (ADS)

Sriharan, S.; Meekins, D.; Comar, M.; Bradshaw, S.; Jackson, L.

2017-12-01

Specifically, a food desert is defined as an area where populations live more than one mile from a supermarket or large grocery store if in an urban area or more than 10 miles from a supermarket or large grocery store if in a rural area (Ver Ploeg et al. 2012). According to the U.S. Department of Agriculture, a food desert is "an area in the United States with limited access to affordable and nutritious food, particularly such an area composed of predominately lower-income neighborhoods and communities" (110th Congress 2008). Three fourths of these food deserts are urban. In the Commonwealth of Virginia, Petersburg City is among the eight primary localities, where its population is living in a food desert. This project will compare those identified food deserts in Virginia (areas around Virginia State University) with focus to where farmers markets and community gardens are being established. The hypothesis of this study is that these minority groups do not get healthy food due to limited access to grocery stores and superstores. To address this problem, the community development activities should focus on partnering local Petersburg convenience stores with farmers and community gardeners to sell fresh produce. Existing data was collected on convenient stores and community gardens in Petersburg City and Chesterfield County. Rare data was generated for Emporia, Lynchburg and Hopewell. The data was compiled through field work and mapping with ArcGIS where markets and gardens are being established, and create a spatial analysis of their location We have localities that reflect both rural and urban areas. The project provides educational support for students who will find solution to community problems by developing activities to: (a) define and examine characteristics of food deserts, (b) identify causes and consequences of food deserts and determine if their community is a food desert, (c) research closest food desert to their school, and (d) design solutions to help

Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

PubMed

Shen, Xianjun; Yi, Li; Jiang, Xingpeng; He, Tingting; Yang, Jincai; Xie, Wei; Hu, Po; Hu, Xiaohua

2017-01-01

How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment). It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

Nutrient profiling can help identify foods of good nutritional quality for their price: a validation study with linear programming.

PubMed

Maillot, Matthieu; Ferguson, Elaine L; Drewnowski, Adam; Darmon, Nicole

2008-06-01

Nutrient profiling ranks foods based on their nutrient content. They may help identify foods with a good nutritional quality for their price. This hypothesis was tested using diet modeling with linear programming. Analyses were undertaken using food intake data from the nationally representative French INCA (enquête Individuelle et Nationale sur les Consommations Alimentaires) survey and its associated food composition and price database. For each food, a nutrient profile score was defined as the ratio between the previously published nutrient density score (NDS) and the limited nutrient score (LIM); a nutritional quality for price indicator was developed and calculated from the relationship between its NDS:LIM and energy cost (in euro/100 kcal). We developed linear programming models to design diets that fulfilled increasing levels of nutritional constraints at a minimal cost. The median NDS:LIM values of foods selected in modeled diets increased as the levels of nutritional constraints increased (P = 0.005). In addition, the proportion of foods with a good nutritional quality for price indicator was higher (P < 0.0001) among foods selected (81%) than among foods not selected (39%) in modeled diets. This agreement between the linear programming and the nutrient profiling approaches indicates that nutrient profiling can help identify foods of good nutritional quality for their price. Linear programming is a useful tool for testing nutrient profiling systems and validating the concept of nutrient profiling.

Cottonseed protein derivatives as nutritional and functional supplements in food formulations.

PubMed

Cherry, J P; Berardi, L C; Zarins, Z M; Wadsworth, J I; Vinnett, C H

1978-01-01

Cottonseeds contain protein with desirable food functional and nutritional properties. Storage globulins make up most of the protein stored in cottonseed and can be separated into five fractions by gel filtration chromatography. Each fraction is distinguishable from the other by its amino acid and polyacrylamide gel electrophoretic properties. Proteins of cottonseed contribute greatly to the functional properties of emulsions, co-isolates, and texturized derivatives. For example, increasing the amount of high protein cottonseed flour in wheat suspensions from 2% to 10% improved the capacity (54-97 ml of oil) and viscosity (5,000-100,000+ cps) of emulsions. The 10% suspension formed emulsions with increasing oil capacity (84-100 ml) and viscosity (28,000-100,000+ cps) as the pH was adjusted from 4.5 to 9.5. Consistencies of the products ranged from that of salad dressing (low percent suspensions, or acid pH) to that of mayonnaise (high percent, or basic pH). These data were utilized to derive a multiple regression model to predict optimum use of cottonseed proteins in emulsions of varying consistencies. A coprecipitated isolate containing greater than 94% protein was prepared from a blend of cottonseed and peanut flours. Amino acid content of the co-isolate reflected that of the protein in the two flours of the composite. The co-isolate has lower gossypol level and improved color and functional properties than a cottonseed protein isolate. Storage protein isolate of cottonseed suspended in aqueous solution and heated with constant stirring forms a texturized product; the quality of the product depends on heat, pH, salt, and the quantity of nonstorage proteins. Protein and amino acid content of meat products were improved by the addition of the texturized protein of cottonseed.

All About the Protein Foods Group

MedlinePlus

... Nutrients and Health Benefits TIPS: Vary Your Veggies Beans and Peas Are Unique Foods Food Gallery Take ... Group? All foods made from meat, poultry, seafood, beans and peas, eggs, processed soy products, nuts, and ...

A systematic analysis of the PARP protein family identifies new functions critical for cell physiology

PubMed Central

Vyas, Sejal; Chesarone-Cataldo, Melissa; Todorova, Tanya; Huang, Yun-Han; Chang, Paul

2013-01-01

The poly(ADP-ribose) polymerase (PARP) family of proteins use NAD+ as their substrate to modify acceptor proteins with adenosine diphosphate-ribose (ADPr) modifications. The function of most PARPs under physiological conditions is unknown. Here, to better understand this protein family, we systematically analyze the cell cycle localization of each PARP and of poly(ADP-ribose), a product of PARP activity, then identify the knock-down phenotype of each protein and perform secondary assays to elucidate function. We show that most PARPs are cytoplasmic, identify cell cycle differences in the ratio of nuclear to cytoplasmic poly(ADP-ribose), and identify four phenotypic classes of PARP function. These include the regulation of membrane structures, cell viability, cell division, and the actin cytoskeleton. Further analysis of PARP14 shows that it is a component of focal adhesion complexes required for proper cell motility and focal adhesion function. In total, we show that PARP proteins are critical regulators of eukaryotic physiology. PMID:23917125

Protein digestibility-corrected amino acid scores for bean and bean-rice infant weaning food products.

PubMed

Kannan, S; Nielsen, S S; Mason, A C

2001-10-01

Vegetable proteins are an integral part of infant weaning diets in Latin America. Protein quality in plant-based products, however, is constrained by amino acid composition and intrinsically present antinutritional factors. The goal of this study was to improve bean protein quality by utilizing fermentation and germination processing. The objectives were to determine if protein quality, as measured by Food and Agricultural Organization (FAO) approved True Protein Digestibility (TPD) and Protein Digestibility-Corrected Amino Acid Scores (PDCAAS), of formulated bean-based weaning products could be improved upon fermentation and germination and if protein quality could be further improved when processed beans were combined with cooked rice. Results showed that the highest TPD and PDCAAS values were obtained for cooked germinated beans combined with rice. The TPD values for products ranged from 80 to 91%, and the PDCAAS values were 0.38-0.51. There was no significant increase (P < 0.05) of either TPD or PDCAAS values upon fermentation. Germination increased TPD of cooked bean products; this increase was not, however, accompanied by an increase in PDCAAS. When combined with rice, the PDCAAS values for all bean products improved significantly, thus supporting the concept of cereal-legume complementation. In conclusion, this study showed the range of PDCAAS in processed black bean and bean-rice infant weaning food products. The potential for incorporation of these products into the diets of weaning age Latin American children would, however, be confirmed only after validation with growth or metabolic balance studies in human infants.

A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways*

PubMed Central

Lecat, Sandra; Matthes, Hans W.D.; Pepperkok, Rainer; Simpson, Jeremy C.; Galzi, Jean-Luc

2015-01-01

Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic proteins was performed using translocation criteria. The screening of 193 fluorescently tagged human proteins identified eight proteins that responded to activation of the tachykinin NK2 receptor by a change in their intracellular localization. Previously we have presented the functional characterization of one of these proteins, REDD1, that translocates to the plasma membrane. Here we report the results of the entire screening. The process of cell activation was recorded on videos at different time points and all the videos can be visualized on a dedicated website. The proteins BAIAP3 and BIN1, partially translocated to the plasma membrane upon activation of NK2 receptors. Proteins ARHGAP12 and PKM2 translocated toward membrane blebs. Three proteins that associate with the cytoskeleton were of particular interest : PLEKHH2 rearranged from individual dots located near the cell-substrate adhesion surface into lines of dots. The speriolin-like protein, SPATC1L, redistributed to cell-cell junctions. The Chloride intracellular Channel protein, CLIC2, translocated from actin-enriched plasma membrane bundles to cell-cell junctions upon activation of NK2 receptors. CLIC2, and one of its close paralogs, CLIC4, were further shown to respond with the same translocation pattern to muscarinic M3 and lysophosphatidic LPA receptors. This screen allowed us to identify potential actors in signaling pathways downstream of G protein-coupled receptors and could be scaled-up for high-content screening. PMID:25759509

A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways.

PubMed

Lecat, Sandra; Matthes, Hans W D; Pepperkok, Rainer; Simpson, Jeremy C; Galzi, Jean-Luc

2015-05-01

Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic proteins was performed using translocation criteria. The screening of 193 fluorescently tagged human proteins identified eight proteins that responded to activation of the tachykinin NK2 receptor by a change in their intracellular localization. Previously we have presented the functional characterization of one of these proteins, REDD1, that translocates to the plasma membrane. Here we report the results of the entire screening. The process of cell activation was recorded on videos at different time points and all the videos can be visualized on a dedicated website. The proteins BAIAP3 and BIN1, partially translocated to the plasma membrane upon activation of NK2 receptors. Proteins ARHGAP12 and PKM2 translocated toward membrane blebs. Three proteins that associate with the cytoskeleton were of particular interest : PLEKHH2 rearranged from individual dots located near the cell-substrate adhesion surface into lines of dots. The speriolin-like protein, SPATC1L, redistributed to cell-cell junctions. The Chloride intracellular Channel protein, CLIC2, translocated from actin-enriched plasma membrane bundles to cell-cell junctions upon activation of NK2 receptors. CLIC2, and one of its close paralogs, CLIC4, were further shown to respond with the same translocation pattern to muscarinic M3 and lysophosphatidic LPA receptors. This screen allowed us to identify potential actors in signaling pathways downstream of G protein-coupled receptors and could be scaled-up for high-content screening. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

More than royal food - Major royal jelly protein genes in sexuals and workers of the honeybee Apis mellifera.

PubMed

Buttstedt, Anja; Moritz, Robin Fa; Erler, Silvio

2013-11-27

In the honeybee Apis mellifera, female larvae destined to become a queen are fed with royal jelly, a secretion of the hypopharyngeal glands of young nurse bees that rear the brood. The protein moiety of royal jelly comprises mostly major royal jelly proteins (MRJPs) of which the coding genes (mrjp1-9) have been identified on chromosome 11 in the honeybee's genome. We determined the expression of mrjp1-9 among the honeybee worker caste (nurses, foragers) and the sexuals (queens (unmated, mated) and drones) in various body parts (head, thorax, abdomen). Specific mrjp expression was not only found in brood rearing nurse bees, but also in foragers and the sexuals. The expression of mrjp1 to 7 is characteristic for the heads of worker bees, with an elevated expression of mrjp1-4 and 7 in nurse bees compared to foragers. Mrjp5 and 6 were higher in foragers compared to nurses suggesting functions in addition to those of brood food proteins. Furthermore, the expression of mrjp9 was high in the heads, thoraces and abdomen of almost all female bees, suggesting a function irrespective of body section. This completely different expression profile suggests mrjp9 to code for the most ancestral major royal jelly protein of the honeybee.

Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion*

PubMed Central

Hung, Chien-Wen; Klein, Tobias; Cassidy, Liam; Linke, Dennis; Lange, Sabrina; Anders, Uwe; Bureik, Matthias; Heinzle, Elmar; Schneider, Konstantin; Tholey, Andreas

2016-01-01

Protein secretion in yeast is a complex process and its efficiency depends on a variety of parameters. We performed a comparative proteome analysis of a set of Schizosaccharomyces pombe strains producing the α-glucosidase maltase in increasing amounts to investigate the overall proteomic response of the cell to the burden of protein production along the various steps of protein production and secretion. Proteome analysis of these strains, utilizing an isobaric labeling/two dimensional LC-MALDI MS approach, revealed complex changes, from chaperones and secretory transport machinery to proteins controlling transcription and translation. We also found an unexpectedly high amount of changes in enzyme levels of the central carbon metabolism and a significant up-regulation of several amino acid biosyntheses. These amino acids were partially underrepresented in the cellular protein compared with the composition of the model protein. Additional feeding of these amino acids resulted in a 1.5-fold increase in protein secretion. Membrane fluidity was identified as a second bottleneck for high-level protein secretion and addition of fluconazole to the culture caused a significant decrease in ergosterol levels, whereas protein secretion could be further increased by a factor of 2.1. In summary, we show that high level protein secretion causes global changes of protein expression levels in the cell and that precursor availability and membrane composition limit protein secretion in this yeast. In this respect, comparative proteome analysis is a powerful tool to identify targets for an efficient increase of protein production and secretion in S. pombe. Data are available via ProteomeXchange with identifiers PXD002693 and PXD003016. PMID:27477394

Allergenic potential of novel foods.

PubMed

Meredith, Clive

2005-11-01

Concerns have been expressed that the introduction of novel foods into the diet might lead to the development of new food allergies in consumers. Novel foods can be conveniently divided into GM and non-GM categories. Decision-tree approaches (e.g. International Life Sciences Institute-International Food Biotechnology Council and WHO/FAO) to assess the allergenic potential of GM foods were developed following the discovery, during product development, of the allergenic potential of GM soyabean expressing a gene encoding a storage protein from Brazil nut (Bertolletia excelsa). Within these decision trees considerations include: the source of the transgene; amino acid homology with known allergens; cross-reactivity with IgE from food-allergic individuals; resistance to proteolysis; prediction using animal models of food allergy. Such decision trees are under constant review as new knowledge and improved models emerge, but they provide a useful framework for the assessment of the allergenic potential of GM foods. For novel non-GM foods the assessment of allergenic potential is more subjective; some foods or food ingredients will need no assessment other than a robust protein assay to demonstrate the absence of protein. Where protein is present in the novel non-GM food, hazard and risk assessments need to be made in terms of the quantity of protein that might be consumed, the identity of individual protein components and their relationships to known food allergens. Where necessary, this assessment would extend to serum screening for potential cross-reactivities, skin-prick tests in previously-sensitised individuals and double-blind placebo-controlled food challenges.

Increased C-reactive protein and fever in Japanese infants with food protein-induced enterocolitis syndrome.

PubMed

Kimura, Mitsuaki; Ito, Yasunori; Tokunaga, Fumika; Meguro, Takaaki; Shimomura, Masaki; Morishita, Hideaki; Seto, Shiro

2016-09-01

Increased C-reactive protein (CRP) and fever are observed in some infants with food protein-induced enterocolitis syndrome (FPIES) in Japan, but the reproducibility of these findings has not yet been confirmed on oral food challenge (OFC). Fourteen infants with FPIES induced by cow's milk (CM) formula were enrolled. OFC using CM formula was performed on each infant once or repeatedly (total 18 tests), with a stepwise incremental protocol in an infection-controlled setting. CRP was measured 24 h after the last ingestion of the CM formula. Increased CRP was observed in 11 of the 18 OFC conducted (median, 2.60 mg/dL; range, 0.22-4.84 mg/dL). Fever was induced in six occasions during OFC. Serum CRP in the patients with fever increased to median 3.76 mg/dL (range, <0.7-4.84 mg/dL), which was significantly higher than that of the patients without fever (median <0.1 mg/dL; range, <0.1-2.6 mg/dL; P < 0.001). CRP during OFC significantly correlated with that at disease onset (rs = 0.62, P < 0.02). Three of the four patients with fever at disease onset also had fever during OFC. Increased CRP and fever are reproducible during OFC in some infants with FPIES, suggesting that these are not accidental phenomena, but instead are associated with FPIES itself in Japanese patients. © 2016 The Authors. Pediatrics International published by John Wiley & Sons Australia, Ltd on behalf of Japan Pediatric Society.

Food mutagens: The role of cooked food in genetic changes

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-07-01

Of all the toxic substances producing during cooking, the most important are likely to be the heterocyclic amines. For 17 years, LLNL researchers have been identifying these food mutagens, measuring their abundance in cooked foods typical of the Western diet, working to understand how they can trigger malignant tumors in laboratory animals that have been exposed to high mutagen doses, and estimating the importance of human exposures. Our success is largely a function of the interdisciplinary approach we have taken to quantify food mutagens and to study their biological effects. LLNL investigators were the first to identify five of themore » most important mutagens in heated food, including PhIP and DiMeIQx. We have shown that fried beef may be the most important single source of heterocyclic amines in the human diet and the PhIP accounts for most of the combined mass of mutagens in fried beef cooked well-done. Most nonmeat foods contain low or undetectable levels of these types of compounds, but some cooked protein-containing foods, such as those high in wheat gluten, have significant levels of unknown aromatic amine mutagens. Cooking time and temperature significantly affect the amounts of mutagens generated. For example, reducing the frying temperature of ground beef from 250 to 200{degrees}C lowers the mutagenic activity by six- to sevenfold. Microwave pretreatment of meat and discarding the liquid that is formed also greatly reduces the formation of heterocyclic amines. Our related work on dose and risk assessment will be described in a forthcoming article.« less

The Involvement of Thaumatin-Like Proteins in Plant Food Cross-Reactivity: A Multicenter Study Using a Specific Protein Microarray

PubMed Central

Palacín, Arantxa; Rivas, Luis A.; Gómez-Casado, Cristina; Aguirre, Jacobo; Tordesillas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; Bonny, José A. Cumplido; Flores, Enrique; García-Alvarez-Eire, Mar G.; García-Nuñez, Ignacio; Fernández, Francisco J.; Gamboa, Pedro; Muñoz, Rosa; Sánchez-Monge, Rosa; Torres, Maria; Losada, Susana Varela; Villalba, Mayte; Vega, Francisco; Parro, Victor; Blanca, Miguel; Salcedo, Gabriel; Díaz-Perales, Araceli

2012-01-01

Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs) in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG) and another against pollens but tolerant to food-plant allergens (PAG), were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%), chestnut TLP (24%) and plane pollen TLP (22%) proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited >50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy. PMID:22970164

A new computational strategy for identifying essential proteins based on network topological properties and biological information.

PubMed

Qin, Chao; Sun, Yongqi; Dong, Yadong

2017-01-01

Essential proteins are the proteins that are indispensable to the survival and development of an organism. Deleting a single essential protein will cause lethality or infertility. Identifying and analysing essential proteins are key to understanding the molecular mechanisms of living cells. There are two types of methods for predicting essential proteins: experimental methods, which require considerable time and resources, and computational methods, which overcome the shortcomings of experimental methods. However, the prediction accuracy of computational methods for essential proteins requires further improvement. In this paper, we propose a new computational strategy named CoTB for identifying essential proteins based on a combination of topological properties, subcellular localization information and orthologous protein information. First, we introduce several topological properties of the protein-protein interaction (PPI) network. Second, we propose new methods for measuring orthologous information and subcellular localization and a new computational strategy that uses a random forest prediction model to obtain a probability score for the proteins being essential. Finally, we conduct experiments on four different Saccharomyces cerevisiae datasets. The experimental results demonstrate that our strategy for identifying essential proteins outperforms traditional computational methods and the most recently developed method, SON. In particular, our strategy improves the prediction accuracy to 89, 78, 79, and 85 percent on the YDIP, YMIPS, YMBD and YHQ datasets at the top 100 level, respectively.

Genetic diversity of functional food species Spinacia oleracea L. by protein markers.

PubMed

Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

2014-01-01

Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers.

EAACI Food Allergy and Anaphylaxis Guidelines. Protecting consumers with food allergies: understanding food consumption, meeting regulations and identifying unmet needs.

PubMed

Muraro, A; Hoffmann-Sommergruber, K; Holzhauser, T; Poulsen, L K; Gowland, M H; Akdis, C A; Mills, E N C; Papadopoulos, N; Roberts, G; Schnadt, S; van Ree, R; Sheikh, A; Vieths, S

2014-11-01

Individuals suffering from IgE-mediated food allergy usually have to practise life-long food allergen avoidance. This document aims to provide an overview of recent evidence-based recommendations for allergen risk assessment and management in the food industry and discusses unmet needs and expectations of the food allergic consumer in that context. There is a general duty of care on the food industry and obligations in European Union legislation to reduce and manage the presence of allergens alongside other food hazards. Current evidence enables quantification of allergen reference doses used to set-up reliable food safety management plans for some foods. However, further work is required to include a wider variety of foods and to understand the impact of the food matrix as well as additional factors which affect the progression and severity of symptoms as a function of dose. Major concerns have been raised by patients, carers and patient groups about the use of precautionary 'may contain' labelling to address the issue of unintended presence of allergens; these therefore need to be reconsidered. New and improved allergen detection methods should be evaluated for their application in food production. There is an urgent requirement for effective communication between healthcare professionals, patient organizations, food industry representatives and regulators to develop a better approach to protecting consumers with food allergies. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Lsa63, a newly identified surface protein of Leptospira interrogans binds laminin and collagen IV.

PubMed

Vieira, Monica L; de Morais, Zenaide M; Gonçales, Amane P; Romero, Eliete C; Vasconcellos, Silvio A; Nascimento, Ana L T O

2010-01-01

Leptospira interrogans is the etiological agent of leptospirosis, a zoonotic disease that affects populations worldwide. We have identified in proteomic studies a protein that is encoded by the gene LIC10314 and expressed in virulent strain of L. interrogans serovar Pomona. This protein was predicted to be surface exposed by PSORT program and contains a p83/100 domain identified by BLAST analysis that is conserved in protein antigens of several strains of Borrelia and Treponema spp. The proteins containing this domain have been claimed antigen candidates for serodiagnosis of Lyme borreliosis. Thus, we have cloned the LIC10314 and expressed the protein in Escherichia coli BL21-SI strain by using the expression vector pAE. The recombinant protein tagged with N-terminal hexahistidine was purified by metal-charged chromatography and characterized by circular dichroism spectroscopy. This protein is conserved among several species of pathogenic Leptospira and absent in the saprophytic strain L. biflexa. We confirm by liquid-phase immunofluorescence assays with living organisms that this protein is most likely a new surface leptospiral protein. The ability of the protein to mediate attachment to ECM components was evaluated by binding assays. The leptospiral protein encoded by LIC10314, named Lsa63 (Leptospiral surface adhesin of 63kDa), binds strongly to laminin and collagen IV in a dose-dependent and saturable fashion. In addition, Lsa63 is probably expressed during infection since it was recognized by antibodies of serum samples of confirmed-leptospirosis patients in convalescent phase of the disease. Altogether, the data suggests that this novel identified surface protein may be involved in leptospiral pathogenesis. 2009 The British Infection Society. Published by Elsevier Ltd. All rights reserved.

Effect of drinking compared with eating sugars or whey protein on short-term appetite and food intake.

PubMed

Akhavan, T; Luhovyy, B L; Anderson, G H

2011-04-01

It is hypothesized that a solid form of food or food components suppresses subjective appetite and short-term food intake (FI) more than a liquid form. To compare the effect of eating solid vs drinking liquid forms of gelatin, sucrose and its component mixtures, and whey protein, on subjective appetite and FI in young men. A randomized crossover design was used in three experiments in which the subjects were healthy males of normal weight. Solid and liquid forms of gelatin (6 g) (experiment 1, n=14), sucrose (75 g) and a mixture of 50% glucose/50% fructose (G50:F50) (experiment 2, n=15), and acid and sweet whey protein (50 g) (experiment 3, n=14) were compared. The controls were water (experiments 1 and 3) and calorie-free sweetened water with gelatin (sweet gelatin, experiment 1) or calorie-free sweetened water (sweet control, experiment 2). Subjective average appetite was measured by visual analog scales over 1 h and ad libitum FI was measured 1 h after treatment consumption. Average appetite area under the curve was not different between solid and liquid forms of sugars, but was larger, indicating greater satiety for solid compared with liquid forms of gelatin and sweet, but not acid whey protein. The FI was not different from that of control because of solid or liquid sugars or gelatin treatments. However, both solid and liquid forms of whey protein, with no difference among them, suppressed FI compared with control (P<0.05). Macronutrient composition is more important than physical state of foods in determining subjective appetite and FI.

Analysis of U.S. Food and Drug Administration food allergen recalls after implementation of the food allergen labeling and consumer protection act.

PubMed

Gendel, Steven M; Zhu, Jianmei

2013-11-01

To avoid potentially life-threatening reactions, food allergic consumers rely on information on food labels to help them avoid exposure to a food or ingredient that could trigger a reaction. To help consumers in the United States obtain the information that they need, the Food Allergen Labeling and Consumer Protection Act of 2004 defined a major food allergen as being one of eight foods or food groups and any ingredient that contains protein from one of these foods or food groups. A food that contains an undeclared major food allergen is misbranded under the U.S. Food, Drug, and Cosmetic Act and is subject to recall. Food allergen labeling problems are the most common cause of recalls for U.S. Food and Drug Administration (FDA)-regulated food products. To help understand why food allergen recalls continue to occur at a high rate, information on each food allergen recall that occurred in fiscal years 2007 through 2012 was obtained from the FDA recall database. This information was analyzed to identify the food, allergen, root cause, and mode of discovery for each food allergen recall. Bakery products were the most frequently recalled food type, and milk was the most frequently undeclared major food allergen. Use of the wrong package or label was the most frequent problem leading to food allergen recalls. These data are the first reported that indicate the importance of label and package controls as public health measures.

Camel milk protein hydrolysates with improved technofunctional properties and enhanced antioxidant potential in in vitro and in food model systems.

PubMed

Al-Shamsi, Kholoud Awad; Mudgil, Priti; Hassan, Hassan Mohamed; Maqsood, Sajid

2018-01-01

Camel milk protein hydrolysates (CMPH) were generated using proteolytic enzymes, such as alcalase, bromelain, and papain, to explore the effect on the technofunctional properties and antioxidant potential under in vitro and in real food model systems. Characterization of the CMPH via degree of hydrolysis, sodium dodecyl sulfate-PAGE, and HPLC revealed that different proteins in camel milk underwent degradation at different degrees after enzymatic hydrolysis using 3 different enzymes for 2, 4, and 6 h, with papain displaying the highest degradation. Technofunctional properties, such as emulsifying activity index, surface hydrophobicity, and protein solubility, were higher in CMPH than unhydrolyzed camel milk proteins. However, the water and fat absorption capacity were lower in CMPH compared with unhydrolyzed camel milk proteins. Antioxidant properties as assessed by 2,2-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging activities and metal-chelating activity were enhanced after hydrolysis, in contrast to ferric-reducing antioxidant power which showed a decrease after hydrolysis. The CMPH were also tested in real food model systems for their potential to inhibit lipid peroxidation in fish mince and grape seed oil-in-water emulsion, and we found that papain-produced hydrolysate displayed higher inhibition than alcalase- and bromelain-produced hydrolysates. Therefore, the CMPH demonstrated effective antioxidant potential in vitro as well as in real food systems and showed enhanced functional properties, which guarantees their potential applications in functional foods. The present study is one of few reports available on CMPH being explored in vitro as well as in real food model systems. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Food safety assessment of an antifungal protein from Moringa oleifera seeds in an agricultural biotechnology perspective.

PubMed

Pinto, Clidia E M; Farias, Davi F; Carvalho, Ana F U; Oliveira, José T A; Pereira, Mirella L; Grangeiro, Thalles B; Freire, José E C; Viana, Daniel A; Vasconcelos, Ilka M

2015-09-01

Mo-CBP3 is an antifungal protein produced by Moringa oleifera which has been investigated as potential candidate for developing transgenic crops. Before the use of novel proteins, food safety tests must be conducted. This work represents an early food safety assessment of Mo-CBP3, using the two-tiered approach proposed by ILSI. The history of safe use, mode of action and results for amino acid sequence homology using the full-length and short contiguous amino acids sequences indicate low risk associated to this protein. Mo-CBP3 isoforms presented a reasonable number of alignments (>35% identity) with allergens in a window of 80 amino acids. This protein was resistant to pepsin degradation up to 2 h, but it was susceptible to digestion using pancreatin. Many positive attributes were presented for Mo-CBP3. However, this protein showed high sequence homology with allergens and resistance to pepsin digestion that indicates that further hypothesis-based testing on its potential allergenicity must be done. Additionally, animal toxicity evaluations (e.g. acute and repeated dose oral exposure assays) must be performed to meet the mandatory requirements of several regulatory agencies. Finally, the approach adopted here exemplified the importance of performing an early risk assessment of candidate proteins for use in plant transformation programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identifying paths of allosteric communication in the protein BirA through simulations

NASA Astrophysics Data System (ADS)

Custer, Gregory; Beckett, Dorothy; Matysiak, Silvina

Biotin ligase/repressor (BirA) is a bifunctional enzyme which adenylates biotin and transfers the product, biotinyl-5'-AMP (bio-5'-AMP) to biotin carboxyl carrier protein (BCCP). In the absence of BCCP, bio-5'-AMP promotes the dimerization of BirA. In dimer form, the BirA.bio-5'-AMP complex is able to bind to the biotin operator and prevents further synthesis of biotin. The bio-5'-AMP binds away from the dimer interface, so it is acting as an allosteric activator. We perform all-atom molecular dynamics simulations with BirA to look at fluctuations within the protein at equilibrium. We simulate apoBirA, liganded BirA, as well as two mutants, M211A and V219A. In agreement with experimental observations, several loops of the protein become stabilized for the liganded BirA when compared to the apo protein. In addition, changes in the dimer interface are observed for the M211A and V219A mutations, which are located in the ligand binding region. Using inter-residue correlation coefficients and pair energies a communication network through the protein is constructed. With this network we have identified paths which have the potential to be important in allosteric activation of BirA. These paths and the methods we use to identify them will be presented.

In-situ Click Reaction Coupled with Quantitative Proteomics for Identifying Protein Targets of Catechol Estrogens.

PubMed

Liang, Huei-Chen; Liu, Yi-Chen; Chen, Hsin; Ku, Ming Chun; Do, Quynh-Trang; Wang, Chih-Yen; Tzeng, Shun-Fen; Chen, Shu-Hui

2018-06-13

Catechol estrogens (CEs) are metabolic electrophiles that actively undergo covalent interaction with cellular proteins, influencing molecular function. There is no feasible method to identify their binders in a living system. Herein, we developed a click chemistry-based approach using ethinylestradiol (EE2) as the precursor probe coupled with quantitative proteomics to identify protein targets of CEs and classify their binding strengths. Using in-situ metabolic conversion and click reaction in liver microsomes, CEs-protein complex was captured by the probe, digested by trypsin, stable isotope labeled via reductive amination, and analyzed by liquid chromatography-mass spectrometry (LC-MS). A total of 334 liver proteins were repeatedly identified (n  2); 274 identified proteins were classified as strong binders based on precursor mass mapping. The binding strength was further scaled by D/H ratio (activity probe/solvent): 259 strong binders had D/H > 5.25; 46 weak binders had 5.25 > D/H > 1; 5 non-specific binders (keratins) had D/H < 1. These results were confirmed using spiked covalent control (strong binder) and noncovalent control (weak binder), as well as in vitro testing of cytochrome c (D/H = 5.9) which showed covalent conjugation with CEs. Many identified strong binders, such as glutathione transferase, catechol-O-methyl transferase, superoxide dismutase, catalase, glutathione peroxidase, and cytochrome c, are involved in cellular redox processes or detoxification activities. CE conjugation was shown to suppress the superoxide oxidase activity of cytochrome c, suggesting that CEs modification may alter the redox action of cellular proteins. Due to structural similarity and inert alkyne group, EE2 probe is very likely to capture protein targets of CEs in general. Thus, this strategy can be adopted to explore the biological impact of CEs modification in living systems.

Foams prepared from whey protein isolate and egg white protein: 2. Changes associated with angel food cake functionality.

PubMed

Berry, Tristan K; Yang, Xin; Foegeding, E Allen

2009-06-01

The effects of sucrose on the physical properties and thermal stability of foams prepared from 10% (w/v) protein solutions of whey protein isolate (WPI), egg white protein (EWP), and their combinations (WPI/EWP) were investigated in wet foams and angel food cakes. Incorporation of 12.8 (w/v) sucrose increased EWP foam stability (drainage 1/2 life) but had little effect on the stability of WPI and WPI/EWP foams. Increased stability was not due to viscosity alone. Sucrose increased interfacial elasticity (E ') of EWP and decreased E' of WPI and WPI/EWP combinations, suggesting that altered interfacial properties increased stability in EWP foams. Although 25% WPI/75% EWP cakes had similar volumes as EWP cakes, cakes containing WPI had larger air cells. Changes during heating showed that EWP foams had network formation starting at 45 degrees C, which was not observed in WPI and WPI/EWP foams. Moreover, in batters, which are foams with additional sugar and flour, a stable foam network was observed from 25 to 85 degrees C for batters made from EWP foams. Batters containing WPI or WPI/EWP mixtures showed signs of destabilization starting at 25 degrees C. These results show that sucrose greatly improved the stability of wet EWP foams and that EWP foams form network structures that remain stable during heating. In contrast, sucrose had minimal effects on stability of WPI and WPI/EWP wet foams, and batters containing these foams showed destabilization prior to heating. Therefore, destabilization processes occurring in the wet foams and during baking account for differences in angel food cake quality.

CoMoDo: identifying dynamic protein domains based on covariances of motion.

PubMed

Wieninger, Silke A; Ullmann, G Matthias

2015-06-09

Most large proteins are built of several domains, compact units which enable functional protein motions. Different domain assignment approaches exist, which mostly rely on concepts of stability, folding, and evolution. We describe the automatic assignment method CoMoDo, which identifies domains based on protein dynamics. Covariances of atomic fluctuations, here calculated by an Elastic Network Model, are used to group residues into domains of different hierarchical levels. The so-called dynamic domains facilitate the study of functional protein motions involved in biological processes like ligand binding and signal transduction. By applying CoMoDo to a large number of proteins, we demonstrate that dynamic domains exhibit features absent in the commonly assigned structural domains, which can deliver insight into the interactions between domains and between subunits of multimeric proteins. CoMoDo is distributed as free open source software at www.bisb.uni-bayreuth.de/CoMoDo.html .

Probabilistic analysis for identifying the driving force of protein folding

NASA Astrophysics Data System (ADS)

Tokunaga, Yoshihiko; Yamamori, Yu; Matubayasi, Nobuyuki

2018-03-01

Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

[Food allergy or food intolerance?].

PubMed

Maître, S; Maniu, C-M; Buss, G; Maillard, M H; Spertini, F; Ribi, C

2014-04-16

Adverse food reactions can be classified into two main categories depending on wether an immune mechanism is involved or not. The first category includes immune mediated reactions like IgE mediated food allergy, eosinophilic oesophagitis, food protein-induced enterocolitis syndrome and celiac disease. The second category implies non-immune mediated adverse food reactions, also called food intolerances. Intoxications, pharmacologic reactions, metabolic reactions, physiologic, psychologic or reactions with an unknown mechanism belong to this category. We present a classification of adverse food reactions based on the pathophysiologic mechanism that can be useful for both diagnostic approach and management.

Using distant supervised learning to identify protein subcellular localizations from full-text scientific articles.

PubMed

Zheng, Wu; Blake, Catherine

2015-10-01

Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to curate knowledge bases with automated approaches that leverage the increased availability of full-text scientific articles. This paper describes experiments that use distant supervised learning to identify protein subcellular localizations, which are important to understand protein function and to identify candidate drug targets. Experiments consider Swiss-Prot, the manually annotated subset of the UniProtKB protein knowledge base, and 43,000 full-text articles from the Journal of Biological Chemistry that contain just under 11.5 million sentences. The system achieves 0.81 precision and 0.49 recall at sentence level and an accuracy of 57% on held-out instances in a test set. Moreover, the approach identifies 8210 instances that are not in the UniProtKB knowledge base. Manual inspection of the 50 most likely relations showed that 41 (82%) were valid. These results have immediate benefit to researchers interested in protein function, and suggest that distant supervision should be explored to complement other manual data curation efforts. Copyright © 2015 Elsevier Inc. All rights reserved.

Protein-tannic acid multilayer films: A multifunctional material for microencapsulation of food-derived bioactives.

PubMed

Lau, Hooi Hong; Murney, Regan; Yakovlev, Nikolai L; Novoselova, Marina V; Lim, Su Hui; Roy, Nicole; Singh, Harjinder; Sukhorukov, Gleb B; Haigh, Brendan; Kiryukhin, Maxim V

2017-11-01

The benefits of various functional foods are often negated by stomach digestion and poor targeting to the lower gastrointestinal tract. Layer-by-Layer assembled protein-tannic acid (TA) films are suggested as a prospective material for microencapsulation of food-derived bioactive compounds. Bovine serum albumin (BSA)-TA and pepsin-TA films demonstrate linear growth of 2.8±0.1 and 4.2±0.1nm per bi-layer, correspondingly, as shown by ellipsometry. Both multilayer films are stable in simulated gastric fluid but degrade in simulated intestinal fluid. Their corresponding degradation constants are 0.026±0.006 and 0.347±0.005nm -1 min -1 . Milk proteins possessing enhanced adhesion to human intestinal surface, Immunoglobulin G (IgG) and β-Lactoglobulin (BLG), are explored to tailor targeting function to BSA-TA multilayer film. BLG does not adsorb onto the multilayer while IgG is successfully incorporated. Microcapsules prepared from the multilayer demonstrate 2.7 and 6.3 times higher adhesion to Caco-2 cells when IgG is introduced as an intermediate and the terminal layer, correspondingly. This developed material has a great potential for oral delivery of numerous active food-derived ingredients. Copyright © 2017 Elsevier Inc. All rights reserved.

A novel assay to identify the trafficking proteins that bind to specific vesicle populations

PubMed Central

Bentley, Marvin; Banker, Gary

2016-01-01

Here we describe a method capable of identifying interactions between candidate trafficking proteins and a defined vesicle population in intact cells. The assay involves the expression of an FKBP12-rapamycin–binding domain (FRB)–tagged candidate vesicle-binding protein that can be inducibly linked to an FKBP-tagged molecular motor. If the FRB-tagged candidate protein binds the labeled vesicles, then linking the FRB and FKBP domains recruits motors to the vesicles and causes a predictable, highly distinctive change in vesicle trafficking. We describe two versions of the assay: a general protocol for use in cells with a typical microtubule-organizing center and a specialized protocol designed to detect protein-vesicle interactions in cultured neurons. We have successfully used this assay to identify kinesins and Rabs that bind to a variety of different vesicle populations. In principle, this assay could be used to investigate interactions between any category of vesicle trafficking proteins and any vesicle population that can be specifically labeled. PMID:26621371

21 CFR 862.1645 - Urinary protein or albumin (nonquantitative) test system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Urinary protein or albumin (nonquantitative) test... Chemistry Test Systems § 862.1645 Urinary protein or albumin (nonquantitative) test system. (a) Identification. A urinary protein or albumin (nonquantitative) test system is a device intended to identify...

21 CFR 862.1645 - Urinary protein or albumin (nonquantitative) test system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Urinary protein or albumin (nonquantitative) test... Chemistry Test Systems § 862.1645 Urinary protein or albumin (nonquantitative) test system. (a) Identification. A urinary protein or albumin (nonquantitative) test system is a device intended to identify...

21 CFR 862.1645 - Urinary protein or albumin (nonquantitative) test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Urinary protein or albumin (nonquantitative) test... Chemistry Test Systems § 862.1645 Urinary protein or albumin (nonquantitative) test system. (a) Identification. A urinary protein or albumin (nonquantitative) test system is a device intended to identify...

21 CFR 862.1645 - Urinary protein or albumin (nonquantitative) test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Urinary protein or albumin (nonquantitative) test... Chemistry Test Systems § 862.1645 Urinary protein or albumin (nonquantitative) test system. (a) Identification. A urinary protein or albumin (nonquantitative) test system is a device intended to identify...

Thresholds of allergenic proteins in foods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hourihane, Jonathan O'B.; Knulst, Andre C.

2005-09-01

Threshold doses or Estimated Eliciting Doses (EEDs) represent an important new field of research in food allergy. Clinicians and regulators have embraced some toxicological concepts such as LOAEL and NOAEL and applied them to an area of significant clinical uncertainty and interest. The impact of intrinsic human factors (e.g., asthma and exercise) and extrinsic event factors (e.g., season, location and especially dose of allergen) on a future allergic reaction in the community needs to be considered carefully when interpreting results of clinical and research low-dose food challenges. The ongoing cooperation of food allergy research groups in medicine, food science andmore » government will surely deliver results of the highest importance to the wider communities of allergology, food science and technology and the increasing number of allergic consumers.« less

Genome wide approaches to identify protein-DNA interactions.

PubMed

Ma, Tao; Ye, Zhenqing; Wang, Liguo

2018-05-29

Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites. This review aims to provide an overview of these three techniques including their experiment procedures, computational approaches, and popular analytic tools. ChIP-chip, ChIP-seq, and ChIP-exo have been the major techniques to study genome-wide in vivo protein-DNA interaction. Due to the rapid development of next-generation sequencing technology, array-based ChIP-chip is deprecated and ChIP-seq has become the most widely used technique to identify transcription factor binding sites in genome-wide. The newly developed ChIP-exo further improves the spatial resolution to single nucleotide. Numerous tools have been developed to analyze ChIP-chip, ChIP-seq and ChIP-exo data. However, different programs may employ different mechanisms or underlying algorithms thus each will inherently include its own set of statistical assumption and bias. So choosing the most appropriate analytic program for a given experiment needs careful considerations. Moreover, most programs only have command line interface so their installation and usage will require basic computation expertise in Unix/Linux. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Proteomic analysis identifies differentially expressed proteins after red propolis treatment in Hep-2 cells.

PubMed

Frozza, Caroline Olivieri da Silva; Ribeiro, Tanara da Silva; Gambato, Gabriela; Menti, Caroline; Moura, Sidnei; Pinto, Paulo Marcos; Staats, Charley Christian; Padilha, Francine Ferreira; Begnini, Karine Rech; de Leon, Priscila Marques Moura; Borsuk, Sibele; Savegnago, Lucielli; Dellagostin, Odir; Collares, Tiago; Seixas, Fabiana Kömmling; Henriques, João Antonio Pêgas; Roesch-Ely, Mariana