WorldWideScience

Sample records for identifying food proteins

  1. vProtein: identifying optimal amino acid complements from plant-based foods.

    Directory of Open Access Journals (Sweden)

    Peter J Woolf

    Full Text Available BACKGROUND: Indispensible amino acids (IAAs are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions, but many plant-based foods provide different proportions of IAAs. To explore how these plant-based foods can be better used in human nutrition, we have created the computational tool vProtein to identify optimal food complements to satisfy human protein needs. METHODS: vProtein uses 1251 plant-based foods listed in the United States Department of Agriculture standard release 22 database to determine the quantity of each food or pair of foods required to satisfy human IAA needs as determined by the 2005 daily recommended intake. The quantity of food in a pair is found using a linear programming approach that minimizes total calories, total excess IAAs, or the total weight of the combination. RESULTS: For single foods, vProtein identifies foods with particularly balanced IAA patterns such as wheat germ, quinoa, and cauliflower. vProtein also identifies foods with particularly unbalanced IAA patterns such as macadamia nuts, degermed corn products, and wakame seaweed. Although less useful alone, some unbalanced foods provide unusually good complements, such as Brazil nuts to legumes. Interestingly, vProtein finds no statistically significant bias toward grain/legume pairings for protein complementation. These analyses suggest that pairings of plant-based foods should be based on the individual foods themselves instead of based on broader food group-food group pairings. Overall, the most efficient pairings include sweet corn/tomatoes, apple/coconut, and sweet corn/cherry. The top pairings also highlight the utility of less common protein sources such as the seaweeds laver and spirulina, pumpkin leaves, and lambsquarters. From a public health perspective, many of the food pairings represent novel, low cost food sources to combat malnutrition. Full analysis results are available online

  2. vProtein: identifying optimal amino acid complements from plant-based foods.

    Science.gov (United States)

    Woolf, Peter J; Fu, Leeann L; Basu, Avik

    2011-04-22

    Indispensible amino acids (IAAs) are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions, but many plant-based foods provide different proportions of IAAs. To explore how these plant-based foods can be better used in human nutrition, we have created the computational tool vProtein to identify optimal food complements to satisfy human protein needs. vProtein uses 1251 plant-based foods listed in the United States Department of Agriculture standard release 22 database to determine the quantity of each food or pair of foods required to satisfy human IAA needs as determined by the 2005 daily recommended intake. The quantity of food in a pair is found using a linear programming approach that minimizes total calories, total excess IAAs, or the total weight of the combination. For single foods, vProtein identifies foods with particularly balanced IAA patterns such as wheat germ, quinoa, and cauliflower. vProtein also identifies foods with particularly unbalanced IAA patterns such as macadamia nuts, degermed corn products, and wakame seaweed. Although less useful alone, some unbalanced foods provide unusually good complements, such as Brazil nuts to legumes. Interestingly, vProtein finds no statistically significant bias toward grain/legume pairings for protein complementation. These analyses suggest that pairings of plant-based foods should be based on the individual foods themselves instead of based on broader food group-food group pairings. Overall, the most efficient pairings include sweet corn/tomatoes, apple/coconut, and sweet corn/cherry. The top pairings also highlight the utility of less common protein sources such as the seaweeds laver and spirulina, pumpkin leaves, and lambsquarters. From a public health perspective, many of the food pairings represent novel, low cost food sources to combat malnutrition. Full analysis results are available online at http://www.foodwiki.com/vprotein.

  3. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  4. Proteomic approach for identifying gonad differential proteins in the oyster (Crassostrea angulata) following food-chain contamination with HgCl2.

    Science.gov (United States)

    Zhang, Qing-Hong; Huang, Lin; Zhang, Yong; Ke, Cai-Huan; Huang, He-Qing

    2013-12-06

    Hg discharged into the environmental waters can generally be bioaccumulated, transformed and transmited by living organisms, thus resulting in the formation of Hg-toxicity food chains. The pathway and toxicology of food chain contaminated with environmental Hg are rarely revealed by proteomics. Here, we showed that differential proteomics had the potential to understand reproduction toxicity mechanism in marine molluscs through the Hg-contaminated food chain. Hg bioaccumulation was found in every link of the HgCl2-Chlorella vulgaris-oyster-mice food chain. Morphological observations identified the lesions in both the oyster gonad and the mice ovary. Differential proteomics was used to study the mechanisms of Hg toxicity in the oyster gonad and to find some biomarkers of Hg contamination in food chain. Using 2-DE and MALDI-TOF/TOF MS, we identified 13 differential protein spots, of which six were up-regulated, six were down-regulated, while one was undecided. A portion of these differential proteins was further confirmed using real-time PCR and western blotting methods. Their major functions involved binding, protein translocation, catalysis, regulation of energy metabolism, reproductive functioning and structural molecular activity. Among these proteins, 14-3-3 protein, GTP binding protein, arginine kinase (AK) and 71kDa heat shock connate protein (HSCP 71) are considered to be suitable biomarkers of environmental Hg contamination. Furthermore, we established the gene correspondence, responding to Hg reproductive toxicity, between mouse and oyster, and then used real-time PCR to analyze mRNA differential expression of the corresponding genes in mice. The results indicated that the mechanism of Hg reproductive toxicity in mouse was similar to that in oyster. We suggest that the proteomics would be further developed in application research of food safety including toxicological mechanism. It is well known that mercury (Hg) is one of the best toxic metal elements in

  5. Identifying gaps in international food safety regulation.

    Science.gov (United States)

    McGrady, Benn; Ho, Christina S

    2011-01-01

    The rise in food importation in countries such as the United States, coupled with food safety incidents, has led to increased concern with the safety of imported food. This concern has prompted discussion of how international law and governance mechanisms might enhance food safety. This paper identifies the objectives underlying multilateral approaches to food safety such as raising food safety standards abroad, information sharing and ensuring market access. The paper then explores how these objectives are integrated into the international system and identifies how the current state of the law creates imbalances in the pursuit of these objectives.

  6. Identifying rural food deserts: Methodological considerations for food environment interventions.

    Science.gov (United States)

    Lebel, Alexandre; Noreau, David; Tremblay, Lucie; Oberlé, Céline; Girard-Gadreau, Maurie; Duguay, Mathieu; Block, Jason P

    2016-06-09

    Food insecurity in an important public health issue and affects 13% of Canadian households. It is associated with poor accessibility to fresh, diverse and affordable food products. However, measurement of the food environment is challenging in rural settings since the proximity of food supply sources is unevenly distributed. The objective of this study was to develop a methodology to identify food deserts in rural environments. In-store evaluations of 25 food products were performed for all food stores located in four contiguous rural counties in Quebec. The quality of food products was estimated using four indices: freshness, affordability, diversity and the relative availability. Road network distance between all residences to the closest food store with a favourable score on the four dimensions was mapped to identify residential clusters located in deprived communities without reasonable access to a "good" food source. The result was compared with the food desert parameters proposed by the US Department of Agriculture (USDA), as well as with the perceptions of a group of regional stakeholders. When food quality was considered, food deserts appeared more prevalent than when only the USDA definition was used. Objective measurements of the food environment matched stakeholders' perceptions. Food stores' characteristics are different in rural areas and require an in-store estimation to identify potential rural food deserts. The objective measurements of the food environment combined with the field knowledge of stakeholders may help to shape stronger arguments to gain the support of decision-makers to develop relevant interventions.

  7. Protein oxidation in aquatic foods

    DEFF Research Database (Denmark)

    Baron, Caroline P.

    2014-01-01

    The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout......, and the second with oxidation in salted herring. The mechanisms responsible for initiation of protein oxidation are unclear, but it is generally accepted that free radical species initiating lipid oxidation can also initiate protein oxidation. The chapter focuses on interaction between protein and lipid...... oxidation. The protein carbonyl group measurement is the widely used method for estimating protein oxidation in foods and has been used in fish muscle. The chapter also talks about the impact of protein oxidation on protein functionality, fish muscle texture, and food nutritional value. Protein oxidation...

  8. Allergenic Proteins in Foods and Beverages

    Directory of Open Access Journals (Sweden)

    Fernanda Cosme

    2013-01-01

    Full Text Available Food allergies can be defined as immunologically mediated hypersensitivity reactions; therefore, a food allergy is also known as food hypersensitivity. The reactions are caused by the immune system response to some food proteins. The eight most common food allergens are proteins from milk, eggs, peanuts, tree nuts, soya, wheat, fish and shellfish. However, many other foods have been identified as allergens for some people, such as certain fruits or vegetables and seeds. It is now recognized that food allergens are an important food safety issue. A food allergy occurs when the body’s immune system reacts to otherwise harmless substances in certain foods. For these reasons, one of the requirements from the European Union is that allergenic food ingredients should be labelled in order to protect allergic consumers. According to the European Federation of Allergy and Airways Diseases Patients’ Associations, about 8 % of children and 4 % of adults suffer from some type of food allergy. Food allergies often develop during infant or early childhood ages, affecting mainly the gastrointestinal tract (stomach and intestines. In some cases, the allergy may persist in adult age, for example, coeliac disease, which is an abnormal immune response to certain proteins present in gluten, a type of protein composite found in wheat and barley. Almost all allergens are proteins, and highly sensitive analytical methods have been developed to detect traces of these compounds in food, such as electrophoretic and immunological methods, enzyme-linked immunosorbent assay (ELISA and polyacrylamide gel electrophoresis. The purpose of this review is to describe the allergenic components of the most common causes of food allergies, followed by a brief discussion regarding their importance in the food industry and for consumer safety. The most important methods used to detect allergenicity in food will also be discussed.

  9. Which functional unit to identify sustainable foods?

    Science.gov (United States)

    Masset, Gabriel; Vieux, Florent; Darmon, Nicole

    2015-09-01

    In life-cycle assessment, the functional unit defines the unit for calculation of environmental indicators. The objective of the present study was to assess the influence of two functional units, 100 g and 100 kcal (420 kJ), on the associations between three dimensions for identifying sustainable foods, namely environmental impact (via greenhouse gas emissions (GHGE)), nutritional quality (using two distinct nutrient profiling systems) and price. GHGE and price data were collected for individual foods, and were each expressed per 100 g and per 100 kcal. Two nutrient profiling models, SAIN,LIM and UK Ofcom, were used to assess foods' nutritional quality. Spearman correlations were used to assess associations between variables. Sustainable foods were identified as those having more favourable values for all three dimensions. The French Individual and National Dietary Survey (INCA2), 2006-2007. Three hundred and seventy-three foods highly consumed in INCA2, covering 65 % of total energy intake of adult participants. When GHGE and price were expressed per 100 g, low-GHGE foods had a lower price and higher SAIN,LIM and Ofcom scores (r=0·59, -0·34 and -0·43, respectively), suggesting a compatibility between the three dimensions; 101 and 100 sustainable foods were identified with SAIN,LIM and Ofcom, respectively. When GHGE and price were expressed per 100 kcal, low-GHGE foods had a lower price but also lower SAIN,LIM and Ofcom scores (r=0·67, 0·51 and 0·47, respectively), suggesting that more environment-friendly foods were less expensive but also less healthy; thirty-four sustainable foods were identified with both SAIN,LIM and Ofcom. The choice of functional unit strongly influenced the compatibility between the sustainability dimensions and the identification of sustainable foods.

  10. Functional Foods Containing Whey Proteins

    Science.gov (United States)

    Whey proteins, modified whey proteins, and whey components are useful as nutrients or supplements for health maintenance. Extrusion modified whey proteins can easily fit into new products such as beverages, confectionery items (e.g., candies), convenience foods, desserts, baked goods, sauces, and in...

  11. Protein oxidation in muscle foods: A review

    DEFF Research Database (Denmark)

    Lund, Marianne; Heinonen, Marina; Baron, Caroline P.

    2011-01-01

    insight into the reactions involved in the oxidative modifications undergone by muscle proteins. Moreover, a variety of products derived from oxidized muscle proteins, including cross-links and carbonyls, have been identified. The impact of oxidation on protein functionality and on specific meat quality...... in this topic has led to highlight the influence that Pox may have on meat quality and human nutrition. Recent studies have contributed to solid scientific knowledge regarding basic oxidation mechanisms, and in advanced methodologies to accurately assess Pox in food systems. Some of these studies have provided......Protein oxidation in living tissues is known to play an essential role in the pathogenesis of relevant degenerative diseases, whereas the occurrence and impact of protein oxidation (Pox) in food systems have been ignored for decades. Currently, the increasing interest among food scientists...

  12. Identifying Foods causing Allergies/ Intolerances among Diabetic ...

    African Journals Online (AJOL)

    Objective: This study was designed to identify the foods that caused allergies / intolerances and symptoms of reaction experienced by diabetic patients attending State Specialist Hospital, Akure. Materials and Methods: Ninety-eight diabetics aged 30-80 years (30 males and 68 females) were included in the study.

  13. Exploring novel food proteins and processing technologies

    NARCIS (Netherlands)

    Avila Ruiz, Geraldine

    2016-01-01

    Foods rich in protein are nowadays high in demand worldwide. To ensure a sustainable supply and a high quality of protein foods, novel food proteins and processing technologies need to be explored to understand whether they can be used for the development of high-quality protein foods. Therefore,

  14. Special low protein foods for phenylketonuria

    DEFF Research Database (Denmark)

    Pena, Maria João; Almeida, Manuela Ferreira; van Dam, Esther

    2015-01-01

    BACKGROUND: Special low protein foods (SLPF) are essential in the nutritional management of patients with phenylketonuria (PKU). The study objectives were to: 1) identify the number of SLPF available for use in eight European countries and Turkey and 2) analyse the nutritional composition of SLPF...

  15. Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

    Science.gov (United States)

    Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

    2013-01-01

    Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

  16. Food protein chemistry: an introduction for food scientists

    National Research Council Canada - National Science Library

    Regenstein, J. M; Regenstein, Carrie; Kochen, Beth

    1984-01-01

    ... Protein Chemistry An Introductio n for Food Scientist s Joe M. Regenstein Department and Institute Cornell Ithaca, of Poultry of Food University New York and Avian Science Sciences Carrie E. Re...

  17. Identifying Protein-Calorie Malnutrition Workshop.

    Science.gov (United States)

    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…

  18. Ontology integration to identify protein complex in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Yang Zhihao

    2011-10-01

    Full Text Available Abstract Background Protein complexes 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 protein complexes detection algorithms. Methods We have developed novel semantic similarity method, 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. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes. Results The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.

  19. Identifying New Small Proteins in Escherichia coli.

    Science.gov (United States)

    VanOrsdel, Caitlin E; Kelly, John P; Burke, Brittany N; Lein, Christina D; Oufiero, Christopher E; Sanchez, Joseph F; Wimmers, Larry E; Hearn, David J; Abuikhdair, Fatimeh J; Barnhart, Kathryn R; Duley, Michelle L; Ernst, Sarah E G; Kenerson, Briana A; Serafin, Aubrey J; Hemm, Matthew R

    2018-04-12

    The number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3' end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins-a 45% success rate. Modeling of detected versus non-detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically-significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification. © 2018 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, Towson University.

  20. Food proteins as potential carriers for phenolics

    NARCIS (Netherlands)

    Bohin, M.C.

    2013-01-01

    The development of phenolic-rich functional foods is often limited by the off-tastes of phenolics that might be counteracted by sequestering these compounds using a carrier, thereby preventing them to interact with bitter taste receptors and salivary proteins. A range of common animal food proteins

  1. The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

    Directory of Open Access Journals (Sweden)

    Leinonen Rasko

    2007-10-01

    Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

  2. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

    Science.gov (United States)

    Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

    2007-10-18

    Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at

  3. How to identify food deserts in Amazonian cities?

    OpenAIRE

    Davies, Gemma; Frausin Bustamante, Gina Giovanna; Parry, Luke Thomas Wyn

    2016-01-01

    Food deserts are areas without affordable access to healthy foods. This paper explores whether food deserts are present within urban areas of the Brazilian Amazon. The availability and price of a variety of food products was surveyed in a total of 304 shops, across 3 cities in 2015. Least-cost distances were calculated to estimate travel distance to access products, with map overlay used to help identify areas with poor access to a variety of healthy food - these were defined as food deserts.

  4. Non-food applications of Jatropha protein

    OpenAIRE

    Lestari, D.

    2012-01-01

    The aim of this thesis is to explore how to gain more value per hectare Jatropha curcas by utilizing Jatropha protein for various applications. Specifically, this research investigated the extractability and functional properties of Jatropha protein for non-food/technical applications. Jatropha press cake and leaves are the potential sources of protein. Jatropha proteins can be extracted from Jatropha seed press cake or leaves, with or without detoxification to remove the toxic phorbol esters...

  5. The use of systems models to identify food waste drivers

    NARCIS (Netherlands)

    Grainger, Matthew James; Aramyan, Lusine; Logatcheva, Katja; Piras, Simone; Righi, Simone; Setti, Marco; Vittuari, Matteo; Stewart, Gavin Bruce

    2018-01-01

    In developed countries, the largest share of food waste is produced at household level. Most studies on consumers’ food waste use models that identify covariates as significant when in fact they may not be, particularly where these models use many variables. Here, using EU-level Eurobarometer data

  6. Non-food applications of Jatropha protein

    NARCIS (Netherlands)

    Lestari, D.

    2012-01-01

    The aim of this thesis is to explore how to gain more value per hectare Jatropha curcas by utilizing Jatropha protein for various applications. Specifically, this research investigated the extractability and functional properties of Jatropha protein for non-food/technical applications. Jatropha

  7. New protein sources and food legislation

    DEFF Research Database (Denmark)

    Belluco, Simone; Halloran, Afton Marina Szasz; Ricci, Antonia

    2017-01-01

    Growing global food demand has generated a greater interest in the consumption of new and diversified protein sources. Novel foodstuffs represent a challenge for food law as they need proper safety assessments before obtaining market permission. The case of edible insects and European law is a good...... framework for a novel food in a regulatory context. Once admitted, edible insects require proper rules to assure consumers and stakeholders of their benefits and safety. This overview highlights the need to develop clearer legislation to govern the future production and consumption of new food in Europe...

  8. Plant protein for food: opportunities and bottlenecks

    Directory of Open Access Journals (Sweden)

    Chardigny Jean-Michel

    2016-07-01

    Full Text Available Dietary proteins represent a key issue for the future regarding worldwide food security. Besides animal sources, plant proteins represent an opportunity to mainly contribute to protein demand. Whether some plant protein sources could appear as deficient in some essential amino acids, mixtures from different sources could represent opportunities to further propose adapted supply regarding specific demand. Such opportunities includes legumes as well as by-products of oil processing, i.e. canola and sunflower cakes. The nutritional benefits of such new sources are still under investigation considering benefits and limits like allergenicity. Finally, consumer behavior and acceptability remains the final bottleneck for developing new protein sources.

  9. Thermoluminescence and photostimulated luminescence techniques to identify irradiated foods

    Energy Technology Data Exchange (ETDEWEB)

    Schreiber, G.A. [BgVV - Federal Inst. for Health Protection of Consumers and Veterinary Medicine, Berlin (Germany). Food Irradiation Lab.

    1996-12-31

    Since the publication of the first report about increased thermoluminescence (TL) of irradiated spices, 10 years have passed. At that time, this effect was observed when spices were heated in a TL reader. Meanwhile, the light sources within the foods have been identified and TL methods applied to various foods for identification of irradiation treatment. The methods have been approved by the Ministry of Agriculture, Fisheries and Food (MAFF) of the United Kingdom and included in the Official Collection of Methods according to article 35 of the German Foods Act (LMBG). A draft European Standard has been formulated for approval by the member states of the European Committee for Standardization (CEN) and most importantly, the method is already routinely used food control authorities to identify irradiation treatment of foods. The strength of TL is its radiation specificity. It counts among the most reliable methods and there is potential for becoming the most sensitive physical method for detection of irradiated foods. Research is still going on to speed up performance, to find new applications and to decrease detection limits. Most recently, a new luminescence technique -photostimulated luminescence - has been introduced which can be rapidly performed and which seems to have the potential to be applied to a similar broad range of foods as TL. (author).

  10. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  11. Identifying hubs in protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Ravishankar R Vallabhajosyula

    Full Text Available In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs, it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks.

  12. Kinetics of fibrilar aggregation of food proteins

    NARCIS (Netherlands)

    Arnaudov, L.N.

    2005-01-01

    In this thesis we study the kinetics of fibrilar aggregation of two model proteins widely used in the food industry -b-lactoglobulin (b-lg) and hen

  13. Newer Approaches to Identify Potential Untoward Effects in Functional Foods.

    Science.gov (United States)

    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.

  14. Identifying Food Insecurity in Africa Using Remote Sensing Datasets

    Science.gov (United States)

    Husak, G. J.; Davenport, F.; Shukla, S.; McNally, A.; Turner, W.

    2016-12-01

    The Famine Early Warning Systems Network (FEWS NET) monitors critical environmental variables that impact food production in developing countries, including over 30 in Africa. However, there is a notable lack of consistent quantitative data accurately capturing crop yields or the number of people facing food insecurity. The recently implemented Integrated Food Security Phase Classification (IPC) protocol seeks to address this issue through a set of protocols that define the severity of food security ranging from "None/Minimal" to "Humanitarian Catastrophe/Famine". The IPC framework considers both the severity of the hazard and the vulnerability of the population, as well as the four dimensions of food security (availability, access, utilization and stability). This framework is applied at a fairly fine sub-national level and its consistent application across national borders provides a large dataset to work with. This presentation reports on an ongoing project to examine correlations between a number of geophysical variables and IPC condition. These variables are rainfall, reference evapotranspiration (ETo) and soil moisture (SM), along with combinations of these variables, such as the Standardized Precipitation Evapotranspiration Index (SPEI). We use the Climate Hazards Group InfraRed Precipitation with Stations (CHIRPS) dataset as the rainfall product and an experimental ETo dataset generated using NASA's MERRA-2 atmospheric forcings. Measures of SM use simulations coming from the FEWSNET Land Data Assimilation System (FLDAS). The variables will be compared based on predicative accuracy of IPC and how that accuracy varies across regions and calendar year. The goal is to identify the optimal geophysical predictor of agricultural drought and food insecurity. The results of this research could prioritize the datasets used in identifying and quantifying food insecurity in Africa, and may allow for accurate and frequent updates of the food security conditions.

  15. Identifying Food Safety Concerns when Communication Barriers Exist

    Science.gov (United States)

    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…

  16. Identifying sources of reporting error using measured food intake.

    Science.gov (United States)

    Rumpler, W V; Kramer, M; Rhodes, D G; Moshfegh, A J; Paul, D R

    2008-04-01

    To investigate the magnitude and relative contribution of different sources of measurement errors present in the estimation of food intake via the 24-h recall technique. We applied variance decomposition methods to the difference between data obtained from the USDA's Automated Multiple Pass Method (AMPM) 24-h recall technique and measured food intake (MFI) from a 16-week cafeteria-style feeding study. The average and the variance of biases, defined as the difference between AMPM and MFI, were analyzed by macronutrient content, subject and nine categories of foods. Twelve healthy, lean men (age, 39+/-9 year; weight, 79.9+/-8.3 kg; and BMI, 24.1+/-1.4 kg/m2). Mean food intakes for AMPM and MFI were not significantly different (no overall bias), but within-subject differences for energy (EI), protein, fat and carbohydrate intakes were 14, 18, 23 and 15% of daily intake, respectively. Mass (incorrect portion size) and deletion (subject did not report foods eaten) errors were each responsible for about one-third of the total error. Vegetables constituted 8% of EI but represented >25% of the error across macronutrients, whereas grains that contributed 32% of EI contributed only 12% of the error across macronutrients. Although the major sources of reporting error were mass and deletion errors, individual subjects differed widely in the magnitude and types of errors they made.

  17. Oral sensitization to food proteins: A Brown Norway rat model

    NARCIS (Netherlands)

    Knippels, L.M.J.; Penninks, A.H.; Spanhaak, S.; Houben, G.F.

    1998-01-01

    Background: Although several in vivo antigenicity assays using parenteral immunization are operational, no adequate enteral sensitization models are available to study food allergy and allergenicity of food proteins. Objective: This paper describes the development of an enteral model for food

  18. Identifying fast-food restaurants using a central register as a measure of the food environment.

    Science.gov (United States)

    Toft, Ulla; Erbs-Maibing, Peter; Glümer, Charlotte

    2011-12-01

    To validate the identification and location of fast-food restaurants according to a government list of inspected food stores and restaurants. Fast-food restaurants in the Capital Region of Denmark were identified using a government list of inspected food stores and restaurants (the Smiley register, spring 2010). Ground-truthing was used as the validation method and was performed in May and June 2010 in 125 randomly selected 250×250 m grid cells. A total of 186 fast-food restaurants was identified by ground-truthing and 99% of these were registered in the same grid cell by the Smiley register. However, only 152 restaurants of these were categorised as fast-food restaurants by both methods. The sensitivity was 82% and the positive predictive value was 92%. The mean±standard deviation position accuracy was 15±24 m. Using a government list of inspected restaurants was found to be a valid and useful alternative to expensive and time-consuming field observation and provided a relatively accurate tool for identifying and locating fast-food restaurants in communities.

  19. Regulatory Monitoring of Fortified Foods: Identifying Barriers and Good Practices

    Science.gov (United States)

    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

  20. Interaction of Proteins Identified in Human Thyroid Cells

    Science.gov (United States)

    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

  1. What foods are identified as animal friendly by Italian consumers?

    Directory of Open Access Journals (Sweden)

    Jorgelina Di Pasquale

    2014-11-01

    Full Text Available In the Italian market, voluntary certifications implying higher levels of animal welfare generally fall into wider production schemes. Despite of the results of EU surveys indicating that about 50% of Italian consumers can easily identify and find animal-friendly products, they still are distributed scarcely or discontinuously in the main retail chains. To assess the apparent contradiction between the intricate information consumers receive from labels and their declared awareness about animal welfare, a survey was conducted in Emilia Romagna region on 355 Italian consumers (face-to-face interviews based on a structured, semi-close-ended questionnaire. Overall, consumers showed a low degree of knowledge about animal welfare attributes, animal farming conditions and animal protection policies (about 30% of correct answers, and a low level of awareness of the effects of their purchasing choices on the welfare of farmed animals (22%. The respondents also showed difficulties in identifying animal-friendly products and often confused them with other certified foods, having sometimes a weak connection (or none at all to animal welfare (e.g., Protected Designation of Origin products. However, most consumers declared to be ready to pay a premium price in name of animal welfare. In conclusion, a labelling system for the welfare content of animal-derived foods is confirmed to be an effective strategy to compensate the efforts of farmers in improving animal welfare, provided that the information given is clear and able to fill the substantial lack of consumer knowledge.

  2. Identifying proteins that can form tyrosine-cysteine crosslinks.

    Science.gov (United States)

    Martinie, Ryan J; Godakumbura, Pahan I; Porter, Elizabeth G; Divakaran, Anand; Burkhart, Brandon J; Wertz, John T; Benson, David E

    2012-10-01

    Protein cofactors represent a unique class of redox active posttranslational protein modifications formed in or by metalloproteins. Once formed, protein cofactors provide a one-electron oxidant, which is tethered to the protein backbone. Twenty-five proteins are known to contain protein cofactors, but this number is likely limited by the use of crystallography as the identification technique. In order to address this limitation, a search of all reported protein structures for chemical environments conducive to forming a protein cofactor through tyrosine and cysteine side chain crosslinking yielded three hundred candidate proteins. Using hydrogen bonding and metal center proximity, the three hundred proteins were narrowed to four highly viable candidates. An orphan metalloprotein (BF4112) was examined to validate this methodology, which identifies proteins capable of crosslinking tyrosine and cysteine sidechains. A tyrosine-cysteine crosslink was formed in BF4112 using copper-dioxygen chemistry, as in galactose oxidase. Liquid chromatography-MALDI mass spectrometry and optical spectroscopy confirmed tyrosine-cysteine crosslink formation in BF4112. This finding demonstrates the efficacy of these predictive methods and the minimal constraints, provided by the BF4112 protein structure, in tyrosine-cysteine crosslink formation. This search method, when coupled with physiological evidence for crosslink formation and function as a cofactor, could identify additional protein-derived cofactors.

  3. Identifying and Measuring Food Deserts in Rural Ohio

    Science.gov (United States)

    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…

  4. Identifying Bacterial Immune Evasion Proteins Using Phage Display.

    Science.gov (United States)

    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.

  5. Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection

    Energy Technology Data Exchange (ETDEWEB)

    Sigdel, Tara K.; Kaushal, Amit; Gritsenko, Marina A.; Norbeck, Angela D.; Qian, Weijun; Xiao, Wenzhong; Camp, David G.; Smith, Richard D.; Sarwal, Minnie M.

    2010-01-04

    Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. We used shotgun proteomics using LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls (HC). A total of 1446 urinary proteins were identified along with a number of NS specific, renal transplantation specific and AR specific proteins. Relative abundance of identified urinary proteins was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific urinary proteins in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (UMOD, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these urinary proteins in AR. This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of urinary proteins for serial, non-invasive clinical monitoring for graft rejection after

  6. Efficacy of Food Proteins as Carriers for Flavonoids

    NARCIS (Netherlands)

    Bohin, M.C.; Vincken, J.P.; Hijden, H.T.W.M.; Gruppen, H.

    2012-01-01

    Enrichment of flavonoids in food is often limited by their off-tastes, which might be counteracted by the use of food proteins as carriers of flavonoids. Various milk proteins, egg proteins, and gelatin hydrolysates were compared for their binding characteristics to two flavan-3-ols. Among the

  7. Modeling of allergen proteins found in sea food products

    Directory of Open Access Journals (Sweden)

    Nataly Galán-Freyle

    2012-06-01

    Full Text Available Shellfish are a source of food allergens, and their consumption is the cause of severe allergic reactions in humans. Tropomyosins, a family of muscle proteins, have been identified as the major allergens in shellfish and mollusks species. Nevertheless, few experimentally determined three-dimensional structures are available in the Protein Data Base (PDB. In this study, 3D models of several homologous of tropomyosins present in marine shellfish and mollusk species (Chaf 1, Met e1, Hom a1, Per v1, and Pen a1 were constructed, validated, and their immunoglobulin E binding epitopes were identified using bioinformatics tools. All protein models for these allergens consisted of long alpha-helices. Chaf 1, Met e1, and Hom a1 had six conserved regions with sequence similarities to known epitopes, whereas Per v1 and Pen a1 contained only one. Lipophilic potentials of identified epitopes revealed a high propensity of hydrophobic amino acids in the immunoglobulin E binding site. This information could be useful to design tropomyosin-specific immunotherapy for sea food allergies.

  8. Protein transport across the small intestine in food allergy.

    Science.gov (United States)

    Reitsma, Marit; Westerhout, Joost; Wichers, Harry J; Wortelboer, Heleen M; Verhoeckx, Kitty C M

    2014-01-01

    In view of the imminent deficiency of protein sources for human consumption in the near future, new protein sources need to be identified. However, safety issues such as the risk of allergenicity are often a bottleneck, due to the absence of predictive, validated and accepted methods for risk assessment. The current strategy to assess the allergenic potential of proteins focuses mainly on homology, stability and cross-reactivity, although other factors such as intestinal transport might be of added value too. In this review, we present an overview of the knowledge of protein transport across the intestinal wall and the methods currently being used to measure this. A literature study reveals that protein transport in sensitised persons occurs para-cellularly with the involvement of mast cells, and trans-cellularly via enterocytes, while in non-sensitised persons micro-fold cells and enterocytes are considered most important. However, there is a lack of comparable systematic studies on transport of allergenic proteins. Knowledge of the multiple protein transport pathways and which model system can be useful to study these processes may be of added value in the risk assessment of food allergenicity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Linear programming can help identify practical solutions to improve the nutritional quality of food aid.

    OpenAIRE

    Rambeloson, ZJ; Darmon, N; Ferguson, EL

    2007-01-01

    : To assess the nutritional quality of food aid delivered by food banks in France and to identify practical modifications to improve it. : National-level data were collected for all food aid distributed by French food banks in 2004, and its nutrient content per 2000 kcal was estimated and compared with French recommendations for adults. Starting with the actual donation and allowing new foods into the food aid donation, linear programming was used to identify the minimum changes required in t...

  10. Proteomic Analysis of the Soybean Symbiosome Identifies New Symbiotic Proteins*

    Science.gov (United States)

    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

  11. Immunomodulatory and anticancer protein hydrolysates (peptides) from food proteins: A review.

    Science.gov (United States)

    Chalamaiah, Meram; Yu, Wenlin; Wu, Jianping

    2018-04-15

    Bioactive peptides are oligopeptides that consist of 2-20 amino acids that can exert beneficial effects on human health in addition to basic nutritional effects. Food derived protein hydrolysates or peptides with immunomodulatory and anticancer activities have been reported from a variety of food protein sources such as milk, egg, fish, rice, soybean, pea, chlorella, spirulina, oyster and mussel. In vitro hydrolysis of food proteins using commercial proteolytic enzymes is the most commonly employed process for the production of immunomodulatory and anticancer food protein hydrolysates. The immunomodulatory and anticancer activities of food derived protein hydrolysates or peptides are related to the amino acid composition, sequence and length. Most immunomodulatory and anticancer food protein hydrolysates or peptides were tested using cell culture and animal models, while a few involved clinical trials. This review provides a comprehensive overview of immunomodulatory and anticancer food derived protein hydrolysates or peptides, their production and mechanisms of action. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Conversion of Food waste to Single Cell Protein using Aspergillus ...

    African Journals Online (AJOL)

    The utilization of food waste into products like single cell protein is an alternative solution to global protein shortage and to alleviate pollution problems. This investigation was carried out with food wastes such as orange, pineapple, banana, watermelon and cucumber waste as growth media for A. niger using standard ...

  13. Identifying Competencies in the Food Service Industry. Final Report.

    Science.gov (United States)

    Wagner, Linda M.

    This report documents a research project conducted to ascertain what specific occupational competencies are necessary for employees in the food service industry. Questionnaires were mailed to employers, in restaurants and hospitals and to graduates of high school and postsecondary food service programs. The respondents completed 316 position…

  14. Clinical importance of non-specific lipid transfer proteins as food allergens

    NARCIS (Netherlands)

    van Ree, R.

    2002-01-01

    Non-specific lipid transfer proteins (nsLTPs) have recently been identified as plant food allergens. They are good examples of true food allergens, in the sense that they are capable of sensitizing, i.e. inducing specific IgE, as well as of eliciting severe symptoms. This is in contrast with most

  15. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  16. Toxicological evaluation of proteins introduced into food crops

    Science.gov (United States)

    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

  17. Protein engineering and its applications in food industry.

    Science.gov (United States)

    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.

  18. Thresholds of allergenic proteins in foods

    International Nuclear Information System (INIS)

    Hourihane, Jonathan O'B.; Knulst, Andre C.

    2005-01-01

    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 and 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

  19. Identifying unexpected therapeutic targets via chemical-protein interactome.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    Full Text Available Drug medications inevitably affect not only their intended protein targets but also other proteins as well. In this study we examined the hypothesis that drugs that share the same therapeutic effect also share a common therapeutic mechanism by targeting not only known drug targets, but also by interacting unexpectedly on the same cryptic targets. By constructing and mining an Alzheimer's disease (AD drug-oriented chemical-protein interactome (CPI using a matrix of 10 drug molecules known to treat AD towards 401 human protein pockets, we found that such cryptic targets exist. We recovered from CPI the only validated therapeutic target of AD, acetylcholinesterase (ACHE, and highlighted several other putative targets. For example, we discovered that estrogen receptor (ER and histone deacetylase (HDAC, which have recently been identified as two new therapeutic targets of AD, might already have been targeted by the marketed AD drugs. We further established that the CPI profile of a drug can reflect its interacting character towards multi-protein sets, and that drugs with the same therapeutic attribute will share a similar interacting profile. These findings indicate that the CPI could represent the landscape of chemical-protein interactions and uncover "behind-the-scenes" aspects of the therapeutic mechanisms of existing drugs, providing testable hypotheses of the key nodes for network pharmacology or brand new drug targets for one-target pharmacology paradigm.

  20. A preliminary approach to identify irradiated foods by thermoluminescence measurements

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Choonshik, E-mail: maggic7@korea.kr [Gyeong-In Regional Korea Food and Drug Administration, Juan-Dong 120, Nam-Gu, Incheon 402-835 (Korea, Republic of); Department of Bioscience and Biotechnology, Konkuk University, Hwayang-Dong 1, Gwangjin-Gu, Seoul 143-701 (Korea, Republic of); Kim, Hyoung-Ook [Gyeong-In Regional Korea Food and Drug Administration, Juan-Dong 120, Nam-Gu, Incheon 402-835 (Korea, Republic of); Lim, Yoongho [Department of Bioscience and Biotechnology, Konkuk University, Hwayang-Dong 1, Gwangjin-Gu, Seoul 143-701 (Korea, Republic of)

    2012-07-15

    Thermoluminescence (TL) is one of the physical methods for the identification of irradiated foods. Among the currently developed methods, TL is the most widely used method for the identification of irradiated foods. However, in order to use this method, silicate minerals should be isolated from food samples. The process for the isolation of silicate minerals is time consuming and laborious. In this work, we have investigated the applicability of the TL method using iron-containing minerals instead of silicate minerals. In the TL analyses of dried spices, TL glow curves of iron-containing minerals showed maximum temperatures between 150 and 250 Degree-Sign C which were the same as those of silicate minerals. The process for the mineral separation of the proposed method is simple, fast, easy, and reliable. Moreover, the analysis results including TL ratio have not shown significant differences compared with the silicate minerals method. As a result, the TL measurements using the iron-containing minerals could be an excellent method for the identification of the irradiated foods, including dried spices. - Highlights: Black-Right-Pointing-Pointer A thermoluminescence method using iron-containing minerals is proposed. Black-Right-Pointing-Pointer Current method using silicate minerals is time consuming and laborious. Black-Right-Pointing-Pointer However, the proposed method is simple, fast, easy, and reliable. Black-Right-Pointing-Pointer Analysis results are similar to those of the silicate minerals method.

  1. A preliminary approach to identify irradiated foods by thermoluminescence measurements

    International Nuclear Information System (INIS)

    Shin, Choonshik; Kim, Hyoung-Ook; Lim, Yoongho

    2012-01-01

    Thermoluminescence (TL) is one of the physical methods for the identification of irradiated foods. Among the currently developed methods, TL is the most widely used method for the identification of irradiated foods. However, in order to use this method, silicate minerals should be isolated from food samples. The process for the isolation of silicate minerals is time consuming and laborious. In this work, we have investigated the applicability of the TL method using iron-containing minerals instead of silicate minerals. In the TL analyses of dried spices, TL glow curves of iron-containing minerals showed maximum temperatures between 150 and 250 °C which were the same as those of silicate minerals. The process for the mineral separation of the proposed method is simple, fast, easy, and reliable. Moreover, the analysis results including TL ratio have not shown significant differences compared with the silicate minerals method. As a result, the TL measurements using the iron-containing minerals could be an excellent method for the identification of the irradiated foods, including dried spices. - Highlights: ► A thermoluminescence method using iron-containing minerals is proposed. ► Current method using silicate minerals is time consuming and laborious. ► However, the proposed method is simple, fast, easy, and reliable. ► Analysis results are similar to those of the silicate minerals method.

  2. Identifying fast-food restaurants using a central register as a measure of the food environment

    DEFF Research Database (Denmark)

    Toft, Ulla; Erbs-Maibing, Peter; Glümer, Charlotte

    2011-01-01

    To validate the identification and location of fast-food restaurants according to a government list of inspected food stores and restaurants.......To validate the identification and location of fast-food restaurants according to a government list of inspected food stores and restaurants....

  3. Identifying Needs of Food Composition Database Users – PortFIR experience

    OpenAIRE

    Dias, M. Graça; Viegas, Silvia; Brazão, Roberto; Oliveira, Luisa

    2013-01-01

    Information sharing and management among all the intervenients in food chain is crucial to improve food safety and to promote and protect public health. It optimizes resources usage and provides evidence support to define and promote policies in food and nutrition and to increase the efficiency of food productive systems. Objectives. To share information among Portuguese Food Composition Table users, to identify their needs, in order to define priorities for the update of the N...

  4. Vegetarian Choices in the Protein Foods Group

    Science.gov (United States)

    ... Price Tag Read the Food Label Kitchen Timesavers Cooking for Your Family Tasty & Low-Cost Recipes Sample 2-Week Menus Resources for Professionals MyPlate Tip Sheets Print Materials Infographics 5 Ways ...

  5. urban dietary heavy metal intake from protein foods and vegetables

    African Journals Online (AJOL)

    Mgina

    portions of pooled samples of the foodstuff. The results showed significant variation in heavy metal concentration among ... Urban dietary heavy metal intake from protein foods … 86 serve breakfast and lunch packages. In the ... portion of the food samples were homogenized, stored in pre-cleaned polythene containers and ...

  6. Dynamic rheology of food protein networks

    Science.gov (United States)

    Small amplitude oscillatory shear analyses of samples containing protein are useful for determining the nature of the protein matrix without damaging it. Elastic modulus, viscous modulus, and loss tangent (the ratio of viscous modulus to elastic modulus) give information on the strength of the netw...

  7. Using non-food information to identify food-choice segment membership

    NARCIS (Netherlands)

    Kornelis, M.; Herpen, van E.; Lans, van der I.A.; Aramyan, L.H.

    2010-01-01

    Food companies, governments, and societal organizations use an increasing number of food-choice motives to persuade consumers to buy food products, and the question which combinations of motives matter for which type of consumer has become of central relevance. In this study, we use a concomitant

  8. The environmental cost of protein food choices.

    Science.gov (United States)

    Sranacharoenpong, Kitti; Soret, Samuel; Harwatt, Helen; Wien, Michelle; Sabaté, Joan

    2015-08-01

    To investigate the resource efficiency and environmental impacts of producing one kilogram of edible protein from two plant- and three animal-protein sources. Primary source data were collected and applied to commodity production statistics to calculate the indices required to compare the environmental impact of producing 1 kg of edible protein from kidney beans, almonds, eggs, chicken and beef. Inputs included land and water for raising animals and growing animal feed, total fuel, and total fertilizer and pesticide for growing the plant commodities and animal feed. Animal waste generated was computed for the animal commodities. Desk-based study at the Department of Nutrition and Department of Occupational and Environmental Health, Loma Linda University. None. To produce 1 kg of protein from kidney beans required approximately eighteen times less land, ten times less water, nine times less fuel, twelve times less fertilizer and ten times less pesticide in comparison to producing 1 kg of protein from beef. Compared with producing 1 kg of protein from chicken and eggs, beef generated five to six times more waste (manure) to produce 1 kg of protein. The substitution of beef with beans in meal patterns will significantly reduce the environmental footprint worldwide and should also be encouraged to reduce the prevalence of non-communicable chronic diseases. Societies must work together to change the perception that red meat (e.g. beef) is the mainstay of an affluent and healthy diet.

  9. Conversion of Food waste to Single Cell Protein using Aspergillus ...

    African Journals Online (AJOL)

    ADOWIE PERE

    2018-03-13

    Mar 13, 2018 ... ABSTRACT: The utilization of food waste into products like single cell protein is an alternative solution to global protein shortage ... as orange, pineapple, banana, watermelon and cucumber waste as growth media for A. niger using standard techniques. ..... Waste to Wealth- Value Recovery from. Agrofood.

  10. CYP1A-immunopositive proteins in bivalves identified as cytoskeletal and major vault proteins

    DEFF Research Database (Denmark)

    Grøsvik, Bjørn Einar; Jonsson, Henrik; Rodríguez-Ortega, Manuel J

    2006-01-01

    To identify possible CYP1A-immunopositive proteins in bivalves, we used anti-fish CYP1A antibodies combined with one- and two-dimensional gel electrophoresis and mass spectrometry, and found that two of the main CYP1A-immunopositive proteins in digestive gland of Mytilus edulis, were cytoskeletal...

  11. Electrospinning of food proteins and polysaccharides

    DEFF Research Database (Denmark)

    Mendes, Ana Carina Loureiro; Boutrup Stephansen, Karen; Chronakis, Ioannis S.

    2017-01-01

    Nano-microfibrous structures of biopolymers with a wide range of compositions, morphologies, mechanical properties and bioactivities could be developed using electrospinning technology. This review focuses on the processing, properties, functionalization and potential applications of electrospun...... biopolymers. Biopolymers include proteins (gelatin, collagen, elastin, silk, soy zein, gliadin, hordein, amaranth, casein, wheat, whey, marine sources proteins), and polysaccharides (chitosan, starch, alginate, cellulose and cellulose derivatives, pullulan, dextran, cyclodextrins)....

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Erwan de Gavelle

    2018-02-01

    Full Text Available 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.

  14. Weighting and indirect effects identify keystone species in food webs.

    Science.gov (United States)

    Zhao, Lei; Zhang, Huayong; O'Gorman, Eoin J; Tian, Wang; Ma, Athen; Moore, John C; Borrett, Stuart R; Woodward, Guy

    2016-09-01

    Species extinctions are accelerating globally, yet the mechanisms that maintain local biodiversity remain poorly understood. The extinction of species that feed on or are fed on by many others (i.e. 'hubs') has traditionally been thought to cause the greatest threat of further biodiversity loss. Very little attention has been paid to the strength of those feeding links (i.e. link weight) and the prevalence of indirect interactions. Here, we used a dynamical model based on empirical energy budget data to assess changes in ecosystem stability after simulating the loss of species according to various extinction scenarios. Link weight and/or indirect effects had stronger effects on food-web stability than the simple removal of 'hubs', demonstrating that both quantitative fluxes and species dissipating their effects across many links should be of great concern in biodiversity conservation, and the potential for 'hubs' to act as keystone species may have been exaggerated to date. © 2016 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  15. Food protein-based phytosterol nanoparticles: fabrication and characterization.

    Science.gov (United States)

    Cao, Wen-Jun; Ou, Shi-Yi; Lin, Wei-Feng; Tang, Chuan-He

    2016-09-14

    The development of food-grade (nano)particles as a delivery system for poorly water soluble bioactives has recently attracted increasing attention. This work is an attempt to fabricate food protein-based nanoparticles as delivery systems for improving the water dispersion and bioaccessibility of phytosterols (PS) by an emulsification-evaporation method. The fabricated PS nanoparticles were characterized in terms of particle size, encapsulation efficiency (EE%) and loading amount (LA), and ξ-potential. Among all the test proteins, including soy protein isolate (SPI), whey protein concentrate (WPC) and sodium caseinate (SC), SC was confirmed to be the most suitable protein for the PS nano-formulation. Besides the type of protein, the particle size, EE% and LA of PS in the nanoparticles varied with the applied protein concentration in the aqueous phase and organic volume fraction. The freeze-dried PS nanoparticles with SC exhibited good water re-dispersion behavior and low crystallinity of PS. The LA of PS in the nanoparticles decreased upon storage, especially at high temperatures (e.g., >25 °C). The PS in the fabricated nanoparticles exhibited much better bioaccessibility than free PS. The findings would be of relevance for the fabrication of food-grade colloidal phytosterols, with great potential to be applied in functional food formulations.

  16. Development of soybeans with low P34 allergen protein concentration for reduced allergenicity of soy foods.

    Science.gov (United States)

    Watanabe, Daisuke; Adányi, Nóra; Takács, Krisztina; Maczó, Anita; Nagy, András; Gelencsér, Éva; Pachner, Martin; Lauter, Kathrin; Baumgartner, Sabine; Vollmann, Johann

    2017-02-01

    In soybean, at least 16 seed proteins have been identified as causing allergenic reactions in sensitive individuals. As a soybean genebank accession low in the immunodominant protein P34 (Gly m Bd 30K) has recently been found, introgression of the low-P34 trait into adapted soybean germplasm has been attempted in order to improve the safety of food products containing soybean protein. Therefore, marker-assisted selection and proteomics were applied to identify and characterize low-P34 soybeans. In low-P34 lines selected from a cross-population, concentrations of the P34 protein as identified with a polyclonal antibody were reduced by 50-70% as compared to P34-containing controls. Using 2D electrophoresis and immunoblotting, the reduction of P34 protein was verified in low-P34 lines. This result was confirmed by liquid chromatographic-tandem mass spectrometric analysis, which revealed either a reduction or complete absence of the authentic P34 protein as suggested from presence or absence of a unique peptide useful for discriminating between conventional and low-P34 lines. Marker-assisted selection proved useful for identifying low-P34 soybean lines for the development of hypoallergenic soy foods. The status of the P34 protein in low-P34 lines needs further characterization. In addition, the food safety relevance of low-P34 soybeans should be tested in clinical studies. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  17. Background on international activities on protein quality assessment of foods.

    Science.gov (United States)

    Gilani, G Sarwar

    2012-08-01

    The subject of protein quality assessment of foods and diets was addressed at the Codex Committee on Vegetable Proteins (1982-1989), FAO/WHO (1989, 2001) and WHO/FAO (2002) expert reviews. These international developments are summarized in this manuscript. In 1989, a Joint FAO/WHO Expert Consultation on Protein Quality Evaluation reviewed knowledge of protein quality assessment of foods, and specifically evaluated amino acid score corrected for protein digestibility, the method recommended by the Codex Committee on Vegetable Proteins. The report of the Consultation published in 1991 concluded that the Protein Digestibility-corrected Amino Acid Score (PDCAAS) method was the most suitable approach for routine evaluation of protein quality for humans. The Consultation recognized that the amino acid scoring pattern proposed by FAO/WHO/UNU (1985) for preschool children was at that time the most suitable pattern for calculating PDCAAS for all ages except infants in which case the amino acid composition of human milk was recommended to be the basis of the scoring pattern. The rat balance method was considered as the most suitable practical method for predicting protein digestibility by humans. Since its adoption by FAO/WHO (1991), the PDCAAS method has been criticised for a number of reasons. The FAO/WHO (2001) Working Group on analytical issues related to protein quality assessed the validity of criticisms of the PDCAAS method. While recognizing a distinct regulatory use of protein quality data, the Working Group recommended that the PDCAAS method may be inappropriate for the routine prediction of protein quality of novel and sole source foods which contain high levels of anti nutritional factors; and that for regulatory purposes, the method should be revised to permit values of >100 for high quality proteins. In evaluating the recommendations of the Working Group, the WHO/FAO (2002) Expert Consultation on Protein and Amino Acid Requirements endorsed the PDCAAS method

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

    Science.gov (United States)

    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.

  19. Dataset of integrin-linked kinase protein: Protein interactions in cardiomyocytes identified by mass spectrometry

    Directory of Open Access Journals (Sweden)

    Alexandra Traister

    2016-06-01

    Full Text Available Using hearts from mice overexpressing integrin linked kinase (ILK behind the cardiac specific promoter αMHC, we have performed immunoprecipitation and mass spectrometry to identify novel ILK protein:protein interactions that regulate cardiomyocyte activity and calcium flux. Integrin linked kinase complexes were captured from mouse heart lysates using a commercial antibody, with subsequent liquid chromatography tandem mass spectral analysis. Interacting partners were identified using the MASCOT server, and important interactions verified using reverse immunoprecipitation and mass spectrometry. All ILK interacting proteins were identified in a non-biased manner, and are stored in the ProteomeXchange Consortium via the PRIDE partner repository (reference ID PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD001053. The functional role of identified ILK interactions in cardiomyocyte function and arrhythmia were subsequently confirmed in human iPSC-cardiomyocytes.

  20. Dataset of integrin-linked kinase protein: Protein interactions in cardiomyocytes identified by mass spectrometry.

    Science.gov (United States)

    Traister, Alexandra; Lu, Mingliang; Coles, John G; Maynes, Jason T

    2016-06-01

    Using hearts from mice overexpressing integrin linked kinase (ILK) behind the cardiac specific promoter αMHC, we have performed immunoprecipitation and mass spectrometry to identify novel ILK protein:protein interactions that regulate cardiomyocyte activity and calcium flux. Integrin linked kinase complexes were captured from mouse heart lysates using a commercial antibody, with subsequent liquid chromatography tandem mass spectral analysis. Interacting partners were identified using the MASCOT server, and important interactions verified using reverse immunoprecipitation and mass spectrometry. All ILK interacting proteins were identified in a non-biased manner, and are stored in the ProteomeXchange Consortium via the PRIDE partner repository (reference ID PRIDE: PXD001053). The functional role of identified ILK interactions in cardiomyocyte function and arrhythmia were subsequently confirmed in human iPSC-cardiomyocytes.

  1. Identification of rice proteins recognized by the IgE antibodies of patients with food allergies.

    Science.gov (United States)

    Goliáš, Jaroslav; Humlová, Zuzana; Halada, Petr; Hábová, Věra; Janatková, Ivana; Tučková, Ludmila

    2013-09-18

    Similarity among food allergens is a great problem affecting the specificity of diagnosis and treatment of allergic patients. We have observed that 80% of patients with food (including wheat) and pollen allergies have increased IgE antibodies against rice proteins. By immunoblotting, we documented that boiling decreased solubility and IgE reactivity of PBS-extracted rice and wheat proteins, yet in SDS extracts this reactivity was only slightly changed. The sera of patients highly positive on the IgE immunoblot and positive in basophil activation and skin prick test with boiled rice components were used for characterizing the IgE-binding proteins separated by 1D or 2D electrophoresis. Using mass spectrometry, we identified 22 rice SDS soluble proteins. Six of them were new thermostable potential rice allergens: glutelin C precursor, granule-bound starch synthase 1 protein, disulfide isomerase-like 1-1 protein, hypothetical protein OsI_13867, putative acid phosphatase precursor 1, and a protein encoded by locus Os02g0453600. All of the identified rice proteins differed from known wheat allergens, except proteins belonging to the α-amylase/trypsin inhibitor family. Furthermore, we would suggest that in patients with high IgE reactivity to wheat and rice components, the IgE immunoblot and skin prick test with boiled rice proteins could be beneficial before diet recommendation.

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

    NARCIS (Netherlands)

    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.

    2014-01-01

    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

  3. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis modified Cry1Ab... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1 are...

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

    Science.gov (United States)

    Shatsky, Maxim; Dong, Ming; Liu, Haichuan; Yang, Lee Lisheng; Choi, Megan; Singer, Mary E.; Geller, Jil T.; Fisher, Susan J.; Hall, Steven C.; Hazen, Terry C.; Brenner, Steven E.; Butland, Gareth; Jin, Jian; Witkowska, H. Ewa; Chandonia, John-Marc; Biggin, Mark D.

    2016-01-01

    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 of 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. PMID:27099342

  5. Cold Atmospheric Plasma Manipulation of Proteins in Food Systems

    DEFF Research Database (Denmark)

    Tolouie, Haniye; Hashemi, Maryam; Mohammadifar, Mohammad Amin

    2017-01-01

    -functional characteristics of processed foods and/or the physico-chemical properties of protein-based films. At the same time, some proteins are responsible for reduction in quality and nutritional value, and/or causing allergic reactions in the human body. This study is a review of the influences of different types...... of plasma on the conformation and function of proteins with food origin, especially enzymes and allergens, as well as protein-made packaging films. In enzyme manipulation with plasma, deactivation has been reported to be either partial or complete. In addition, an activity increase has been observed in some...... factors, including treatment power, time, and gas type, as well as the nature of the substance and the treatment environment....

  6. Cow's milk protein allergy and other food hypersensitivities in infants.

    Science.gov (United States)

    Venter, Carina

    2009-01-01

    Food hypersensitivity (FHS) is the umbrella term used to describe both food allergy, which involves the immune system, and food intolerances, which do not. It is therefore important that the diagnosis is made by a specialist health care professional such as a paediatrician or allergist. Some experienced dietitians and health visitors may be able to assist in making a diagnosis. The diagnostic work-up includes a medical history and blood tests/skin tests (where applicable). A food and symptom diary followed by a special test diet to identify the foods causing the infant's symptoms may also be needed. Once a diagnosis is made, dietary advice should be given to eliminate or reduce the intake of the offending foods. For cow's milk hypersensitivity in infants, this will include choosing the most appropriate specialised infant formula.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    ... many egg whites as you want. Eat plant protein foods more often Try beans and peas (kidney, pinto, black, or white beans; split peas; chickpeas; hummus), soy products (tofu, tempeh, veggie burgers), nuts, ...

  9. Identifying foods with good nutritional quality and price for the Opticourses intervention research project.

    Science.gov (United States)

    Dubois, Christophe; Tharrey, Marion; Darmon, Nicole

    2017-12-01

    People on a limited budget want to know the 'good price' of foods. Here we report the methodology used to produce an educational tool designed to help recognize foods with good nutritional quality and price, and assess the validity and relevancy of the tool. A 'Good Price Booklet' presenting a list of foods with good nutritional quality and price was constructed. The validity of the in-booklet prices was assessed by comparing them with prices actually paid by households from the Opticourses project. The relevancy of the booklet tool was assessed by semi-structured interviews with Opticourses participants. Socio-economically disadvantaged neighbourhoods of Marseille, France. Ninety-one participants collected household food-purchase receipts over a 1-month period. Based on the French food database, foods with higher-than-median nutritional quality were identified. After grouping similar foods, 100 foods were selected and their corresponding in-booklet prices were derived based on the distribution of average national prices by food group. Household food purchases data revealed that of the 2386 purchases of foods listed in the booklet, 67·1 % were bought at prices lower than the in-booklet prices. Nineteen semi-structured interviews showed that participants understood the tool and most continued using it more than a month after the intervention. A method was developed to ease the identification of foods with good nutritional quality and price. The Good Price Booklet is an effective tool to help guide people shopping on a low budget.

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

    Science.gov (United States)

    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

  11. Linear programming can help identify practical solutions to improve the nutritional quality of food aid.

    Science.gov (United States)

    Rambeloson, Zo J; Darmon, Nicole; Ferguson, Elaine L

    2008-04-01

    To assess the nutritional quality of food aid delivered by food banks in France and to identify practical modifications to improve it. National-level data were collected for all food aid distributed by French food banks in 2004, and its nutrient content per 2000 kcal was estimated and compared with French recommendations for adults. Starting with the actual donation and allowing new foods into the food aid donation, linear programming was used to identify the minimum changes required in the actual donation to achieve the French recommendations. French food-bank-delivered food aid does not achieve the French recommendations for dietary fibre, ascorbic acid, vitamin D, folate, magnesium, docosahexaenoic acid, alpha-linolenic acid and the percentage of energy from saturated fatty acids. Linear programming analysis showed that these recommendations are achievable if more fruits, vegetables, legumes and fish were collected and less cheese, refined cereals and foods rich in fat, sugar and/or salt. In addition, new foods not previously collected are needed, particularly nuts, wholemeal bread and rapeseed oil. These changes increased the total edible weight (42%) and economic value (55%) of the food aid donation, with one-third of its edible weight coming from fruits and vegetables, one-third from staples, one-quarter from dairy products and approximately a tenth from meat/fish/eggs. Important changes in the types and amounts of food collected will improve the nutritional quality of food-bank-delivered food aid in France. Such changes are recommended to improve the diets of deprived French populations.

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

    Directory of Open Access Journals (Sweden)

    Malgorzata Teodorowicz

    2017-08-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  14. Improved Functional Characteristics of Whey Protein Hydrolysates in Food Industry

    Science.gov (United States)

    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

  15. Food protein-induced enterocolitis syndrome: pitfalls in the diagnosis.

    Science.gov (United States)

    Guibas, George V; Tsabouri, Sophia; Makris, Michael; Priftis, Kostas N

    2014-11-01

    Food protein-induced enterocolitis syndrome (FPIES) represents the severe end of the spectrum of gastrointestinal food hypersensitivity; its acute episodes can culminate in severe dehydration and hypovolemic shock, and its chronic form entails considerable morbidity associated with feeding difficulty and failure to thrive. Nevertheless, awareness for this syndrome remains rather low. Many factors hamper the establishment of FPIES diagnosis. Such factors pertain to the pathophysiological mechanism of the syndrome, causal food proteins, clinical manifestations, diagnostic procedures, differential diagnosis considerations, and prevailing perceptions which may require critical appraisal. Throughout this review, we will present and discuss these issues and put the focus on factors that could lead to under-diagnosis of FPIES, cause numerous acute episodes, and substantially increase the diseases morbidity and financial burden. We will also address other issues that are clinically relevant to FPIES. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Interactions between plant proteins/enzymes and other food components, and their effects on food quality.

    Science.gov (United States)

    Lv, Chenyan; Zhao, Guanghua; Ning, Yong

    2017-05-24

    Plant proteins are the main sources of dietary protein for humans, especially for vegetarians. There are a variety of components with different properties coexisting in foodstuffs, so the interactions between these components are inevitable to occur, thereby affecting food quality. Among these interactions, the interplay between plant proteins/enzymes from fruits and vegetables, cereals, and legumes and other molecules plays an important role in food quality, which recently has gained a particular scientific interest. Such interactions not only affect the appearances of fruits and vegetables and the functionality of cereal products but also the nutritive properties of plant foods. Non-covalent forces, such as hydrogen bond, hydrophobic interaction, electrostatic interaction, and van der Waals forces, are mainly responsible for these interactions. Future outlook is highlighted with aim to suggest a research line to be followed in further studies.

  17. Food protein induced enterocolitis syndrome caused by rice beverage.

    Science.gov (United States)

    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.

  18. Allergenic sensitization versus elicitation risk criteria for novel food proteins.

    Science.gov (United States)

    Herman, Rod A; Ladics, Gregory S

    2018-02-23

    The value of criteria used in the weight-of-evidence assessment of allergenic risk of genetically modified (GM) crops has been debated. This debate may originate, in part, from not specifying if the criteria are intended to contribute to the assessment of sensitization risk or elicitation risk. Here, this distinction is explicitly discussed in the context of exposure and hazard. GM crops with structural relationships with known allergens or sourced from an organism known to cause allergy (hazard) are screened for IgE-antibody reactivity using serum from sensitized individuals. If IgE reactivity is observed, the GM crop is not developed. While digestive and heat stability impact exposure and thus the elicitation risk to sensitized individuals, these attributes are not interpretable relative to sensitization risk. For novel food proteins with no identified hazard, heat stability cannot be validly assessed because relevant IgE antibodies are not available. Likewise, the uncertain and sometime non-monotonic dose relationship between oral exposure to allergens and sensitization makes digestive stability a poor predictor of sensitization risk. It is hoped that by explicitly distinguishing between sensitization risk and elicitation risk, some of the debate surrounding the weight-of evidence criteria for predicting the allergenic risk of GM crops can be resolved. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Changchuan Yin

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  2. Protein micro-structuring as a tool to texturize protein foods

    NARCIS (Netherlands)

    Purwanti, N.; Peters, J.P.C.M.; Goot, van der A.J.

    2013-01-01

    Structuring protein foods to control the textural properties receives growing attention nowadays. It requires decoupling of the product properties such as water holding capacity and the mechanical properties from the actual protein concentration in the product. From an application point of view,

  3. Protein enrichment of familiar foods as an innovative strategy to increase protein intake in institutionalized elderly

    NARCIS (Netherlands)

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

    2017-01-01

    Objective
    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

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

    Directory of Open Access Journals (Sweden)

    James Kaufman

    2014-07-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  7. Positive effect of protein-supplemented hospital food on protein intake in patients at nutritional risk

    DEFF Research Database (Denmark)

    Munk, T; Beck, A M; Holst, M

    2014-01-01

    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. RESULTS: 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...... of hospital stay did not differ between groups. CONCLUSIONS: 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....

  8. Yellow Mealworm Protein for Food Purposes - Extraction and Functional Properties.

    Directory of Open Access Journals (Sweden)

    Xue Zhao

    Full Text Available 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.

  9. Yellow Mealworm Protein for Food Purposes - Extraction and Functional Properties

    Science.gov (United States)

    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

  10. Identifying bacterial immune evasion proteins using phage display

    NARCIS (Netherlands)

    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

  11. Protein transport across the small intestine in food allergy

    NARCIS (Netherlands)

    Reitsma, M.; Westerhout, J.; Wichers, H.J.; Wortelboer, H.M.; Verhoeckx, K.C.M.

    2014-01-01

    In view of the imminent deficiency of protein sources for human consumption in the near future, new protein sources need to be identified. However, safety issues such as the risk of allergenicity are often a bottleneck, due to the absence of predictive, validated and accepted methods for risk

  12. Protein transport across the small intestine in food hypersensitivity

    NARCIS (Netherlands)

    Reitsma, M.; Westerhout, J.; Wichers, H.J.; Wortelboer, H.; Verhoeckx, K.C.M.

    2014-01-01

    In view of the imminent deficiency of protein sources for human consumption in the near future, new protein sources need to be identified. However, safety issues such as the risk of allergenicity are often a bottleneck, due to the absence of predictive, validated and accepted methods for risk

  13. A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy

    DEFF Research Database (Denmark)

    Moreira, Irina S.; da Silva Martins, João Miguel; Coimbra, João T.S.

    2015-01-01

    the most correct one, in particular when a single answer is asked for. With such a low success rate it is difficult to point out one docked structure as being native-like. Here we present a new, high accuracy, scoring method to identify the 3D structure of P-P complexes among a set of trial poses...... the trial structures and identifies the native-like structures with unprecedented accuracy (∼94%), providing the correct P-P 3D structures that biochemists and molecular biologists need to pursue their studies. With such a success rate, the bottleneck of protein-protein docking moves from the scoring....... It incorporates alanine scanning mutagenesis experimental data that need to be obtained a priori. The scoring scheme works by matching the computational and the experimental alanine scanning mutagenesis results. The size of the trial P-P interface area is also taken into account. We show that the method ranks...

  14. Amaranth-protein interaction in food system and its impact on tryptic digestibility

    International Nuclear Information System (INIS)

    Saeed, S.M.G.; Sayeed, S.A.; Ashraf, S.; Qureshi, A.; Kausar, R.

    2013-01-01

    Amaranth, a food color, is used in variety of food products to attract consumers, especially children. The purpose of the present study was to identify the component present in the food system which acts as a carrier of color and its distribution. The protein is the most possible candidate for color-conjugates and this was first explored by staining the resolved food proteins on PAGE simultaneously and separately with Amaranth as well as by Coomassie brilliant blue R250. It is the most widely used dye for protein assay. The color intensity of the Amaranth-protein complexes was slightly less than those of Coomassie brilliant blue R250, although the bands stained by Amaranth were very sharp, clearly separated and distinct. The staining procedure followed for Amaranth was quick. The impact of tryptic digestibility on amaranth-protein complexes has illustrated that dye may safely be used without any adverse effect. The possible moode of conjugation between amino acid and azo-bond is also discussed. (author)

  15. Differential diagnosis of food protein-induced enterocolitis syndrome.

    Science.gov (United States)

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

    2014-06-01

    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. 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. 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.

  16. Identify drug repurposing candidates by mining the protein data bank.

    Science.gov (United States)

    Moriaud, Fabrice; Richard, Stéphane B; Adcock, Stewart A; Chanas-Martin, Laetitia; Surgand, Jean-Sébastien; Ben Jelloul, Marouane; Delfaud, François

    2011-07-01

    Predicting off-targets by computational methods is gaining increasing interest in early-stage drug discovery. Here, we present a computational method based on full 3D comparisons of 3D structures. When a similar binding site is detected in the Protein Data Bank (PDB) (or any protein structure database), it is possible that the corresponding ligand also binds to that similar site. On one hand, this target hopping case is probably rare because it requires a high similarity between the binding sites. On the other hand, it could be a strong rational evidence to highlight possible off-target reactions and possibly a potential undesired side effect. This target-based drug repurposing can be extended a significant step further with the capability of searching the full surface of all proteins in the PDB, and therefore not relying on pocket detection. Using this approach, we describe how MED-SuMo reproduces the repurposing of tadalafil from PDE5A to PDE4A and a structure of PDE4A with tadalafil. Searching for local protein similarities generates more hits than for whole binding site similarities and therefore fragment repurposing is more likely to occur than for drug-sized compounds. In this work, we illustrate that by mining the PDB for proteins sharing similarities with the hinge region of protein kinases. The experimentally validated examples, biotin carboxylase and synapsin, are retrieved. Further to fragment repurposing, this approach can be applied to the detection of druggable sites from 3D structures. This is illustrated with detection of the protein kinase hinge motif in the HIV-RT non-nucleosidic allosteric site.

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

    Science.gov (United States)

    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.

  18. Neurosecretory protein GL stimulates food intake, de novo lipogenesis, and onset of obesity.

    Science.gov (United States)

    Iwakoshi-Ukena, Eiko; Shikano, Kenshiro; Kondo, Kunihiro; Taniuchi, Shusuke; Furumitsu, Megumi; Ochi, Yuta; Sasaki, Tsutomu; Okamoto, Shiki; Bentley, George E; Kriegsfeld, Lance J; Minokoshi, Yasuhiko; Ukena, Kazuyoshi

    2017-08-11

    Mechanisms underlying the central regulation of food intake and fat accumulation are not fully understood. We found that neurosecretory protein GL (NPGL), a newly-identified neuropeptide, increased food intake and white adipose tissue (WAT) in rats. NPGL-precursor gene overexpression in the hypothalamus caused increases in food intake, WAT, body mass, and circulating insulin when fed a high calorie diet. Intracerebroventricular administration of NPGL induced de novo lipogenesis in WAT, increased insulin, and it selectively induced carbohydrate intake. Neutralizing antibody administration decreased the size of lipid droplets in WAT. Npgl mRNA expression was upregulated by fasting and low insulin levels. Additionally, NPGL-producing cells were responsive to insulin. These results point to NPGL as a novel neuronal regulator that drives food intake and fat deposition through de novo lipogenesis and acts to maintain steady-state fat level in concert with insulin. Dysregulation of NPGL may be a root cause of obesity.

  19. A novel proteogenomics approach identifying key proteins in severe COPD

    NARCIS (Netherlands)

    Brandsma, C.A.; Guryev, V.; Timens, W.; Postma, D.S.; Bischoff, R.; Yakovleva, M.; Marko-Varga, G.; Fehniger, T.; Van Den Berge, M.; Horvatovich, P.

    2017-01-01

    Rationale COPD is influenced by many genetic and environmental factors. Genetic studies provided insights in the molecular mechanisms underlying COPD, but did not inform on protein changes. We propose that whichever factor contributes to disease, the final common pathway for disease development lies

  20. Target and identify: triazene linker helps identify azidation sites of labelled proteins via click and cleave strategy.

    Science.gov (United States)

    Lohse, Jonas; Schindl, Alexandra; Danda, Natasha; Williams, Chris P; Kramer, Karl; Kuster, Bernhard; Witte, Martin D; Médard, Guillaume

    2017-10-31

    A method for identifying probe modification of proteins via tandem mass spectrometry was developed. Azide bearing molecules are immobilized on functionalised sepharose beads via copper catalysed Huisgen-type click chemistry and selectively released under acidic conditions by chemical cleavage of the triazene linkage. We applied this method to identify the modification site of targeted-diazotransfer on BirA.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Functionally relevant domains of the prion protein identified in vivo.

    Directory of Open Access Journals (Sweden)

    Frank Baumann

    2009-09-01

    Full Text Available The prion consists essentially of PrP(Sc, a misfolded and aggregated conformer of the cellular protein PrP(C. Whereas PrP(C deficient mice are clinically healthy, expression of PrP(C variants lacking its central domain (PrP(DeltaCD, or of the PrP-related protein Dpl, induces lethal neurodegenerative syndromes which are repressed by full-length PrP. Here we tested the structural basis of these syndromes by grafting the amino terminus of PrP(C (residues 1-134, or its central domain (residues 90-134, onto Dpl. Further, we constructed a soluble variant of the neurotoxic PrP(DeltaCD mutant that lacks its glycosyl phosphatidyl inositol (GPI membrane anchor. Each of these modifications abrogated the pathogenicity of Dpl and PrP(DeltaCD in transgenic mice. The PrP-Dpl chimeric molecules, but not anchorless PrP(DeltaCD, ameliorated the disease of mice expressing truncated PrP variants. We conclude that the amino proximal domain of PrP exerts a neurotrophic effect even when grafted onto a distantly related protein, and that GPI-linked membrane anchoring is necessary for both beneficial and deleterious effects of PrP and its variants.

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

    Directory of Open Access Journals (Sweden)

    Sha Zhang

    2015-10-01

    Full Text Available 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.

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

    Science.gov (United States)

    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 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.

  6. Nanodiamond MALDI support for enhancing the credibility of identifying proteins.

    Science.gov (United States)

    Wei, Li-Ming; Xue, Yan; Zhou, Xin-Wen; Jin, Hong; Shi, Qian; Lu, Hao-Jie; Yang, Peng-Yuan

    2008-02-15

    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a standard analytical tool for protein identification and peptide sequencing. High sensitivity and resolution are two critical parameters for recording good peptide mass fingerprinting (PMF) of low abundance proteins. Here, we report a novel nanodiamond (ND) (normal size 3-10nm) support for MALDI-MS target, over which alpha-cyano-4-hydrocinnamic acid (CCA) crystallizes evenly. Good reproducibility of relative peak intensity (R.S.D. less than 11.8%) among sample spot (from ring to center) is achieved on ND support. Therefore, the search for "hot spots" during the analysis is not necessary, which is supporting for the automatic acquisition of data. Due to high absorbability of energy from the laser, the ND support improves ionization efficiency of samples. In general, the sensitivity of MS obtained on ND support can be enhanced three to four times compared to the conventional MALDI sample preparation technique. Sensitivity obtained on ND support ranges from 62.5 amol of Arg-vasopressin standard peptide to 1.0 fmol of myoglobin tryptic peptide mixture. Reduced spot size and increased sensitivity in MALDI-MS are also accomplished by ND support. With spot size reduced, the signal intensity of cytochrome c (Cyt c) tryptic peptide obtained on ND support is at least seven times greater than it acquired on stainless steel. And ND support has been found better tolerance for salt (up to 500 mM NaCl) to MALDI-MS analysis. All these properties make ND support a valuable tool for MALDI-MS identification of proteins.

  7. Electrospinning of food-grade nanofibres from whey protein.

    Science.gov (United States)

    Zhong, Jie; Mohan, Saeed D; Bell, Alan; Terry, Ann; Mitchell, Geoffrey R; Davis, Fred J

    2018-02-19

    In this study, electrospinning has been employed to produce micro to nano scale fibres of whey protein in order to investigate their potential for use in the food industry. Initially, spinning of pure whey protein proved challenging; so in order to facilitate the spinning of freshly prepared aqueous solutions, small amounts of polyethylene oxide (as low as 1% w/w in solution) were incorporated in the spinning solutions. The electrospun composite polyethylene-oxide/whey fibres exhibited diameters in the region of 100 to 400 nm, showing the potential to build fibre bundles from this size up. Time-dependent examinations of pure whey protein aqueous solutions were conducted using rheometery and small angle neutron scattering techniques, with the results showing a substantial change in the solution properties with time and stirring; and allowing the production of fibres, albeit with large diameters, without the need for an additive. The spinability is related to the potential of the whey protein composites to form aggregate structures, either through hydration and interaction with neighbouring proteins, or through interaction with the polyethylene oxide. Copyright © 2018. Published by Elsevier B.V.

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

    DEFF Research Database (Denmark)

    Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L.

    2015-01-01

    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...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Laura Acevedo-Pacheco

    2016-10-01

    Full Text Available 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

  14. Methods and systems for identifying ligand-protein binding sites

    KAUST Repository

    Gao, Xin

    2016-05-06

    The invention provides a novel integrated structure and system-based approach for drug target prediction that enables the large-scale discovery of new targets for existing drugs Novel computer-readable storage media and computer systems are also provided. Methods and systems of the invention use novel sequence order-independent structure alignment, hierarchical clustering, and probabilistic sequence similarity techniques to construct a probabilistic pocket ensemble (PPE) that captures even promiscuous structural features of different binding sites for a drug on known targets. The drug\\'s PPE is combined with an approximation of the drug delivery profile to facilitate large-scale prediction of novel drug- protein interactions with several applications to biological research and drug development.

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

    Directory of Open Access Journals (Sweden)

    Edgar Denova-Gutiérrez

    2016-12-01

    Full Text Available Objective. To examine the validity of a semi-quantitative food frequency questionnaire (SFFQ to identify dietary patterns in an adult Mexican population. Materials and methods. 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. Results. 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 oefficients 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. Conclusions. Our data indicate reasonable validity of the SFFQ, using fac­tor analysis, to derive major dietary patterns in comparison with two 24DR.

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

    Science.gov (United States)

    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.

  17. The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection.

    Science.gov (United States)

    Perkowski, E F; Zulauf, K E; Weerakoon, D; Hayden, J D; Ioerger, T R; Oreper, D; Gomez, S M; Sacchettini, J C; Braunstein, M

    2017-04-25

    Exported proteins of bacterial pathogens function both in essential physiological processes and in virulence. Past efforts to identify exported proteins were limited by the use of bacteria growing under laboratory ( in vitro ) conditions. Thus, exported proteins that are exported only or preferentially in the context of infection may be overlooked. To solve this problem, we developed a genome-wide method, named EXIT ( ex ported i n vivo t echnology), to identify proteins that are exported by bacteria during infection and applied it to Mycobacterium tuberculosis during murine infection. Our studies validate the power of EXIT to identify proteins exported during infection on an unprecedented scale (593 proteins) and to reveal in vivo induced exported proteins (i.e., proteins exported significantly more during in vivo infection than in vitro ). Our EXIT data also provide an unmatched resource for mapping the topology of M. tuberculosis membrane proteins. As a new approach for identifying exported proteins, EXIT has potential applicability to other pathogens and experimental conditions. IMPORTANCE There is long-standing interest in identifying exported proteins of bacteria as they play critical roles in physiology and virulence and are commonly immunogenic antigens and targets of antibiotics. While significant effort has been made to identify the bacterial proteins that are exported beyond the cytoplasm to the membrane, cell wall, or host environment, current methods to identify exported proteins are limited by their use of bacteria growing under laboratory ( in vitro ) conditions. Because in vitro conditions do not mimic the complexity of the host environment, critical exported proteins that are preferentially exported in the context of infection may be overlooked. We developed a novel method to identify proteins that are exported by bacteria during host infection and applied it to identify Mycobacterium tuberculosis proteins exported in a mouse model of tuberculosis

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

    Science.gov (United States)

    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.

  19. Economic approach to environmental sustainability of protein foods

    NARCIS (Netherlands)

    Zhu, X.; Ierland, van E.C.

    2006-01-01

    Intensive animal production systems in Europe, particularly in the Netherlands result in a series of environmental problems mainly due to manure surplus. This study aims to make contributions to identifying the solutions to the problems related to protein production and consumption. The first

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

    Science.gov (United States)

    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.

  1. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    Science.gov (United States)

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  2. Eating energy-Identifying possibilities for reduced energy use in the future food supply system

    International Nuclear Information System (INIS)

    Wallgren, Christine; Hoejer, Mattias

    2009-01-01

    This paper explores the possibilities for reducing future energy use for eating to a sustainable level. A backcasting approach is used to generate an image of the future where energy use for eating is 60% lower in 2050 than in 2000. The currently known potential to reduce energy use in the food supply system for producing, transporting, storing, cooking and eating food is explored and described in terms of a number of distinct changes that are numbered consecutively and presented in both a quantitative and qualitative way. Sweden is used as the case and all data regarding energy use apply for Swedish conditions. An exercise like this illustrates the possible outcome of taking sustainability seriously. If sustainability is to be achieved, some images of the future are needed so that potential targets can be identified. This paper does not present forecasts, but illustrates the kind of changes needed in order to achieve sustainable energy use in the food system.

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

    Science.gov (United States)

    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.

  4. Backcasting to identify food waste prevention and mitigation opportunities for infant feeding in maternity services.

    Science.gov (United States)

    Ryan-Fogarty, Yvonne; Becker, Genevieve; Moles, Richard; O'Regan, Bernadette

    2017-03-01

    Food waste in hospitals is of major concern for two reasons: one, healthcare needs to move toward preventative and demand led models for sustainability and two, food system sustainability needs to seek preventative measures such as diet adaptation and waste prevention. The impact of breast-milk substitute use on health services are well established in literature in terms of healthcare implications, cost and resourcing, however as a food demand and waste management issue little has been published to date. This paper presents the use of a desk based backcasting method to analyse food waste prevention, mitigation and management options within the Irish Maternity Service. Best practice in healthcare provision and waste management regulations are used to frame solutions. Strategic problem orientation revealed that 61% of the volume of ready to use breast-milk substitutes purchased by maternity services remains unconsumed and ends up as waste. Thirteen viable strategies to prevent and manage this waste were identified. Significant opportunities exist to prevent waste and also decrease food demand leading to both positive health and environmental outcomes. Backcasting methods display great promise in delivering food waste management strategies in healthcare settings, especially where evidenced best practice policies exist to inform solution forming processes. In terms of food waste prevention and management, difficulties arise in distinguishing between demand reduction, waste prevention and waste reduction measures under the current Waste Management Hierarchy definitions. Ultimately demand reduction at source requires prioritisation, a strategy which is complimentary to health policy on infant feeding. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. How to identify food deserts: measuring physical and economic access to supermarkets in King County, Washington.

    Science.gov (United States)

    Jiao, Junfeng; Moudon, Anne V; Ulmer, Jared; Hurvitz, Philip M; Drewnowski, Adam

    2012-10-01

    We explored new ways to identify food deserts. We estimated physical and economic access to supermarkets for 5 low-income groups in Seattle-King County, Washington. We used geographic information system data to measure physical access: service areas around each supermarket were delineated by ability to walk, bicycle, ride transit, or drive within 10 minutes. We assessed economic access by stratifying supermarkets into low, medium, and high cost. Combining income and access criteria generated multiple ways to estimate food deserts. The 5 low-income group definitions yielded total vulnerable populations ranging from 4% to 33% of the county's population. Almost all of the vulnerable populations lived within a 10-minute drive or bus ride of a low- or medium-cost supermarket. Yet at most 34% of the vulnerable populations could walk to any supermarket, and as few as 3% could walk to a low-cost supermarket. The criteria used to define low-income status and access to supermarkets greatly affect estimates of populations living in food deserts. Measures of access to food must include travel duration and mode and supermarket food costs.

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

    Directory of Open Access Journals (Sweden)

    Alfonso Clemente

    Full Text Available 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

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

    Science.gov (United States)

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

    2018-03-07

    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 identify patients for malnutrition 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 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 protein/albumin ratio, and impaired self-feeding at admission were independently associated with critically reduced energy and protein intake. Middle

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

    Science.gov (United States)

    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®

  9. Human protein status modulates brain reward responses to food cues1–3

    NARCIS (Netherlands)

    Griffioen-Roose, S.; Smeets, P.A.M.; Heuvel, van den E.M.; Boesveldt, S.; Finlayson, G.; Graaf, de C.

    2014-01-01

    Background: Protein is indispensable in the human diet, and its intake appears tightly regulated. The role of sensory attributes of foods in protein intake regulation is far from clear. Objective: We investigated the effect of human protein status on neural responses to different food cues with the

  10. Dietary guidance for pulses: the challenge and opportunity to be part of both the vegetable and protein food groups.

    Science.gov (United States)

    Havemeier, Stefanie; Erickson, Jennifer; Slavin, Joanne

    2017-03-01

    Pulses are a dry, edible variety of beans, peas, and lentils that have been consumed for 10,000 years. Pulses are rich in plant-based protein and fiber, as well as micronutrients such as iron and potassium. The satiating effect of both fiber and protein assists in managing weight and combating obesity. The high fiber content and low glycemic index of pulses aid people with diabetes in maintaining blood glucose and insulin levels. Pulse consumption may improve serum lipid levels to reduce the risk of cardiovascular disease. Pulses developed as a member of both the protein and vegetable food groups as a result of its high content of plant-based protein and dietary fiber. The last two revisions of the Dietary Guidelines saw the transformation from the MyPyramid "meat and beans group" to the MyPlate "protein foods group," a nutrient name rather than a food source. Research suggests that consumers better identify with food source examples rather than nutrient names. The 2015 Dietary Guidelines also came with a new area: sustainable diets. Encouraging the consumption of sustainable food sources, like pulses, is imperative to ensuring a secure, healthy food supply for the U.S. population over time and for future generations. © 2017 New York Academy of Sciences.

  11. Interaction of Quillaja bark saponins with food-relevant proteins.

    Science.gov (United States)

    Kezwon, Aleksandra; Wojciechowski, Kamil

    2014-07-01

    The surface activity and aggregation behaviour of two Quillaja bark saponins (QBS) are compared using surface tension, conductometry and light scattering. Despite formally of the same origin (bark of the Quillaja saponaria Molina tree), the two QBS show markedly different ionic characters and critical micelle concentrations (7.7·10(-6) mol·dm(-3) and 1.2·10(-4) mol·dm(-3)). The new interpretation of the surface tension isotherms for both QBS allowed us to propose an explanation for the previous discrepancy concerning the orientation of the saponin molecules in the adsorbed layer. The effect of three food-related proteins (hen egg lysozyme, bovine β-lactoglobulin and β-casein) on surface tension of the saponins is also described. Dynamic surface tension was measured at fixed protein concentrations and QBS concentrations varying in the range 5·10(-7)-1·10(-3) mol·dm(-3). Both dynamic and extrapolated equilibrium surface tensions of the protein/QBS mixtures depend not only on the protein, but also on the QBS source. In general, the surface tension for mixtures of the QBS with lower CMC and less ionic character shows less pronounced synergistic effects. This is especially well visible for β-casein/QBS mixtures, where a characteristic maximum in the surface tension isotherm around the molar ratio of one can be noticed for one saponin product, but not for the other. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat

    DEFF Research Database (Denmark)

    Yang, Fen; Jensen, Jens D.; Svensson, Birte

    2012-01-01

    or wheat flour as the sole nutrient source to mimic the host–pathogen interaction. A gel‐based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty‐nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation......Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley...... of cell walls, starch and proteins. Of these proteins, 35% had not been identified in previous in planta or in vitro studies, 70% were predicted to contain signal peptides and a further 16% may be secreted in a nonclassical manner. Proteins identified in the 72 spots showing differential appearance...

  13. A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks.

    Science.gov (United States)

    Li, Min; Lu, Yu; Wang, Jianxin; Wu, Fang-Xiang; Pan, Yi

    2015-01-01

    Essential proteins are indispensable for cellular life. It is of great significance to identify essential proteins that can help us understand the minimal requirements for cellular life and is also very important for drug design. However, identification of essential proteins based on experimental approaches are typically time-consuming and expensive. With the development of high-throughput technology in the post-genomic era, more and more protein-protein interaction data can be obtained, which make it possible to study essential proteins from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. Most of these topology based essential protein discovery methods were to use network centralities. In this paper, we investigate the essential proteins' topological characters from a completely new perspective. To our knowledge it is the first time that topology potential is used to identify essential proteins from a protein-protein interaction (PPI) network. The basic idea is that each protein in the network can be viewed as a material particle which creates a potential field around itself and the interaction of all proteins forms a topological field over the network. By defining and computing the value of each protein's topology potential, we can obtain a more precise ranking which reflects the importance of proteins from the PPI network. The experimental results show that topology potential-based methods TP and TP-NC outperform traditional topology measures: degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), subgraph centrality (SC), eigenvector centrality (EC), information centrality (IC), and network centrality (NC) for predicting essential proteins. In addition, these centrality measures are improved on their performance for identifying essential proteins in biological network when controlled by topology potential.

  14. Identifying Practical Solutions to Meet America’s Fiber Needs: Proceedings from the Food & Fiber Summit

    Science.gov (United States)

    Mobley, Amy R.; Jones, Julie Miller; Rodriguez, Judith; Slavin, Joanne; Zelman, Kathleen M.

    2014-01-01

    Fiber continues to be singled out as a nutrient of public health concern. Adequate intakes of fiber are associated with reduced risk for cardiovascular disease, cancer, diabetes, certain gastrointestinal disorders and obesity. Despite ongoing efforts to promote adequate fiber through increased vegetable, fruit and whole-grain intakes, average fiber consumption has remained flat at approximately half of the recommended daily amounts. Research indicates that consumers report increasingly attempting to add fiber-containing foods, but there is confusion around fiber in whole grains. The persistent and alarmingly low intakes of fiber prompted the “Food & Fiber Summit,” which assembled nutrition researchers, educators and communicators to explore fiber’s role in public health, current fiber consumption trends and consumer awareness data with the objective of generating opportunities and solutions to help close the fiber gap. The summit outcomes highlight the need to address consumer confusion and improve the understanding of sources of fiber, to recognize the benefits of various types of fibers and to influence future dietary guidance to provide prominence and clarity around meeting daily fiber recommendations through a variety of foods and fiber types. Potential opportunities to increase fiber intake were identified, with emphasis on meal occasions and food categories that offer practical solutions for closing the fiber gap. PMID:25006857

  15. Identifying Practical Solutions to Meet America’s Fiber Needs: Proceedings from the Food & Fiber Summit

    Directory of Open Access Journals (Sweden)

    Amy R. Mobley

    2014-07-01

    Full Text Available Fiber continues to be singled out as a nutrient of public health concern. Adequate intakes of fiber are associated with reduced risk for cardiovascular disease, cancer, diabetes, certain gastrointestinal disorders and obesity. Despite ongoing efforts to promote adequate fiber through increased vegetable, fruit and whole-grain intakes, average fiber consumption has remained flat at approximately half of the recommended daily amounts. Research indicates that consumers report increasingly attempting to add fiber-containing foods, but there is confusion around fiber in whole grains. The persistent and alarmingly low intakes of fiber prompted the “Food & Fiber Summit,” which assembled nutrition researchers, educators and communicators to explore fiber’s role in public health, current fiber consumption trends and consumer awareness data with the objective of generating opportunities and solutions to help close the fiber gap. The summit outcomes highlight the need to address consumer confusion and improve the understanding of sources of fiber, to recognize the benefits of various types of fibers and to influence future dietary guidance to provide prominence and clarity around meeting daily fiber recommendations through a variety of foods and fiber types. Potential opportunities to increase fiber intake were identified, with emphasis on meal occasions and food categories that offer practical solutions for closing the fiber gap.

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

    Science.gov (United States)

    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

  17. The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection

    Science.gov (United States)

    Perkowski, E. F.; Zulauf, K. E.; Weerakoon, D.; Hayden, J. D.; Ioerger, T. R.; Oreper, D.; Gomez, S. M.; Sacchettini, J. C.

    2017-01-01

    ABSTRACT Exported proteins of bacterial pathogens function both in essential physiological processes and in virulence. Past efforts to identify exported proteins were limited by the use of bacteria growing under laboratory (in vitro) conditions. Thus, exported proteins that are exported only or preferentially in the context of infection may be overlooked. To solve this problem, we developed a genome-wide method, named EXIT (exported in vivo technology), to identify proteins that are exported by bacteria during infection and applied it to Mycobacterium tuberculosis during murine infection. Our studies validate the power of EXIT to identify proteins exported during infection on an unprecedented scale (593 proteins) and to reveal in vivo induced exported proteins (i.e., proteins exported significantly more during in vivo infection than in vitro). Our EXIT data also provide an unmatched resource for mapping the topology of M. tuberculosis membrane proteins. As a new approach for identifying exported proteins, EXIT has potential applicability to other pathogens and experimental conditions. PMID:28442606

  18. Food protein-induced enterocolitis syndrome in Australia: A population-based study, 2012-2014.

    Science.gov (United States)

    Mehr, Sam; Frith, Katie; Barnes, Elizabeth H; Campbell, Dianne E

    2017-11-01

    Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated gastrointestinal allergic disorder. Large population-based FPIES studies are lacking. We sought to determine the incidence and clinical characteristics of FPIES in Australian infants. An Australia-wide survey (2012-2014) was undertaken through the Australian Paediatric Surveillance Unit, with monthly notification of new cases of acute FPIES in infants aged less than 24 months by 1400 participating pediatricians. Two hundred thirty infants with FPIES were identified. The incidence of FPIES in Australian infants (disease and FPIES to fruits, vegetables, or both. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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.

  20. Genomes2Drugs: identifies target proteins and lead drugs from proteome data.

    LENUS (Irish Health Repository)

    Toomey, David

    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.

  1. Genomes2Drugs: identifies target proteins and lead drugs from proteome data.

    Directory of Open Access Journals (Sweden)

    David Toomey

    Full Text Available 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.

  2. Identifying possible non-thermal effects of radio frequency energy on inactivating food microorganisms.

    Science.gov (United States)

    Kou, Xiaoxi; Li, Rui; Hou, Lixia; Zhang, Lihui; Wang, Shaojin

    2018-03-23

    Radio frequency (RF) heating has been successfully used for inactivating microorganisms in agricultural and food products. Athermal (non-thermal) effects of RF energy on microorganisms have been frequently proposed in the literature, resulting in difficulties for developing effective thermal treatment protocols. The purpose of this study was to identify if the athermal inactivation of microorganisms existed during RF treatments. Escherichia coli and Staphylococcus aureus in apple juice and mashed potato were exposed to both RF and conventional thermal energies to compare their inactivation populations. A thermal death time (TDT) heating block system was used as conventional thermal energy source to simulate the same heating treatment conditions, involving heating temperature, heating rate and uniformity, of a RF treatment at a frequency of 27.12 MHz. Results showed that a similar and uniform temperature distribution in tested samples was achieved in both heating systems, so that the central sample temperature could be used as representative one for evaluating thermal inactivation of microorganisms. The survival patterns of two target microorganisms in two food samples were similar both for RF and heating block treatments since their absolute difference of survival populations was  0.05) in inactivating bacteria between the RF and the heating block treatments at each set of temperatures. The solid temperature and microbial inactivation data demonstrated that only thermal effect of RF energy at 27.12 MHz was observed on inactivating microorganisms in foods. Copyright © 2018 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

    Tjernsbekk, M. T.; Tauson, Anne-Helene; Matthiesen, Connie Frank

    2016-01-01

    The present study evaluated growing mink (Neovison vison) 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...... by the European Pet Food Industry Federation. It was concluded that growth studies with mink kits can provide valuable information in protein quality assessment of extruded dog foods. Furthermore, the study showed that to ensure nutritional adequacy of dog food and to be able to compare protein quality of dog...

  4. Pea proteins based food products as meat replacers: the Profetas concept

    NARCIS (Netherlands)

    Jongen, W.M.F.; Meerdink, G.

    2001-01-01

    Profetas (Protein Foods, Environment, Technology and Society) is a Dutch trans-disciplinary research programme, aiming to develop more sustainable food systems. The central theme of the programme is the question: is a transition feasible from a diet based primarily on animal proteins to a diet based

  5. Scientific bases of protein paste technology for baby food with a long shelf life

    Directory of Open Access Journals (Sweden)

    Наталія Андріївна Ткаченко

    2015-03-01

    Full Text Available The article shows the development prospects of technologies of protein food pastes for children from 8 months; the basic principles underlying production technology by thermostatic way are given; the choice of physiologically functional food ingredients is grounded for the adaptation of the product to the milk of women and parameters of the process using thermal acid coagulation of skim milk proteins

  6. Effects of Protein Foods on the Nutritional Status of Adults with ...

    African Journals Online (AJOL)

    Revd Dr Olaleye

    Effects of Protein Foods on the Nutritional Status of. Adults with Moderate Chronic Renal Failure. Fadupin Grace T. Department of Human Nutrition, College of Medicine, University Of Ibadan. Ibadan. ABSTRACT: This study compares the efficacy of low- protein foods, from cooked beef (diet A), smoked cat fish (diet B),.

  7. HOUSEHOLD DECISION ANALYSIS ON ANIMAL PROTEIN FOOD CONSUMPTION: EVIDENCE FROM D.I YOGYAKARTA PROVINCE

    Directory of Open Access Journals (Sweden)

    Mujtahidah Anggriani Ummul Muzayyanah

    2017-05-01

    Full Text Available Food consumption pattern in Indonesia has change. Consumption of animal protein food is increasing as income increase. Animal protein foods are come from fish products and livestock products. The aim of this study is to analyze household decision on animal protein food consumption based on socioeconomics determinant of the households. Household expenditure data were used in this study. Discrete choice model is used to measure household decision in consuming these foods. Socioeconomics determinants are measured by Binary Logistic regression to know the influence of these to the household’s decision. Marginal effect value from binary logistic regression analysis showed that households tend to increase consuming animal protein food from livestock products varies from 0.5 to 6.09 times associated to socioeconomic factors of the households. Further research need to analyze nutritional status of the household’s members.

  8. Molecular Interaction Between Salivary Proteins and Food Tannins.

    Science.gov (United States)

    Silva, Mafalda Santos; García-Estévez, Ignacio; Brandão, Elsa; Mateus, Nuno; de Freitas, Victor; Soares, Susana

    2017-08-09

    Polyphenols interaction with salivary proteins (SP) has been related with organoleptic features such as astringency. The aim of this work was to study the interaction between some human SP and tannins through two spectroscopic techniques, fluorescence quenching, and saturation transfer difference-nuclear magnetic resonance (STD-NMR). Generally, the results showed a significant interaction between SP and both condensed tannins and ellagitannins. Herein, STD-NMR proved to be a useful tool to map tannins' epitopes of binding, while fluorescence quenching allowed one to discriminate binding affinities. Ellagitannins showed the greatest binding constants values (K SV from 20.1 to 94.1 mM -1 ; K A from 0.7 to 8.3 mM -1 ) in comparison with procyanidins (K SV from 5.4 to 40.0 mM -1 ; K A from 1.1 to 2.7 mM -1 ). In fact, punicalagin was the tannin that demonstrated the highest affinity for all three SP. Regarding SP, P-B peptide was the one with higher affinity for ellagitannins. On the other hand, cystatins showed in general the lower K SV and K A values. In the case of condensed tannins, statherin was the SP with the highest affinity, contrasting with the other two SP. Altogether, these results are evidence that the distinct SP present in the oral cavity have different abilities to interact with food tannins class.

  9. Proteomic profiling of human plasma exosomes identifies PPARγ as an exosome-associated protein

    International Nuclear Information System (INIS)

    Looze, Christopher; Yui, David; Leung, Lester; Ingham, Matthew; Kaler, Maryann; Yao, Xianglan; Wu, Wells W.; Shen Rongfong; Daniels, Mathew P.; Levine, Stewart J.

    2009-01-01

    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-γ (PPARγ), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatory cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPARγ as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.

  10. B56δ-related protein phosphatase 2A dysfunction identified in patients with intellectual disability

    NARCIS (Netherlands)

    Houge, Gunnar; Haesen, Dorien; Vissers, Lisenka E L M; Mehta, Sarju; Parker, Michael J.; Wright, Michael; Vogt, Julie; McKee, Shane; Tolmie, John L.; Cordeiro, Nuno; Kleefstra, Tjitske; Willemsen, Marjolein H.; Reijnders, Margot R F; Berland, Siren; Hayman, Eli; Lahat, Eli; Brilstra, Eva H.; Van Gassen, Koen L I; Zonneveld-Huijssoon, Evelien; De Bie, Charlotte I.; Hoischen, Alexander; Eichler, Evan E.; Holdhus, Rita; Steen, Vidar M.; Døskeland, Stein Ove; Hurles, Matthew E.; FitzPatrick, David R.; Janssens, Veerle

    2015-01-01

    Here we report inherited dysregulation of protein phosphatase activity as a cause of intellectual disability (ID). De novo missense mutations in 2 subunits of serine/threonine (Ser/Thr) protein phosphatase 2A (PP2A) were identified in 16 individuals with mild to severe ID, long-lasting hypotonia,

  11. B56delta-related protein phosphatase 2A dysfunction identified in patients with intellectual disability

    NARCIS (Netherlands)

    Houge, G.; Haesen, D.; Vissers, L.E.L.M.; Mehta, S.; Parker, M.J.; Wright, M.; Vogt, J.; McKee, S.; Tolmie, J.L.; Cordeiro, N.; Kleefstra, T.; Willemsen, M.H.; Reijnders, M.R.F.; Berland, S.; Hayman, E.; Lahat, E.; Brilstra, E.H.; Gassen, K.L. van; Zonneveld-Huijssoon, E.; Bie, C.I. De; Hoischen, A.; Eichler, E.E.; Holdhus, R.; Steen, V.M.; Doskeland, S.O.; Hurles, M.E.; FitzPatrick, D.R.; Janssens, V.

    2015-01-01

    Here we report inherited dysregulation of protein phosphatase activity as a cause of intellectual disability (ID). De novo missense mutations in 2 subunits of serine/threonine (Ser/Thr) protein phosphatase 2A (PP2A) were identified in 16 individuals with mild to severe ID, long-lasting hypotonia,

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

    Science.gov (United States)

    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

  13. Semantic integration to identify overlapping functional modules in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Ramanathan Murali

    2007-07-01

    Full Text Available Abstract 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.

  14. Determination of ortho-tyrosine in irradiated protein containing foods by HPLC

    International Nuclear Information System (INIS)

    Mischke, J.; Voehringer, M.; Helle, N.; Boegl K.W.; Schreiber, G.A.

    1993-01-01

    In order to control the processing and trading of irradiated foodstuffs several chemical and physical methods have been developed to identify irradiation induced changes. The three most promising methods are gas chromatorgraphic determination of radiation induced volatiles from the lipid content of foods, thermoluminescence measurements on minerals and e.s.r.-spectroscopic measurements on solids and food contents with a low water amount. There is a lack in detecting the irradiation in foods with a high protein content. It is based on the radiation induced hydroxylation of phenylalanine, forming small amounts of ortho- (and meta-) tyrosine. This method can be useful for foods with a low lipid content such as shrimps and pure egg-white. The results obtained on shrimps and egg-white are promising. All shrimp samples showed a good dose dependence which was similar to results reported by Chuaqui-Offermanns and McDougall obtained on frozen materials (chicken) irradiated at a slightly higher dose rate. There are not enough data about o-tyrosine-contents in different kinds of unirradiated shrimps. Therfore next step will be the analysis of a great number of various samples. With these information and by the use of an internal standard it should be possible to apply the HPLC method for routine analysis. As internal standards α-methyltyrosine or 4-hydroxyphenylglycine could be used. (orig./vhe)

  15. Advances in food packaging films from milk proteins

    Science.gov (United States)

    Most commercial petroleum-based food packaging films are poor oxygen barriers, do not biodegrade, and some are suspected to even leach compounds into the food product. For instance, three-perfluorinated coatings were banned from convenience food packaging earlier this year. These shortcomings are a ...

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

    Science.gov (United States)

    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.

  17. Identifying food deserts and swamps based on relative healthy food access: a spatio-temporal Bayesian approach.

    Science.gov (United States)

    Luan, Hui; Law, Jane; Quick, Matthew

    2015-12-30

    Obesity and other adverse health outcomes are influenced by individual- and neighbourhood-scale risk factors, including the food environment. At the small-area scale, past research has analysed spatial patterns of food environments for one time period, overlooking how food environments change over time. Further, past research has infrequently analysed relative healthy food access (RHFA), a measure that is more representative of food purchasing and consumption behaviours than absolute outlet density. This research applies a Bayesian hierarchical model to analyse the spatio-temporal patterns of RHFA in the Region of Waterloo, Canada, from 2011 to 2014 at the small-area level. RHFA is calculated as the proportion of healthy food outlets (healthy outlets/healthy + unhealthy outlets) within 4-km from each small-area. This model measures spatial autocorrelation of RHFA, temporal trend of RHFA for the study region, and spatio-temporal trends of RHFA for small-areas. For the study region, a significant decreasing trend in RHFA is observed (-0.024), suggesting that food swamps have become more prevalent during the study period. For small-areas, significant decreasing temporal trends in RHFA were observed for all small-areas. Specific small-areas located in south Waterloo, north Kitchener, and southeast Cambridge exhibited the steepest decreasing spatio-temporal trends and are classified as spatio-temporal food swamps. This research demonstrates a Bayesian spatio-temporal modelling approach to analyse RHFA at the small-area scale. Results suggest that food swamps are more prevalent than food deserts in the Region of Waterloo. Analysing spatio-temporal trends of RHFA improves understanding of local food environment, highlighting specific small-areas where policies should be targeted to increase RHFA and reduce risk factors of adverse health outcomes such as obesity.

  18. Hydrolyzed collagen (gelatin decreases food efficiency and the bioavailability of high-quality protein in rats

    Directory of Open Access Journals (Sweden)

    Cláudia Cantelli Daud BORDIN

    2015-08-01

    Full Text Available Objective Although deficient in all indispensable amino acids, gelatin is used in protein-restricted diets. Food efficiency and protein quality of casein and gelatin mixtures in low protein diets in Wistar rats were investigated. Methods The rats were treated with protein-restricted diets (10.0 and 12.5% containing casein (control diets, casein with gelatin mixtures (4:1 of protein content, and gelatin as sources of protein. The food conversion ratio, protein efficiency ratio, relative and corrected protein efficiency ratio, true protein digestibility, and hepatic parameters were estimated. Results After 28 days of the experiment, food efficiency of 10.0% casein/gelatin diet decreased when compared to that of 10.0% casein diet, and the protein efficiency ratio of the casein/gelatin mixtures (10.0%=2.41 and 12.5%=2.03 were lower than those of the casein (10.0%=2.90 and 12.5%=2.32. After 42 days of the experiment, the weight of the liver of the animals treated with 10.0 and 12.5% casein/gelatin diets, and the liver protein retention of the 12.5% casein/gelatin diet group of animals were lower than those of the control group. Conclusion Gelatin decreases food efficiency and high-quality protein bioavailability in protein-restricted diets.

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

    International Nuclear Information System (INIS)

    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 ( 3 H-EFDA), and were characterized by electrophoretic analysis. A protocol was developed which allowed detection of 3 H-EFDA that was covalently linked to proteins upon exposure to ultraviolet light at 254 nm. Quantification of protein-linked 3 H-EFDA by liquid scintillation spectrometry took advantage of the differential solubility of unlinked 3 H-EFDA in toluene alone, and of the protein-linked 3 H-EFDA in toluene plus the detergent, Triton X-100. Competition between EFDA and juvenile hormone (JH) for 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

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

    Science.gov (United States)

    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.

  1. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  2. Irradiated foods and allergy. From a perspective of irradiation chemistry of proteins

    International Nuclear Information System (INIS)

    Miyahara, Makoto

    2003-01-01

    A change of protein in irradiated food has been known. There are a few reports on change of allergy of irradiated foods. Two kinds of allergy such as the immediate allergy (I type) and delayed allergy (IV type) are taken ill by foods. I type is related to irradiated foods. Allergen enters body through digestive tract. Anti body (IgE) is protein with from 10,000 to 100,000 molecular weight. Allergic disease is originated mainly by egg, milk, wheat, buckwheat, peanut and shrimp. When food is irradiated, the proteins are decomposed and produced higher and lower molecular compounds at the same time. Change of the viscosity and the sedimentation coefficient and deactivation of enzymes of β-lactoglobulin, cow albumin, egg albumin and casein were investigated. There is no report of increasing allergy by irradiation. However, some paper indicated that immunogenicity of protein was decreased by irradiation. (S.Y.)

  3. The fundament of food, crop protein production, is threatened by climate change

    DEFF Research Database (Denmark)

    Ingvordsen, Cathrine Heinz; Gislum, René; Jørgensen, Johannes Ravn

    2016-01-01

    Income growth, urbanization, and changes in lifestyles and food preferences combined with continuing population growth lead to increasing demand for plant protein production worldwide. All the proteins we eat are produced by crops, including the proteins we get from animals, which initially come...

  4. The effect of within-meal protein content and taste on subsequent food choice and satiety

    NARCIS (Netherlands)

    Griffioen-Roose, S.; Mars, M.; Finlayson, G.; Blundell, J.E.; Graaf, de C.

    2011-01-01

    It is posed that protein intake is tightly regulated by the human body. The role of sensory qualities in the satiating effects of protein, however, requires further clarification. Our objective was to determine the effect of within-meal protein content and taste on subsequent food choice and

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

    Science.gov (United States)

    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...

  6. Proteomics strategy for identifying candidate bioactive proteins in complex mixtures: application to the platelet releasate.

    LENUS (Irish Health Repository)

    O'Connor, Roisin

    2010-01-01

    Proteomic approaches have proven powerful at identifying large numbers of proteins, but there are fewer reports of functional characterization of proteins in biological tissues. Here, we describe an experimental approach that fractionates proteins released from human platelets, linking bioassay activity to identity. We used consecutive orthogonal separation platforms to ensure sensitive detection: (a) ion-exchange of intact proteins, (b) SDS-PAGE separation of ion-exchange fractions and (c) HPLC separation of tryptic digests coupled to electrospray tandem mass spectrometry. Migration of THP-1 monocytes in response to complete or fractionated platelet releasate was assessed and located to just one of the forty-nine ion-exchange fractions. Over 300 proteins were identified in the releasate, with a wide range of annotated biophysical and biochemical properties, in particular platelet activation, adhesion, and wound healing. The presence of PEDF and involucrin, two proteins not previously reported in platelet releasate, was confirmed by western blotting. Proteins identified within the fraction with monocyte promigratory activity and not in other inactive fractions included vimentin, PEDF, and TIMP-1. We conclude that this analytical platform is effective for the characterization of complex bioactive samples.

  7. msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks

    Directory of Open Access Journals (Sweden)

    Yuan Zhang

    2014-01-01

    Full Text Available Dynamics of protein-protein interactions (PPIs reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process.

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

    Directory of Open Access Journals (Sweden)

    Xianjun Shen

    Full Text Available 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mudenda, Lwiindi; Aguilar Pierle, Sebastian; Turse, Joshua E.; Scoles, Glen A.; Purvine, Samuel O.; Nicora, Carrie D.; Clauss, Therese RW; Ueti, Massaro W.; Brown, Wendy C.; Brayton, Kelly A.

    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 opportunity 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.

  10. Protein and amino acid bioavailability estimates for canine foods

    NARCIS (Netherlands)

    Hendriks, W.H.; Bakker, E.J.; Bosch, G.

    2015-01-01

    Estimates of nutrient bioavailability are required for establishing dietary nutrient requirements and to evaluate the nutritional value of food ingredients or foods that are exposed to processing or extended storage. This study aimed to generate estimates for the bioavailability of dietary CP and AA

  11. Allergic sensitization: food- and protein-related factors

    NARCIS (Netherlands)

    McClain, Scott; Bowman, Christal; Fernández-Rivas, Montserrat; Ladics, Gregory S.; van Ree, Ronald

    2014-01-01

    Presented here are emerging capabilities to precisely measure endogenous allergens in soybean and maize, consideration of food matrices on allergens, and proteolytic activity of allergens. Also examined are observations of global allergy surveys and the prevalence of food allergy across different

  12. Dissection of the Ascaris Sperm Motility Machinery Identifies Key Proteins Involved in Major Sperm Protein-based Amoeboid Locomotion

    Science.gov (United States)

    Buttery, Shawnna M.; Ekman, Gail C.; Seavy, Margaret; Stewart, Murray; Roberts, Thomas M.

    2003-01-01

    Although Ascaris sperm motility closely resembles that seen in many other types of crawling cells, the lamellipodial dynamics that drive movement result from modulation of a cytoskeleton based on the major sperm protein (MSP) rather than actin. The dynamics of the Ascaris sperm cytoskeleton can be studied in a cell-free in vitro system based on the movement of plasma membrane vesicles by fibers constructed from bundles of MSP filaments. In addition to ATP, MSP, and a plasma membrane protein, reconstitution of MSP motility in this cell-free extract requires cytosolic proteins that orchestrate the site-specific assembly and bundling of MSP filaments that generates locomotion. Here, we identify a fraction of cytosol that is comprised of a small number of proteins but contains all of the soluble components required to assemble fibers. We have purified two of these proteins, designated MSP fiber proteins (MFPs) 1 and 2 and demonstrated by immunolabeling that both are located in the MSP cytoskeleton in cells and in fibers. These proteins had reciprocal effects on fiber assembly in vitro: MFP1 decreased the rate of fiber growth, whereas MFP2 increased the growth rate. PMID:14565983

  13. Identifying vegetarians and their food consumption according to self-identification and operationalized definition in Finland.

    Science.gov (United States)

    Vinnari, Markus; Montonen, Jukka; Härkänen, Tommi; Männistö, Satu

    2009-04-01

    To determine the prevalence and sociodemographic factors related to vegetarians according to different definitions in Finland and to compare the consumption of selected foodstuffs and nutritional intakes among vegetarians and omnivores. Information about subjects' identification as vegetarians in a survey was used as a basis for self-defined vegetarianism. Foodstuffs consumed and their frequencies of consumption were obtained, and the reported consumption frequencies of meat, fish, milk and eggs or food portions containing these foodstuffs were used as a basis for an operationalized definition of different types of vegetarianism. Reported consumption was used to estimate foodstuff and nutritional intakes. Three large nationwide surveys in Finland. In total, 24 393 participants aged between 18 and 79 years were included. The proportion of self-identified vegetarians was 3.3 % of the total population in Finland. According to responses to questions on consumption frequency, 1.4 % of the population were pesco-lacto-ovo-vegetarians, 0.43 % were vegans, lacto-vegetarians or lacto-ovo-vegetarians, and 0.18 % were vegans or lacto-vegetarians. Eighty per cent of the self-identified vegetarians did not follow a vegetarian diet according to the operationalized definition, but they consumed fewer meat products (P fish, but they follow a healthier diet than self-defined omnivores. In the same sample self-identification indicated more than double the incidence of vegetarianism than the operationalized definition. Therefore self-identification is not a good method for observing the prevalence of vegetarianism.

  14. Identifying food-related life style segments by a cross-culturally valid scaling device

    DEFF Research Database (Denmark)

    Brunsø, Karen; Grunert, Klaus G.

    1994-01-01

    We present a new view of life style, based on a cognitive perspective, which makes life style specific to certain areas of consumption. The specific area of consumption studied here is food, resulting in a concept of food-related life style. An instrument is developed that can measure food-relate...

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

    Science.gov (United States)

    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.

  16. Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system.

    Science.gov (United States)

    Liao, Qi; Yuan, Xiongying; Xiao, Hui; Liu, Changning; Lv, Zhiyue; Zhao, Yi; Wu, Zhongdao

    2011-01-01

    Schistosoma japonicum is a major infectious agent of schistosomiasis. It has been reported that large number of proteins excreted and secreted by S. japonicum during its life cycle are important for its infection and survival in definitive hosts. These proteins can be used as ideal candidates for vaccines or drug targets. In this work, we analyzed the protein sequences of S. japonicum and found that compared with other proteins in S. japonicum, excretory/secretory (ES) proteins are generally longer, more likely to be stable and enzyme, more likely to contain immune-related binding peptides and more likely to be involved in regulation and metabolism processes. Based on the sequence difference between ES and non-ES proteins, we trained a support vector machine (SVM) with much higher accuracy than existing approaches. Using this SVM, we identified 191 new ES proteins in S. japonicum, and further predicted 7 potential interactions between these ES proteins and human immune proteins. Our results are useful to understand the pathogenesis of schistosomiasis and can serve as a new resource for vaccine or drug targets discovery for anti-schistosome.

  17. Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system.

    Directory of Open Access Journals (Sweden)

    Qi Liao

    Full Text Available Schistosoma japonicum is a major infectious agent of schistosomiasis. It has been reported that large number of proteins excreted and secreted by S. japonicum during its life cycle are important for its infection and survival in definitive hosts. These proteins can be used as ideal candidates for vaccines or drug targets. In this work, we analyzed the protein sequences of S. japonicum and found that compared with other proteins in S. japonicum, excretory/secretory (ES proteins are generally longer, more likely to be stable and enzyme, more likely to contain immune-related binding peptides and more likely to be involved in regulation and metabolism processes. Based on the sequence difference between ES and non-ES proteins, we trained a support vector machine (SVM with much higher accuracy than existing approaches. Using this SVM, we identified 191 new ES proteins in S. japonicum, and further predicted 7 potential interactions between these ES proteins and human immune proteins. Our results are useful to understand the pathogenesis of schistosomiasis and can serve as a new resource for vaccine or drug targets discovery for anti-schistosome.

  18. Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays.

    Science.gov (United States)

    Low, Jason K K; Im, Hogune; Erce, Melissa A; Hart-Smith, Gene; Snyder, Michael P; Wilkins, Marc R

    2016-02-01

    Arginine methylation on nonhistone proteins is associated with a number of cellular processes including RNA splicing, protein localization, and the formation of protein complexes. In this manuscript, Saccharomyces cerevisiae proteome arrays carrying 4228 proteins were used with an antimethylarginine antibody to first identify 88 putatively arginine-methylated proteins. By treating the arrays with recombinant arginine methyltransferase Hmt1, 42 proteins were found to be possible substrates of this enzyme. Analysis of the putative arginine-methylated proteins revealed that they were predominantly nuclear or nucleolar in localization, consistent with the localization of Hmt1. Many are involved in known methylarginine-associated functions, such as RNA processing and ribonucleoprotein complex biogenesis, yet others are of newer classes, namely RNA/DNA helicases and tRNA-associated proteins. Using ex vivo methylation and MS/MS, a set of 12 proteins (Brr1, Dia4, Hts1, Mpp10, Mrd1, Nug1, Prp43, Rpa43, Rrp43, Spp381, Utp4, and Npl3), including the RNA helicase Prp43 and tRNA ligases Dia4 and Hts1, were all validated as Hmt1 substrates. Interestingly, the majority of these also had human orthologs, or family members, that have been documented elsewhere to carry arginine methylation. These results confirm arginine methylation as a widespread modification and Hmt1 as the major arginine methyltransferase in the S. cerevisiae cell. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    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

  20. Identifying common metalloprotease inhibitors by protein fold types using Fourier transform mass spectrometry.

    Science.gov (United States)

    Mitchell, Jennifer K; Pitcher, Desley; McArdle, Bernadette M; Alnefelt, Terese; Duffy, Sandra; Avery, Vicky; Quinn, Ronald J

    2007-12-01

    Fourteen natural products, known to inhibit other proteins of the Zincin-like fold class, were screened for inhibition of the Zincin-like fold metalloprotease thermolysin using mass spectrometry. Fourier Transform Mass Spectrometry was successful in identifying actinonin, a known inhibitor of astacin and stromelysin, to be an inhibitor of thermolysin. Molecular modelling studies have shown that specificity within the Zincin-like fold is determined by Protein Fold Topology.

  1. A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma

    DEFF Research Database (Denmark)

    Havelund, Jesper F; Wojdyla, Katarzyna Iwona; Davies, Michael J

    2017-01-01

    preparation and chromatography. For the first time MS/MS data analysis utilising diagnostic biotin fragment ions is used to pinpoint sites of biotin labelling and improve the confidence of carbonyl peptide assignments. We identified a total of 125 carbonylated residues in bovine serum albumin after extensive...... at the protein level and help to understand how carbonylation affects protein structure and function. The challenge for future research is to identify the type and nature of oxidised residues to gain a deeper understanding of the mechanism(s) governing carbonylation in cells and organisms and assess their role...

  2. Geochemistry and mercury contamination in receiving environments of artisanal mining wastes and identified concerns for food safety

    International Nuclear Information System (INIS)

    Reichelt-Brushett, Amanda J.; Stone, Jane; Howe, Pelli; Thomas, Bernard; Clark, Malcolm; Male, Yusthinus; Nanlohy, Albert; Butcher, Paul

    2017-01-01

    Artisanal small-scale gold mining (ASGM) using mercury (Hg) amalgamation has been occurring on Buru Island, Indonesia since early 2012, and has caused rapid accumulation of high Hg concentrations in river, estuary and marine sediments. In this study, sediment samples were collected from several sites downstream of the Mount Botak ASGM site, as well as in the vicinity of the more recently established site at Gogrea where no sampling had previously been completed. All sediment samples had total Hg (THg) concentrations exceeding Indonesian sediment quality guidelines and were up to 82 times this limit at one estuary site. The geochemistry of sediments in receiving environments indicates the potential for Hg-methylation to form highly bioavailable Hg species. To assess the current contamination threat from consumption of local seafood, samples of fish, molluscs and crustaceans were collected from the Namlea fish market and analysed for THg concentrations. The majority of edible tissue samples had elevated THg concentrations, which raises concerns for food safety. This study shows that river, estuary and marine ecosystems downstream of ASGM operations on Buru Island are exposed to dangerously high Hg concentrations, which are impacting aquatic food chains, and fisheries resources. Considering the high dietary dependence on marine protein in the associated community and across the Mollucas Province, and the short time period since ASGM operations commenced in this region, the results warrant urgent further investigation, risk mitigation, and community education. - Highlights: • Mercury contamination of sediments and seafood due to artisanal gold mining. • Considerable risks to human and ecosystem health are identified. • Results emphasise the urgent need for risk mitigation and community education.

  3. Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein

    DEFF Research Database (Denmark)

    Sørensen, Rikke Kruse; Krantz, James; Barker, Natalie

    2017-01-01

    and built a CLASP2 protein network in 3T3-L1 adipocytes. Using two different commercially available antibodies for CLASP2 and an antibody for epitope-tagged, overexpressed CLASP2, we performed multiple affinity purification coupled with mass spectrometry (AP-MS) experiments in combination with label-free......, glycogen synthase, and glycogenin. Investigating the SOGA1 interactome confirmed SOGA1 can reciprocal co-IP both CLASP2 and MARK2 as well as glycogen synthase and glycogenin. SOGA1 was confirmed to colocalize with CLASP2 and also with tubulin, which identifies SOGA1 as a new microtubule-associated protein...

  4. A feedback framework for protein inference with peptides identified from tandem mass spectra

    Directory of Open Access Journals (Sweden)

    Shi Jinhong

    2012-11-01

    Full Text Available Abstract Background Protein inference is an important computational step in proteomics. There exists a natural nest relationship between protein inference and peptide identification, but these two steps are usually performed separately in existing methods. We believe that both peptide identification and protein inference can be improved by exploring such nest relationship. Results In this study, a feedback framework is proposed to process peptide identification reports from search engines, and an iterative method is implemented to exemplify the processing of Sequest peptide identification reports according to the framework. The iterative method is verified on two datasets with known validity of proteins and peptides, and compared with ProteinProphet and PeptideProphet. The results have shown that not only can the iterative method infer more true positive and less false positive proteins than ProteinProphet, but also identify more true positive and less false positive peptides than PeptideProphet. Conclusions The proposed iterative method implemented according to the feedback framework can unify and improve the results of peptide identification and protein inference.

  5. Mass Spectrometry-Based Methods for Identifying Oxidized Proteins in Disease: Advances and Challenges

    Directory of Open Access Journals (Sweden)

    Ivan Verrastro

    2015-04-01

    Full Text Available Many inflammatory diseases have an oxidative aetiology, which leads to oxidative damage to biomolecules, including proteins. It is now increasingly recognized that oxidative post-translational modifications (oxPTMs of proteins affect cell signalling and behaviour, and can contribute to pathology. Moreover, oxidized proteins have potential as biomarkers for inflammatory diseases. Although many assays for generic protein oxidation and breakdown products of protein oxidation are available, only advanced tandem mass spectrometry approaches have the power to localize specific oxPTMs in identified proteins. While much work has been carried out using untargeted or discovery mass spectrometry approaches, identification of oxPTMs in disease has benefitted from the development of sophisticated targeted or semi-targeted scanning routines, combined with chemical labeling and enrichment approaches. Nevertheless, many potential pitfalls exist which can result in incorrect identifications. This review explains the limitations, advantages and challenges of all of these approaches to detecting oxidatively modified proteins, and provides an update on recent literature in which they have been used to detect and quantify protein oxidation in disease.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Aflatoxins in body fluids and food of Nigerian children with protein ...

    African Journals Online (AJOL)

    Aflatoxins are natural contaminants of food crops implicated in the pathogenesis of various human diseases. This study aimed to determine the associations between aflatoxins and protein- energy malnutrition (PEM) by measurements of aflatoxins in serum, urine and food on plate of Nigerian children with PEM. A cross- ...

  10. Advances in structure formation of anisotropic protein-rich foods through novel processing concepts

    NARCIS (Netherlands)

    Manski, J.M.; Goot, van der A.J.; Boom, R.M.

    2007-01-01

    Development of protein-rich food products is currently limited by lack of scientific insights in structuring processes. The application of well-defined flow appears to be a good tool to create novel anisotropic food structures, on one hand, and to improve understanding of the behavior of

  11. Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery

    Directory of Open Access Journals (Sweden)

    Yuri Pevzner

    2015-08-01

    Full Text Available Inherent biological viability and diversity of natural products make them a potentially rich source for new therapeutics. However, identification of bioactive compounds with desired therapeutic effects and identification of their protein targets is a laborious, expensive process. Extracts from organism samples may show desired activity in phenotypic assays but specific bioactive compounds must be isolated through further separation methods and protein targets must be identified by more specific phenotypic and in vitro experimental assays. Still, questions remain as to whether all relevant protein targets for a compound have been identified. The desire is to understand breadth of purposing for the compound to maximize its use and intellectual property, and to avoid further development of compounds with insurmountable adverse effects. Previously we developed a Virtual Target Screening system that computationally screens one or more compounds against a collection of virtual protein structures. By scoring each compound-protein interaction, we can compare against averaged scores of synthetic drug-like compounds to determine if a particular protein would be a potential target of a compound of interest. Here we provide examples of natural products screened through our system as we assess advantages and shortcomings of our current system in regards to natural product drug discovery.

  12. Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery

    Directory of Open Access Journals (Sweden)

    Yuri Pevzner

    2014-05-01

    Full Text Available Inherent biological viability and diversity of natural products make them a potentially rich source for new therapeutics. However, identification of bioactive compounds with desired therapeutic effects and identification of their protein targets is a laborious, expensive process. Extracts from organism samples may show desired activity in phenotypic assays but specific bioactive compounds must be isolated through further separation methods and protein targets must be identified by more specific phenotypic and in vitro experimental assays. Still, questions remain as to whether all relevant protein targets for a compound have been identified. The desire is to understand breadth of purposing for the compound to maximize its use and intellectual property, and to avoid further development of compounds with insurmountable adverse effects. Previously we developed a Virtual Target Screening system that computationally screens one or more compounds against a collection of virtual protein structures. By scoring each compound-protein interaction, we can compare against averaged scores of synthetic drug-like compounds to determine if a particular protein would be a potential target of a compound of interest. Here we provide examples of natural products screened through our system as we assess advantages and shortcomings of our current system in regards to natural product drug discovery.

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

    Science.gov (United States)

    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.

  14. A retrospective chart review to identify perinatal factors associated with food allergies

    Science.gov (United States)

    2012-01-01

    Background Gut flora are important immunomodulators that may be disrupted in individuals with atopic conditions. Probiotic bacteria have been suggested as therapeutic modalities to mitigate or prevent food allergic manifestations. We wished to investigate whether perinatal factors known to disrupt gut flora increase the risk of IgE-mediated food allergies. Methods Birth records obtained from 192 healthy children and 99 children diagnosed with food allergies were reviewed retrospectively. Data pertaining to delivery method, perinatal antibiotic exposure, neonatal nursery environment, and maternal variables were recorded. Logistic regression analysis was used to assess the association between variables of interest and subsequent food allergy diagnosis. Results Retrospective investigation did not find perinatal antibiotics, NICU admission, or cesarean section to be associated with increased risk of food allergy diagnosis. However, associations between food allergy diagnosis and male gender (66 vs. 33; p=0.02) were apparent in this cohort. Additionally, increasing maternal age at delivery was significantly associated with food allergy diagnosis during childhood (OR, 1.05; 95% CI, 1.017 to 1.105; p=0.005). Conclusions Gut flora are potent immunomodulators, but their overall contribution to immune maturation remains to be elucidated. Additional understanding of the interplay between immunologic, genetic, and environmental factors underlying food allergy development need to be clarified before probiotic therapeutic interventions can routinely be recommended for prevention or mitigation of food allergies. Such interventions may be well-suited in male infants and in infants born to older mothers. PMID:23078601

  15. A retrospective chart review to identify perinatal factors associated with food allergies

    Directory of Open Access Journals (Sweden)

    Karpa Kelly

    2012-10-01

    Full Text Available Abstract Background Gut flora are important immunomodulators that may be disrupted in individuals with atopic conditions. Probiotic bacteria have been suggested as therapeutic modalities to mitigate or prevent food allergic manifestations. We wished to investigate whether perinatal factors known to disrupt gut flora increase the risk of IgE-mediated food allergies. Methods Birth records obtained from 192 healthy children and 99 children diagnosed with food allergies were reviewed retrospectively. Data pertaining to delivery method, perinatal antibiotic exposure, neonatal nursery environment, and maternal variables were recorded. Logistic regression analysis was used to assess the association between variables of interest and subsequent food allergy diagnosis. Results Retrospective investigation did not find perinatal antibiotics, NICU admission, or cesarean section to be associated with increased risk of food allergy diagnosis. However, associations between food allergy diagnosis and male gender (66 vs. 33; p=0.02 were apparent in this cohort. Additionally, increasing maternal age at delivery was significantly associated with food allergy diagnosis during childhood (OR, 1.05; 95% CI, 1.017 to 1.105; p=0.005. Conclusions Gut flora are potent immunomodulators, but their overall contribution to immune maturation remains to be elucidated. Additional understanding of the interplay between immunologic, genetic, and environmental factors underlying food allergy development need to be clarified before probiotic therapeutic interventions can routinely be recommended for prevention or mitigation of food allergies. Such interventions may be well-suited in male infants and in infants born to older mothers.

  16. Brief assessment of food insecurity accurately identifies high-risk US adults.

    Science.gov (United States)

    Gundersen, Craig; Engelhard, Emily E; Crumbaugh, Amy S; Seligman, Hilary K

    2017-06-01

    To facilitate the introduction of food insecurity screening into clinical settings, we examined the test performance of two-item screening questions for food insecurity against the US Department of Agriculture's Core Food Security Module. We examined sensitivity, specificity and accuracy of various two-item combinations of questions assessing food insecurity in the general population and high-risk population subgroups. 2013 Current Population Survey December Supplement, a population-based US survey. All survey participants from the general population and high-risk subgroups. The test characteristics of multiple two-item combinations of questions assessing food insecurity had adequate sensitivity (>97 %) and specificity (>70 %) for widespread adoption as clinical screening measures. We recommend two specific items for clinical screening programmes based on their widespread current use and high sensitivity for detecting food insecurity. These items query how often the household 'worried whether food would run out before we got money to buy more' and how often 'the food that we bought just didn't last and we didn't have money to get more'. The recommended items have sensitivity across high-risk population subgroups of ≥97 % and a specificity of ≥74 % for food insecurity.

  17. A retrospective chart review to identify perinatal factors associated with food allergies.

    Science.gov (United States)

    Dowhower Karpa, Kelly; Paul, Ian M; Leckie, J Alexander; Shung, Sharon; Carkaci-Salli, Nurgul; Vrana, Kent E; Mauger, David; Fausnight, Tracy; Poger, Jennifer

    2012-10-19

    Gut flora are important immunomodulators that may be disrupted in individuals with atopic conditions. Probiotic bacteria have been suggested as therapeutic modalities to mitigate or prevent food allergic manifestations. We wished to investigate whether perinatal factors known to disrupt gut flora increase the risk of IgE-mediated food allergies. Birth records obtained from 192 healthy children and 99 children diagnosed with food allergies were reviewed retrospectively. Data pertaining to delivery method, perinatal antibiotic exposure, neonatal nursery environment, and maternal variables were recorded. Logistic regression analysis was used to assess the association between variables of interest and subsequent food allergy diagnosis. Retrospective investigation did not find perinatal antibiotics, NICU admission, or cesarean section to be associated with increased risk of food allergy diagnosis. However, associations between food allergy diagnosis and male gender (66 vs. 33; p=0.02) were apparent in this cohort. Additionally, increasing maternal age at delivery was significantly associated with food allergy diagnosis during childhood (OR, 1.05; 95% CI, 1.017 to 1.105; p=0.005). Gut flora are potent immunomodulators, but their overall contribution to immune maturation remains to be elucidated. Additional understanding of the interplay between immunologic, genetic, and environmental factors underlying food allergy development need to be clarified before probiotic therapeutic interventions can routinely be recommended for prevention or mitigation of food allergies. Such interventions may be well-suited in male infants and in infants born to older mothers.

  18. A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis.

    Science.gov (United States)

    Burstein, David; Gould, Sven B; Zimorski, Verena; Kloesges, Thorsten; Kiosse, Fuat; Major, Peter; Martin, William F; Pupko, Tal; Dagan, Tal

    2012-02-01

    The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, the most widespread nonviral sexually transmitted disease in humans. It possesses hydrogenosomes-anaerobic mitochondria that generate H(2), CO(2), and acetate from pyruvate while converting ADP to ATP via substrate-level phosphorylation. T. vaginalis hydrogenosomes lack a genome and translation machinery; hence, they import all their proteins from the cytosol. To date, however, only 30 imported proteins have been shown to localize to the organelle. A total of 226 nuclear-encoded proteins inferred from the genome sequence harbor a characteristic short N-terminal presequence, reminiscent of mitochondrial targeting peptides, which is thought to mediate hydrogenosomal targeting. Recent studies suggest, however, that the presequences might be less important than previously thought. We sought to identify new hydrogenosomal proteins within the 59,672 annotated open reading frames (ORFs) of T. vaginalis, independent of the N-terminal targeting signal, using a machine learning approach. Our training set included 57 gene and protein features determined for all 30 known hydrogenosomal proteins and 576 nonhydrogenosomal proteins. Several classifiers were trained on this set to yield an import score for all proteins encoded by T. vaginalis ORFs, predicting the likelihood of hydrogenosomal localization. The machine learning results were tested through immunofluorescence assay and immunodetection in isolated cell fractions of 14 protein predictions using hemagglutinin constructs expressed under the homologous SCSα promoter in transiently transformed T. vaginalis cells. Localization of 6 of the 10 top predicted hydrogenosome-localized proteins was confirmed, and two of these were found to lack an obvious N-terminal targeting signal.

  19. Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity

    DEFF Research Database (Denmark)

    Lasonder, Edwin; Janse, Chris J; van Gemert, Geert-Jan

    2008-01-01

    Plasmodium falciparum sporozoites that develop and mature inside an Anopheles mosquito initiate a malaria infection in humans. Here we report the first proteomic comparison of different parasite stages from the mosquito -- early and late oocysts containing midgut sporozoites, and the mature...... whose annotation suggest an involvement in sporozoite maturation, motility, infection of the human host and associated metabolic adjustments. Analyses of proteins identified in the P. falciparum sporozoite proteomes by orthologous gene disruption in the rodent malaria parasite, P. berghei, revealed...... three previously uncharacterized Plasmodium proteins that appear to be essential for sporozoite development at distinct points of maturation in the mosquito. This study sheds light on the development and maturation of the malaria parasite in an Anopheles mosquito and also identifies proteins that may...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  2. Proteomic analysis of exosomes from nasopharyngeal carcinoma cell identifies intercellular transfer of angiogenic proteins

    KAUST Repository

    Chan, Yuk-kit

    2015-04-01

    Exosomes, a group of secreted extracellular nanovesicles containing genetic materials and signaling molecules, play a critical role in intercellular communication. During tumorigenesis, exosomes have been demonstrated to promote tumor angiogenesis and metastasis while their biological functions in nasopharyngeal carcinoma (NPC) are poorly understood. In this study, we focused on the role of NPC-derived exosomes on angiogenesis. Exosomes derived from the NPC C666-1 cells and immortalized nasopharyngeal epithelial cells (NP69 and NP460) were isolated using ultracentrifugation. The molecular profile and biophysical characteristics of exosomes were verified by Western blotting, sucrose density gradient, and electron microscopy. We showed that the C666-1 exosomes (10 and 20 μg/ml) could significantly increase the tubulogenesis, migration and invasion of human umbilical vein endothelial cells (HUVECs) in a dose-dependent manner. Subsequently, an iTRAQ-based quantitative proteomics was used to identify the differentially expressed proteins in C666-1 exosomes. Among the 640 identified proteins, 51 and 89 proteins were considered as up- and down-regulated (≥ 1.5-fold variations) in C666-1 exosomes compared to the normal counterparts, respectively. As expected, pro-angiogenic proteins including intercellular adhesion molecule-1 (ICAM-1) and CD44 variant isoform 5 (CD44v5) are among the up-regulated proteins, whereas angio-suppressive protein, thrombospondin-1 (TSP-1) was down-regulated in C666-1 exosomes. Further confocal microscopic study and Western blotting clearly demonstrated that the alteration of ICAM-1, and TSP-1 expressions in recipient HUVECs are due to internalization of exosomes. Taken together, these data strongly indicated the critical roles of identified angiogenic proteins in the involvement of exosomes-induced angiogenesis, which could potentially be developed as therapeutic targets in future. This article is protected by copyright. All rights reserved.

  3. A cohort of new adhesive proteins identified from transcriptomic analysis of mussel foot glands.

    Science.gov (United States)

    DeMartini, Daniel G; Errico, John M; Sjoestroem, Sebastian; Fenster, April; Waite, J Herbert

    2017-06-01

    The adaptive attachment of marine mussels to a wide range of substrates in a high-energy, saline environment has been explored for decades and is a significant driver of bioinspired wet adhesion research. Mussel attachment relies on a fibrous holdfast known as the byssus, which is made by a specialized appendage called the foot. Multiple adhesive and structural proteins are rapidly synthesized, secreted and moulded by the foot into holdfast threads. About 10 well-characterized proteins, namely the mussel foot proteins (Mfps), the preCols and the thread matrix proteins, are reported as representing the bulk of these structures. To explore how robust this proposition is, we sequenced the transcriptome of the glandular tissues that produce and secrete the various holdfast components using next-generation sequencing methods. Surprisingly, we found around 15 highly expressed genes that have not previously been characterized, but bear key similarities to the previously defined mussel foot proteins, suggesting additional contribution to byssal function. We verified the validity of these transcripts by polymerase chain reaction, cloning and Sanger sequencing as well as confirming their presence as proteins in the byssus. These newly identified proteins greatly expand the palette of mussel holdfast biochemistry and provide new targets for investigation into bioinspired wet adhesion. © 2017 The Author(s).

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

    Science.gov (United States)

    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.

  5. Food choice by Blue-gray Tanagers in relation to protein content.

    Science.gov (United States)

    Bosque, Carlos; Calchi, Rosanna

    2003-06-01

    We tested discriminatory ability and food choice in relation to protein content of the diet in wild-caught Blue-gray Tanagers (Thraupis episcopus), a generalist tropical frugivorous bird. In two sets of experiments we offered to five individual birds in pair-wise choice trials two nearly iso-caloric experimental diets differing in their protein content only. Protein contents of the experimental diets were 4.6 vs. 1.4% in the first experiment and 3.2 and 1.5% (dry matter basis) in the second experiment. Response varied among individual tanagers, but 6 of the 10 birds showed a clear preference for the food highest in protein. Two individuals displayed a strong positional preference. When testing each treatment group, birds ate daily significantly more of the food that had higher protein content. We conclude that Blue-gray Tanagers prefer richer nitrogen foods. Our results also demonstrate that Blue-gray Tanagers have remarkable discriminatory abilities, they reacted to differences in protein content as small as 0.09% fresh matter. We show for the first time discriminatory ability and preference of wild frugivorous birds for foods richer in protein under controlled conditions. Our findings support the hypothesis that frugivorous birds can act as selective agents for fruit pulp composition.

  6. Inflammatory and fibrotic proteins proteomically identified as key protein constituents in urine and stone matrix of patients with kidney calculi.

    Science.gov (United States)

    Boonla, Chanchai; Tosukhowong, Piyaratana; Spittau, Björn; Schlosser, Andreas; Pimratana, Chaowat; Krieglstein, Kerstin

    2014-02-15

    To uncover whether urinary proteins are incorporated into stones, the proteomic profiles of kidney stones and urine collected from the same patients have to be explored. We employed 1D-PAGE and nanoHPLC-ESI-MS/MS to analyze the proteomes of kidney stone matrix (n=16), nephrolithiatic urine (n=14) and healthy urine (n=3). We identified 62, 66 and 22 proteins in stone matrix, nephrolithiatic urine and healthy urine, respectively. Inflammation- and fibrosis-associated proteins were frequently detected in the stone matrix and nephrolithiatic urine. Eighteen proteins were exclusively found in the stone matrix and nephrolithiatic urine, considered as candidate biomarkers for kidney stone formation. S100A8 and fibronectin, representatives of inflammation and fibrosis, respectively, were up-regulated in nephrolithiasis renal tissues. S100A8 was strongly expressed in infiltrated leukocytes. Fibronectin was over-expressed in renal tubular cells. S100A8 and fibronectin were immunologically confirmed to exist in nephrolithiatic urine and stone matrix, but in healthy urine they were undetectable. Conclusion, both kidney stones and urine obtained from the same patients greatly contained inflammatory and fibrotic proteins. S100A8 and fibronectin were up-regulated in stone-baring kidneys and nephrolithiatic urine. Therefore, inflammation and fibrosis are suggested to be involved in the formation of kidney calculi. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Pandey, Aarti; Chakraborty, Subhra; Datta, Asis; Chakraborty, Niranjan

    2008-01-01

    Dehydration or water-deficit is one of the most important environmental stress factors that greatly influences plant growth and development and limits crop productivity. Plants respond and adapt to such stress by altering their cellular metabolism and activating various defense machineries. Mechanisms that operate signal perception, transduction, and downstream regulatory events provide valuable information about the underlying pathways involved in environmental stress responses. The nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. To gain a better understanding of dehydration response in plants, we have developed a comparative nuclear proteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water and the changes in the nuclear proteome were examined using two-dimensional gel electrophoresis. Approximately 205 protein spots were found to be differentially regulated under dehydration. Mass spectrometry analysis allowed the identification of 147 differentially expressed proteins, presumably involved in a variety of functions including gene transcription and replication, molecular chaperones, cell signaling, and chromatin remodeling. The dehydration responsive nuclear proteome of chickpea revealed a coordinated response, which involves both the regulatory as well as the functional proteins. This study, for the first time, provides an insight into the complex metabolic network operating in the nucleus during dehydration.

  8. Identifying the source of food-borne disease outbreaks: An application of Bayesian variable selection.

    NARCIS (Netherlands)

    Jacobs, Rianne; Lesaffre, Emmanuel; Teunis, Peter Fm; Höhle, Michael; van de Kassteele, Jan

    2017-01-01

    Early identification of contaminated food products is crucial in reducing health burdens of food-borne disease outbreaks. Analytic case-control studies are primarily used in this identification stage by comparing exposures in cases and controls using logistic regression. Standard epidemiological

  9. Evaluation of scientific criteria for identifying allergenic foods of public health importance

    NARCIS (Netherlands)

    Bilsen, J.H.M. van; Ronsmans, S.; Crevel, R.W.R.; Rona, R.J.; Przyrembel, H.; Penninks, A.H.; Contor, L.; Houben, G.F.

    2011-01-01

    Identification of allergenic foods of public health importance should be based on well-defined criteria. Björkstén et al. (2008) proposed that the criteria should assess the evidence for an IgE mechanism, the reaction, the potency and the severity of the effect of the food and its prevalence. This

  10. Proteomic screen in the simple metazoan Hydra identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Ca2+ signalling

    Directory of Open Access Journals (Sweden)

    Imhof Axel

    2007-07-01

    Full Text Available Abstract Background 14-3-3 proteins have been implicated in many signalling mechanisms due to their interaction with Ser/Thr phosphorylated target proteins. They are evolutionarily well conserved in eukaryotic organisms from single celled protozoans and unicellular algae to plants and humans. A diverse array of target proteins has been found in higher plants and in human cell lines including proteins involved in cellular metabolism, apoptosis, cytoskeletal organisation, secretion and Ca2+ signalling. Results We found that the simple metazoan Hydra has four 14-3-3 isoforms. In order to investigate whether the diversity of 14-3-3 target proteins is also conserved over the whole animal kingdom we isolated 14-3-3 binding proteins from Hydra vulgaris using a 14-3-3-affinity column. We identified 23 proteins that covered most of the above-mentioned groups. We also isolated several novel 14-3-3 binding proteins and the Hydra specific secreted fascin-domain-containing protein PPOD. In addition, we demonstrated that one of the 14-3-3 isoforms, 14-3-3 HyA, interacts with one Hydra-Bcl-2 like protein in vitro. Conclusion Our results indicate that 14-3-3 proteins have been ubiquitous signalling components since the start of metazoan evolution. We also discuss the possibility that they are involved in the regulation of cell numbers in response to food supply in Hydra.

  11. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.

    Directory of Open Access Journals (Sweden)

    Matt eGeisler

    2015-06-01

    Full Text Available Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6,004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.

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

    Science.gov (United States)

    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.

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

    NARCIS (Netherlands)

    Blom, W.M.; Kruizinga, A.G.; Rubingh, C.M.; Remington, B.C.; Crevel, R.W.R.; Houben, G.F.

    2017-01-01

    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

  14. Food proteins as a source of bioactive peptides with diverse functions.

    Science.gov (United States)

    Rutherfurd-Markwick, Kay J

    2012-08-01

    In addition to supplying essential nutrients, some food proteins can confer additional health benefits beyond nutrition. The presence of bioactive proteins and peptides in different foods is a factor not currently taken into consideration when assessing the dietary quality of food proteins. The range of described physiological benefits attributed to bioactive proteins and peptides is diverse. Multiple factors can potentially impact on the ability of a bioactive peptide or protein to elicit an effect. Although some food proteins act directly in their intact form to elicit their effects, generally it is peptides derived from digestion, hydrolysis or fermentation that are of most interest. The levels of bioactive peptides generated must be sufficient to elicit a response, but should not be so high as to be unsafe, thus causing negative effects. In addition, some peptides cause systemic effects and therefore must be absorbed, again in sufficient amounts to elicit their action. Many studies to date have been carried out in vitro; therefore it is important that further trials are conducted in vivo to assess efficacy, dose response and safety of the peptides, particularly if health related claims are to be made. Therefore, methods must be developed and standardised that enable the measurement of health benefits and also the level of bioactive peptides which are absorbed into the bloodstream. Once standardised, such methods may provide a new perspective and an additional mechanism for analysing protein quality which is currently not encompassed by the use of the protein digestibility-corrected amino acid score (PDCAAS).

  15. [Assessment of protein quality in foods by calculating the amino acids score corrected by digestibility].

    Science.gov (United States)

    Suárez López, M M; Kizlansky, A; López, L B

    2006-01-01

    The protein score reflects its amino acids (AA) content in comparison with the ideal protein. However, when there is a need to know the use of AA by the organism it is necessary to do a correction of the score value by protein digestibility (PDCAAS). Since this information is not available for usually consumed foods, the present work aimed at calculating the PDCAAS values of these foods. The score was calculated the limiting AA of 70 foods, taking as reference protein the AA pattern for children > 1 year old and adults proposed by the U.S. National Academy of Sciences for the year 2002. The PDCAAS value was obtained in each case by multiplying the score value by the digestibility index. For vegetable foods the obtained score values and PDCAAS were, respectively: vegetables 88.5% / 73.4%, tubercles 89.44% / 74.24%, fresh fruits 75.6% / 64.3%, dried fruits 65.6% / 48.1%, legumes in general 89.2% / 69.58%, chickpea and soybean 100% / 78%, cereals and derivatives 68.8% / 58.5%. Creation of table that contents the score values, digestibility values, and PDCAAS of foods is a useful tool when food selection for a dietary plan based on its protein quality is desirable.

  16. Production of Pharmaceutical Proteins in Solanaceae Food Crops

    Directory of Open Access Journals (Sweden)

    Giorgio De Guzman

    2013-01-01

    Full Text Available The benefits of increased safety and cost-effectiveness make vegetable crops appropriate systems for the production and delivery of pharmaceutical proteins. In particular, Solanaceae edible crops could be inexpensive biofactories for oral vaccines and other pharmaceutical proteins that can be ingested as minimally processed extracts or as partially purified products. The field of crop plant biotechnology is advancing rapidly due to novel developments in genetic and genomic tools being made available today for the scientific community. In this review, we briefly summarize data now available regarding genomic resources for the Solanaceae family. In addition, we describe novel strategies developed for the expression of foreign proteins in vegetable crops and the utilization of these techniques to manufacture pharmaceutical proteins.

  17. Protein and amino acid bioavailability estimates for canine foods.

    Science.gov (United States)

    Hendriks, W H; Bakker, E J; Bosch, G

    2015-10-01

    Estimates of nutrient bioavailability are required for establishing dietary nutrient requirements and to evaluate the nutritional value of food ingredients or foods that are exposed to processing or extended storage. This study aimed to generate estimates for the bioavailability of dietary CP and AA for adult dogs using existing literature data and to evaluate the accuracy of estimates currently used in 3 authoritative publications. A regression equation was derived relating apparent fecal N outflow to standardized ileal N outflow from a data set containing information on 158 individual diets and their N digestibility when fed to adult dogs. Standardized ileal digestibility (sID) of N (sID) was shown to be nearly perfectly correlated to the sID of the sum of N of AA in 24 diets for which AA digestibility data were available. Regression equations between sID of individual AA and sID were calculated. Bioavailability estimates were subsequently derived from simulated sID values of N and essential and nonessential AA for 10 diets varying in CP content (18 to 42%) and apparent fecal N digestibility (70 and 80%) for an adult dog of 20 kg BW. Calculated bioavailability estimates of the NRC for maintenance dog foods do not lead to realistic nutrient allowance estimates for CP and AA. Estimates used by the Association of American Feed Control Officials and the European Pet Food Industry Federation were closer to calculated values, although the majority were too low, with the exception of CP, Arg, and Lys. Bioavailability estimates for Lys, Met, and Cys as calculated here require further veracity as the chemical form in which these AA are present in commercial pet foods may significantly reduce their bioavailability.

  18. Identifying and selecting edible luminescent probes as sensors of food quality

    Directory of Open Access Journals (Sweden)

    Maria G. Corradini

    2016-06-01

    Full Text Available Foods contain a plethora of aromatic molecules—natural colors, synthetic dyes, flavors, vitamins, antioxidants, etc.—that are luminescent, exhibiting prompt fluorescence or delayed phosphorescence. Although food autofluorescence has been used to detect specific contaminants (e.g., aflatoxins or to authenticate specific foods (olive oil, much of the potential of using the optical luminescence of intrinsic molecules for sensing properties of foods is unrealized. We summarize here work characterizing the photophysical properties of some edible, and potentially GRAS (generally-recognized-as-safe, chromophores and especially their sensitivity to, and thus potential for sensing, various physical—viscosity, mobility/rigidity—or chemical—polarity, pH—properties of food known to reflect or be indicative of food quality, stability, and safety. A thorough-going characterization of and robust protocols for interpretation of the luminescent signals from edible chromophores can expand the repertoire of analytical techniques available to monitor quality, and even safety, of the food supply at various stages of production, distribution and storage or even at point of sale.

  19. Characterization of Enterococcus faecalis alkaline phosphatase and use in identifying Streptococcus agalactiae secreted proteins.

    Science.gov (United States)

    Lee, M H; Nittayajarn, A; Ross, R P; Rothschild, C B; Parsonage, D; Claiborne, A; Rubens, C E

    1999-09-01

    We have identified and characterized an Enterococcus faecalis alkaline phosphatase (AP, encoded by phoZ). The predicted gene product shows homology with alkaline phosphatases from a variety of species; it has especially high similarity with two alkaline phosphatases from Bacillus subtilis. Expression of phoZ in Escherichia coli, E. faecalis, Streptococcus agalactiae (group B streptococcus [GBS]), or Streptococcus pyogenes (group A streptococcus [GAS]) produces a blue-colony phenotype on plates containing a chromogenic substrate, 5-bromo-4-chloro-3-indolylphosphate (XP or BCIP). Two tests were made to determine if the activity of the enzyme is dependent upon the enzyme's subcellular location. First, elimination of the signal sequence reduced AP activity to 3% of the wild-type activity (or less) in three species of gram-positive bacteria. Restoration of export, using the signal sequence from C5a peptidase, restored AP activity to at least 50% of that of the wild type. Second, we engineered two chimeric proteins in which AP was fused to either a periplasmic domain or a cytoplasmic domain of lactose permease (a membrane protein). In E. coli, the periplasmic fusion had 17-fold-higher AP activity than the cytoplasmic fusion. We concluded that AP activity is export dependent. The signal sequence deletion mutant, phoZDeltass, was used to identify random genomic fragments from GBS that encode exported proteins or integral membrane proteins. Included in this set of fragments were genes that exhibited homology with the Rib protein (a cell wall protein from GBS) or with DppB (an integral membrane protein from GAS). AP acts as a reporter enzyme in GBS, GAS, and E. faecalis and is expected to be useful in a variety of gram-positive bacteria.

  20. Identifying neuropeptide and protein hormone receptors in Drosophila melanogaster by exploiting genomic data

    DEFF Research Database (Denmark)

    Hauser, Frank; Williamson, Michael; Cazzamali, Giuseppe

    2006-01-01

    insect genome, that of the fruitfly Drosophila melanogaster, was sequenced in 2000, and about 200 GPCRs have been annnotated in this model insect. About 50 of these receptors were predicted to have neuropeptides or protein hormones as their ligands. Since 2000, the cDNAs of most of these candidate...... receptors have been cloned and for many receptors the endogenous ligand has been identified. In this review, we will give an update about the current knowledge of all Drosophila neuropeptide and protein hormone receptors, and discuss their phylogenetic relationships. Udgivelsesdato: 2006-Feb...

  1. Ineffectiveness of a fluorometric method for identifying irradiated food base on thymine glycol

    International Nuclear Information System (INIS)

    Ewing, D.D.; Stepanik, T.M.

    1992-01-01

    At dosages used for food irradiation, some of the thymine present in the DNA of irradiated food may be converted to thymine glycol. A fluorometric assay for thymine glycol was investigated as a possible method of detecting irradiated foods based on this effect. Experiments were performed on homogenates of irradiated chicken breast meat and on DNA isolated from irradiated chicken breast meat. In both cases the assay was subject to interference from one of the reagents, o-aminobenzaldehyde, and lacked the necessary sensitivity to detect the thymine glycol produced by radiolysis of the DNA at relevant dosages

  2. Food Proteins and Bioactive Peptides: New and Novel Sources, Characterisation Strategies and Applications

    Directory of Open Access Journals (Sweden)

    Maria Hayes

    2018-03-01

    Full Text Available By 2050, the world population is estimated to reach 9.6 billion, and this growth continues to require more food, particularly proteins. Moreover, the Westernisation of society has led to consumer demand for protein products that taste good and are convenient to consume, but additionally have nutritional and health maintenance and well-being benefits. Proteins provide energy, but additionally have a wide range of functions from enzymatic activities in the body to bioactivities including those associated with heart health, diabetes-type 2-prevention and mental health maintenance; stress relief as well as a plethora of other health beneficial attributes. Furthermore, proteins play an important role in food manufacture and often provide the binding, water- or oil-holding, emulsifying, foaming or other functional attributes required to ensure optimum sensory and taste benefits for the consumer. The purpose of this issue is to highlight current and new protein sources and their associated functional, nutritional and health benefits as well as best practices for quantifying proteins and bioactive peptides in both a laboratory and industry setting. The bioaccessibility, bioavailability and bioactivities of proteins from dairy, cereal and novel sources including seaweeds and insect protein and how they are measured and the relevance of protein quality measurement methods including the Protein Digestibility Amino Acid Score (PDCAAS and Digestible Indispensable Amino Acid Score (DIAAS are highlighted. In addition, predicted future protein consumption trends and new markets for protein and peptide products are discussed.

  3. Food Proteins and Bioactive Peptides: New and Novel Sources, Characterisation Strategies and Applications.

    Science.gov (United States)

    Hayes, Maria

    2018-03-14

    By 2050, the world population is estimated to reach 9.6 billion, and this growth continues to require more food, particularly proteins. Moreover, the Westernisation of society has led to consumer demand for protein products that taste good and are convenient to consume, but additionally have nutritional and health maintenance and well-being benefits. Proteins provide energy, but additionally have a wide range of functions from enzymatic activities in the body to bioactivities including those associated with heart health, diabetes-type 2-prevention and mental health maintenance; stress relief as well as a plethora of other health beneficial attributes. Furthermore, proteins play an important role in food manufacture and often provide the binding, water- or oil-holding, emulsifying, foaming or other functional attributes required to ensure optimum sensory and taste benefits for the consumer. The purpose of this issue is to highlight current and new protein sources and their associated functional, nutritional and health benefits as well as best practices for quantifying proteins and bioactive peptides in both a laboratory and industry setting. The bioaccessibility, bioavailability and bioactivities of proteins from dairy, cereal and novel sources including seaweeds and insect protein and how they are measured and the relevance of protein quality measurement methods including the Protein Digestibility Amino Acid Score (PDCAAS) and Digestible Indispensable Amino Acid Score (DIAAS) are highlighted. In addition, predicted future protein consumption trends and new markets for protein and peptide products are discussed.

  4. Identifying research advancements in supply chain risk management for Agri-food Industries: Literature review

    Science.gov (United States)

    Septiani, W.; Astuti, P.

    2017-12-01

    Agri-food supply chain has different characteristics related to the raw materials it uses. Food supply chain has a high risk of damage, thus drawing a lot of attention from researchers in supply chain management. This research aimed to investigate the development of supply chain risk management research on agri-food industries. These reviews were arranged in steps systematically, ranging from searching related to the review of SCRM paper, reviewing the general framework of SCRM and the framework of agri-food SCRM. Selection of literature review papers in the period 2005-2017, and obtained 45 papers. The results of the identification research were illustrated in a supply chain risk management framework model. This provided insight toward future research directions and needs.

  5. Modulation of protein quality control systems by food phytochemicals.

    Science.gov (United States)

    Murakami, Akira

    2013-05-01

    There is compelling evidence showing that dietary phytochemicals have exhibited pronounced bioactivities in a number of experimental models. In addition, a variety of epidemiological surveys have demonstrated that frequent ingestion of vegetables and fruits, which contain abundant phytochemicals, lowers the risk of onset of some diseases. However, the action mechanisms by which dietary phytochemicals show bioactivity remain to be fully elucidated and a fundamental question is why this class of chemicals has great potential for regulating health. Meanwhile, maintenance and repair of biological proteins by molecular chaperones, such as heat shock proteins, and clearance of abnormal proteins by the ubiquitin-proteasome system and autophagy play central roles in health, some disease prevention, and longevity. Interestingly, several recent studies have revealed that phytochemicals, including curcumin (yellow pigment in turmeric), resveratrol (phytoalexin in grapes), quercetin (general flavonol in onions and others), and isothiocyanates (preferentially present in cruciferous vegetables, such as broccoli and cabbage), are remarkable regulators of protein quality control systems, suggesting that their physiological and biological functions are exerted, at least in part, through activation of such unique mechanisms. This review article highlights recent findings regarding the effects of representative phytochemicals on protein quality control systems and their possible molecular mechanisms.

  6. SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets.

    Science.gov (United States)

    Ponzoni, Luca; Polles, Guido; Carnevale, Vincenzo; Micheletti, Cristian

    2015-08-04

    Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for characterizing functionally oriented structural changes via a parsimonious set of degrees of freedom. In fact, the relative displacements of few dynamical domains usually suffice to rationalize the mechanics underpinning biological functionality in proteins and can even be exploited for structure determination or refinement purposes. Here we present SPECTRUS, a general scheme that, by solely using amino acid distance fluctuations, can pinpoint the innate quasi-rigid domains of single proteins or large complexes in a robust way. Consistent domains are usually obtained by using either a pair of representative structures or thousands of conformers. The functional insights offered by the approach are illustrated for biomolecular systems of very different size and complexity such as kinases, ion channels, and viral capsids. The decomposition tool is available as a software package and web server at spectrus.sissa.it. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Food-grade protein-based nanoparticles and microparticles for bioactive delivery: fabrication, characterization, and utilization.

    Science.gov (United States)

    Davidov-Pardo, Gabriel; Joye, Iris J; McClements, David Julian

    2015-01-01

    Proteins can be used to fabricate nanoparticles and microparticles suitable for use as delivery systems for bioactive compounds in pharmaceutical, food, cosmetic, and other products. Food proteins originate from various animal or vegetal sources and exhibit a wide diversity of molecular and physicochemical characteristics, e.g., molecular weight, conformation, flexibility, polarity, charge, isoelectric point, solubility, and interactions. As a result, protein particles can be assembled using numerous different preparation methods, from one or more types of protein or from a combination of a protein and another type of biopolymer (usually a polysaccharide). The final characteristics of the particles produced are determined by the proteins and/or polysaccharides used, as well as the fabrication techniques employed. This chapter provides an overview of the functional properties of food proteins that can be used to assemble nanoparticles and microparticles, the fabrication techniques available to create those particles, the factors that influence their stability, and their potential applications within the food industry. © 2015 Elsevier Inc. All rights reserved.

  8. Small-strain dynamic rheology of food protein networks.

    Science.gov (United States)

    Tunick, Michael H

    2011-03-09

    Small-amplitude oscillatory shear analyses of samples containing protein are useful for determining the nature of the protein matrix without damaging it. G' (elastic or storage modulus), G'' (viscous or loss modulus), and tan δ (loss tangent, the ratio of G'' to G') give information on the properties of the network. Strain, frequency, time, and temperature sweeps provide information on the linear viscoelastic region, structural assembly, and thermal characteristics. The gelation point may be determined by locating the time at which tan δ is independent of frequency or the temperature at which G' becomes greater than G''. The logarithm of η* (complex viscosity) may be plotted against the reciprocal of the absolute temperature, with the slope being proportional to the activation energy. Dynamic tests of protein-containing samples reveal a great deal about their rheological characteristics.

  9. Novel snail1 target proteins in human colon cancer identified by proteomic analysis.

    Directory of Open Access Journals (Sweden)

    María Jesús Larriba

    2010-04-01

    Full Text Available The transcription factor Snail1 induces epithelial-to-mesenchymal transition (EMT, a process responsible for the acquisition of invasiveness during tumorigenesis. Several transcriptomic studies have reported Snail1-regulated genes in different cell types, many of them involved in cell adhesion. However, only a few studies have used proteomics as a tool for the characterization of proteins mediating EMT.We identified by proteomic analysis using 2D-DIGE electrophoresis combined with MALDI-TOF-TOF and ESI-linear ion trap mass spectrometry a number of proteins with variable functions whose expression is modulated by Snail1 in SW480-ADH human colon cancer cells. Validation was performed by Western blot and immunofluorescence analyses. Snail1 repressed several members of the 14-3-3 family of phosphoserine/phosphothreonine binding proteins and also the expression of the Proliferation-associated protein 2G4 (PA2G4 that was mainly localized at the nuclear Cajal bodies. In contrast, the expression of two proteins involved in RNA processing, the Cleavage and polyadenylation specificity factor subunit 6 (CPSF6 and the Splicing factor proline/glutamine-rich (SFPQ, was higher in Snail1-expressing cells than in controls. The regulation of 14-3-3epsilon, 14-3-3tau, 14-3-3zeta and PA2G4 by Snail1 was reproduced in HT29 colon cancer cells. In addition, we found an inverse correlation between 14-3-3sigma and Snail1 expression in human colorectal tumors.We have identified a set of novel Snail1 target proteins in colon cancer that expand the cellular processes affected by Snail1 and thus its relevance for cell function and phenotype.

  10. Negative regulation of active zone assembly by a newly identified SR protein kinase.

    Science.gov (United States)

    Johnson, Ervin L; Fetter, Richard D; Davis, Graeme W

    2009-09-01

    Presynaptic, electron-dense, cytoplasmic protrusions such as the T-bar (Drosophila) or ribbon (vertebrates) are believed to facilitate vesicle movement to the active zone (AZ) of synapses throughout the nervous system. The molecular composition of these structures including the T-bar and ribbon are largely unknown, as are the mechanisms that specify their synapse-specific assembly and distribution. In a large-scale, forward genetic screen, we have identified a mutation termed air traffic controller (atc) that causes T-bar-like protein aggregates to form abnormally in motoneuron axons. This mutation disrupts a gene that encodes for a serine-arginine protein kinase (SRPK79D). This mutant phenotype is specific to SRPK79D and is not secondary to impaired kinesin-dependent axonal transport. The srpk79D gene is neuronally expressed, and transgenic rescue experiments are consistent with SRPK79D kinase activity being necessary in neurons. The SRPK79D protein colocalizes with the T-bar-associated protein Bruchpilot (Brp) in both the axon and synapse. We propose that SRPK79D is a novel T-bar-associated protein kinase that represses T-bar assembly in peripheral axons, and that SRPK79D-dependent repression must be relieved to facilitate site-specific AZ assembly. Consistent with this model, overexpression of SRPK79D disrupts AZ-specific Brp organization and significantly impairs presynaptic neurotransmitter release. These data identify a novel AZ-associated protein kinase and reveal a new mechanism of negative regulation involved in AZ assembly. This mechanism could contribute to the speed and specificity with which AZs are assembled throughout the nervous system.

  11. Negative regulation of active zone assembly by a newly identified SR protein kinase.

    Directory of Open Access Journals (Sweden)

    Ervin L Johnson

    2009-09-01

    Full Text Available Presynaptic, electron-dense, cytoplasmic protrusions such as the T-bar (Drosophila or ribbon (vertebrates are believed to facilitate vesicle movement to the active zone (AZ of synapses throughout the nervous system. The molecular composition of these structures including the T-bar and ribbon are largely unknown, as are the mechanisms that specify their synapse-specific assembly and distribution. In a large-scale, forward genetic screen, we have identified a mutation termed air traffic controller (atc that causes T-bar-like protein aggregates to form abnormally in motoneuron axons. This mutation disrupts a gene that encodes for a serine-arginine protein kinase (SRPK79D. This mutant phenotype is specific to SRPK79D and is not secondary to impaired kinesin-dependent axonal transport. The srpk79D gene is neuronally expressed, and transgenic rescue experiments are consistent with SRPK79D kinase activity being necessary in neurons. The SRPK79D protein colocalizes with the T-bar-associated protein Bruchpilot (Brp in both the axon and synapse. We propose that SRPK79D is a novel T-bar-associated protein kinase that represses T-bar assembly in peripheral axons, and that SRPK79D-dependent repression must be relieved to facilitate site-specific AZ assembly. Consistent with this model, overexpression of SRPK79D disrupts AZ-specific Brp organization and significantly impairs presynaptic neurotransmitter release. These data identify a novel AZ-associated protein kinase and reveal a new mechanism of negative regulation involved in AZ assembly. This mechanism could contribute to the speed and specificity with which AZs are assembled throughout the nervous system.

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

    Science.gov (United States)

    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

  13. Identifying Key Proteins in Hg Methylation Pathways of Desulfovibrio by Global Proteomics, Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Summers, Anne O. [Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology; Miller, Susan M. [Univ. of California, San Francisco, CA (United States). Dept. of Pharmaceutical Chemistry; Wall, Judy [Univ. of Missouri, Columbia, MO (United States). Dept. of Biochemistry; Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-18

    Elemental mercury, Hg(0) is a contaminant at many DOE sites, especially at Oak Ridge National Laboratory (ORNL) where the spread of spilled Hg and its effects on microbial populations have been monitored for decades. To explore the microbial interactions with Hg, we have devised a global proteomic approach capable of directly detecting Hg-adducts of proteins. This technique developed in the facultative anaerobe, Escherichia coli, allows us to identify the proteins most vulnerable to acute exposure to organomercurials phenyl- and ethyl-mercury (as surrogates for the highly neurotoxic methyl-Hg) (Polacco, et al, 2011). We have found >300 such proteins in all metabolic functional groups and cellular compartments; most are highly conserved and can serve as markers for acute Hg exposure (Zink, et al. 2016, in preparation). We have also discovered that acute Hg exposure severely disrupts thiol, iron and redox homeostases, and electrolyte balance (LaVoie, et al., 2015) Thus, we proposed to bring these techniques to bear on the central problem of identifying the cellular proteins involved in bacterial uptake and methylation of mercury and its release from the cell.

  14. Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

    Science.gov (United States)

    2013-01-01

    Background Biomarker discovery datasets created using mass spectrum protein profiling of complex mixtures of proteins contain many peaks that represent the same protein with different charge states. Correlated variables such as these can confound the statistical analyses of proteomic data. Previously we developed an algorithm that clustered mass spectrum peaks that were biologically or technically correlated. Here we demonstrate an algorithm that clusters correlated technical aliases only. Results In this paper, we propose a preprocessing algorithm that can be used for grouping technical aliases in mass spectrometry protein profiling data. The stringency of the variance allowed for clustering is customizable, thereby affecting the number of peaks that are clustered. Subsequent analysis of the clusters, instead of individual peaks, helps reduce difficulties associated with technically-correlated data, and can aid more efficient biomarker identification. Conclusions This software can be used to pre-process and thereby decrease the complexity of protein profiling proteomics data, thus simplifying the subsequent analysis of biomarkers by decreasing the number of tests. The software is also a practical tool for identifying which features to investigate further by purification, identification and confirmation. PMID:24010718

  15. Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis*

    Science.gov (United States)

    Scholz, Roland; Imami, Koshi; Scott, Nichollas E.; Trimble, William S.; Foster, Leonard J.; Finlay, B. Brett

    2015-01-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation

  16. A sensitive enzyme-linked immunosorbent assay for the determination of fish protein in processed foods.

    Science.gov (United States)

    Shibahara, Yusuke; Uesaka, Yoshihiko; Wang, Jun; Yamada, Shoichi; Shiomi, Kazuo

    2013-01-15

    Fish is one of the most common causes of food allergy and its major allergen is parvalbumin, a 12 kDa muscular protein. In this study, a sandwich enzyme-linked immunosorbent assay (ELISA) for the determination of fish protein in processed foods was developed using a polyclonal antibody raised against Pacific mackerel parvalbumin. The developed sandwich ELISA showed 22.6-99.0% reactivity (based on the reactivity to Pacific mackerel parvalbumin) to parvalbumins from various species of fish. The limits of detection and quantitation were estimated to be 0.23 and 0.70 μg protein per g of food, respectively. When the sandwich ELISA was subjected to inter-laboratory validation, spiked fish protein was recovered from five model processed foods in the range of 69.4-84.8% and the repeatability and reproducibility relative standard deviations were satisfactorily low (≤ 10.5%). Thus, the sandwich ELISA was judged to be a useful tool to determine fish protein in processed foods. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

    OpenAIRE

    Laura Acevedo-Pacheco; Sergio O. Serna-Saldívar

    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 valu...

  18. Identifying potential strategies in the key sectors of China’s food chain to implement sustainable phosphorus management

    NARCIS (Netherlands)

    Li, Guohua; Huang, Gaoqiang; Li, Haigang; Ittersum, van M.K.; Leffelaar, P.A.; Zhang, Fusuo

    2016-01-01

    High extraction of phosphate reserves and low phosphorus utilization efficiency in the food chain in China result in large P losses and serious environmental pollution. The P fertilizer industry, soil P surplus, livestock manure P and wastewater P recycling have been identified as the priority

  19. Identifying interventions to help rural Kenyan mothers cope with food insecurity: results of a focused ethnographic study

    OpenAIRE

    Pelto, Gretel H.; Armar?Klemesu, Margaret

    2016-01-01

    Abstract An ethnographic study was conducted in two areas in southern and western Kenya to identify potential interventions to improve the quality, availability and affordability of foods consumed by infants and young children. A cultural?ecological model of determinants of nutrition identified the sectors of information for data collection related to infant and young child (IYC) diet and feeding?related behaviours, and the focused ethnographic study manual was used to guide the research. The...

  20. A genome-wide association study identifies protein quantitative trait loci (pQTLs.

    Directory of Open Access Journals (Sweden)

    David Melzer

    2008-05-01

    Full Text Available There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8x10(-57, CCL4L1 (p = 3.9x10(-21, IL18 (p = 6.8x10(-13, LPA (p = 4.4x10(-10, GGT1 (p = 1.5x10(-7, SHBG (p = 3.1x10(-7, CRP (p = 6.4x10(-6 and IL1RN (p = 7.3x10(-6 genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R, altered secretion rates of different sized proteins (LPA, variation in gene copy number (CCL4L1 and altered transcription (GGT1. We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha levels (p = 6.8x10(-40, but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis

  1. Identifying the role of Wilms tumor 1 associated protein in cancer prediction using integrative genomic analyses.

    Science.gov (United States)

    Wu, Li-Sheng; Qian, Jia-Yi; Wang, Minghai; Yang, Haiwei

    2016-09-01

    The Wilms tumor suppressor, WT1 was first identified due to its essential role in the normal development of the human genitourinary system. Wilms tumor 1 associated protein (WTAP) was subsequently revealed to interact with WT1 using yeast two-hybrid screening. The present study identified 44 complete WTAP genes in the genomes of vertebrates, including fish, amphibians, birds and mammals. The vertebrate WTAP proteins clustered into the primate, rodent and teleost lineages using phylogenetic tree analysis. From 1,347 available SNPs in the human WTAP gene, 19 were identified to cause missense mutations. WTAP was expressed in bladder, blood, brain, breast, colorectal, esophagus, eye, head and neck, lung, ovarian, prostate, skin and soft tissue cancers. A total of 17 out of 328 microarrays demonstrated an association between WTAP gene expression and cancer prognosis. However, the association between WTAP gene expression and prognosis varied in distinct types of cancer, and even in identical types of cancer from separate microarray databases. By searching the Catalogue of Somatic Mutations in Cancer database, 65 somatic mutations were identified in the human WTAP gene from the cancer tissue samples. These results suggest that the function of WTAP in tumor formation may be multidimensional. Furthermore, signal transducer and activator of transcription 1, forkhead box protein O1, interferon regulatory factor 1, glucocorticoid receptor and peroxisome proliferator-activated receptor γ transcription factor binding sites were identified in the upstream (promoter) region of the human WTAP gene, suggesting that these transcription factors may be involved in WTAP functions in tumor formation.

  2. Effects of whey protein and its two major protein components on satiety and food intake in normal-weight women.

    Science.gov (United States)

    Chungchunlam, Sylvia M S; Henare, Sharon J; Ganesh, Siva; Moughan, Paul J

    2017-06-01

    Protein is the most satiating macronutrient and is source dependent, with whey protein thought to be particularly satiating. The purported satiating effect of whey protein may be due to the unique mixture of proteins in whey or to the major constituent individual proteins (β-lactoglobulin and α-lactalbumin). The objective of the study was to compare the effects of isoenergetic (~2100kJ, ~500kcal) preload meals enriched (~50g protein) with either whey protein isolate (WP), β-lactoglobulin (BL) isolate or α-lactalbumin (AL) isolate, on food intake at an ad libitum test meal 120min later and subjective ratings of appetite (hunger, desire to eat, prospective food consumption and fullness) using visual analogue scales (VAS). Twenty adult normal-weight women (mean age 24.2±0.8years; mean BMI 22.7±0.4kg/m 2 ) participated in the study which used a single-blind completely randomised block design, where each subject consumed each of the three preload meals. Energy intake at the ad libitum test meal and total energy intakes (preload+test meal) did not differ between the three preload meals (p>0.05). There were no significant differences observed for the VAS scores and net incremental area under the curve (net iAUC) during the 120min following consumption of the three preload meals for subjective ratings of appetite (p>0.05). The findings show that the satiating effect of whey protein was similar to that of BL or AL individually and suggest that the major whey protein components BL and AL do not mediate the satiating effect of whey protein. The present human trial was registered with the Australian New Zealand Clinical Trials Registry (www.anzctr.org.au) as ACTRN12615000344594. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Fiber, protein, and lupin-enriched foods: role for improving cardiovascular health.

    Science.gov (United States)

    Belski, Regina

    2012-01-01

    Cardiovascular diseases (CVD) are the leading cause of death globally (World Health Organisation, 2011). Many of the risk factors for CVD are modifiable, including overweight and obesity. Numerous strategies have been proposed to fight CVD, with a special focus being placed on dietary interventions for weight management. The literature suggests that two nutrients, fiber and protein, may play significant roles in weight control and hence cardiovascular health. Increasing both protein and fiber in the diet can be difficult because popular low-carbohydrate and high-protein diets tend to have considerably low-fiber intakes (Slavin, 2005). One approach to obtain both is to develop functional foods using unique ingredients. Lupin flour is a novel food ingredient derived from the endosperm of lupin. It contains 40-45% protein, 25-30% fiber, and negligible sugar and starch (Petterson and Crosbie, 1990). Research conducted to date reveals that lupin-enriched foods, which are naturally high in protein and fiber, may have a significant effect on CVD risk factors. This review explores whether there is a role for fiber-, protein-, and lupin-enriched foods in improving cardiovascular health. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Protein Digestion-Derived Peptides and the Peripheral Regulation of Food Intake

    Directory of Open Access Journals (Sweden)

    Benoit Cudennec

    2017-04-01

    Full Text Available The gut plays a central role in energy homeostasis. Food intake regulation strongly relies on the gut–brain axis, and numerous studies have pointed out the significant role played by gut hormones released from enteroendocrine cells. It is well known that digestive products of dietary protein possess a high satiating effect compared to carbohydrates and fat. Nevertheless, the processes occurring in the gut during protein digestion involved in the short-term regulation of food intake are still not totally unraveled. This review provides a concise overview of the current data concerning the implication of food-derived peptides in the peripheral regulation of food intake with a focus on the gut hormones cholecystokinin and glucagon-like peptide 1 regulation and the relationship with some aspects of glucose homeostasis.

  5. Identifying biological concepts from a protein-related corpus with a probabilistic topic model

    Directory of Open Access Journals (Sweden)

    Lu Xinghua

    2006-02-01

    Full Text Available Abstract Background Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE© titles and abstracts by applying a probabilistic topic model. Results The latent Dirichlet allocation (LDA model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO terms based on mutual information. Conclusion The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text.

  6. The systematic functional analysis of plasmodium protein kinases identifies essential regulators of mosquito transmission

    KAUST Repository

    Tewari, Rita

    2010-10-21

    Although eukaryotic protein kinases (ePKs) contribute to many cellular processes, only three Plasmodium falciparum ePKs have thus far been identified as essential for parasite asexual blood stage development. To identify pathways essential for parasite transmission between their mammalian host and mosquito vector, we undertook a systematic functional analysis of ePKs in the genetically tractable rodent parasite Plasmodium berghei. Modeling domain signatures of conventional ePKs identified 66 putative Plasmodium ePKs. Kinomes are highly conserved between Plasmodium species. Using reverse genetics, we show that 23 ePKs are redundant for asexual erythrocytic parasite development in mice. Phenotyping mutants at four life cycle stages in Anopheles stephensi mosquitoes revealed functional clusters of kinases required for sexual development and sporogony. Roles for a putative SR protein kinase (SRPK) in microgamete formation, a conserved regulator of clathrin uncoating (GAK) in ookinete formation, and a likely regulator of energy metabolism (SNF1/KIN) in sporozoite development were identified. 2010 Elsevier Inc.

  7. Identifying the Learning Styles and Instructional Tool Preferences of Beginning Food Science and Human Nutrition Majors

    Science.gov (United States)

    Bohn, D. M.; Rasmussen, C. N.; Schmidt, S. J.

    2004-01-01

    Learning styles vary among individuals, and understanding which instructional tools certain learning styles prefer can be utilized to enhance student learning. Students in the introductory Food Science and Human Nutrition course (FSHN 101), taught at the Univ. of Illinois at Urbana-Champaign, were asked to complete Gregorc's Learning Style…

  8. EPR spectroscopy as a potential approach to identify irradiated food and radiation dosimetry - an overview

    International Nuclear Information System (INIS)

    Sanyal, Bhaskar; Chawla, S.P.

    2017-01-01

    The need for reliable and routine tests to determine whether or not food has been irradiated has arisen as a result of the progress made in commercialization of the food irradiation technology. The effectiveness of food irradiation depends on proper delivery of absorbed dose and its reliable measurement. Electron Paramagnetic Resonance (EPR) spectroscopy has been established as an essential tool both for detection of irradiated food and radiation measurements. This presentation demonstrates the behavior of the radicals produced in irradiated cashew nut and orange. In addition the role of EPR spectroscopy will be discussed to understand thermoluminescence behavior of CaSO 4 dosimeter. Cashew nut and orange samples were exposed to gamma radiation in the dose range of 0.25 to 2 kGy. CaSO 4 crystals were irradiated at 0.5-7 kGy. Electron Paramagnetic Resonance (EPR) spectroscopy was carried out using EMX model EPR spectrometer (BRUKER, Germany) with a microwave frequency of 9.42 GHz

  9. From Nutrients to Wellbeing Identifying Discourses of Food in Relation to Health in Syllabi

    Science.gov (United States)

    Oljans, Emma; Elmståhl, Helena; Mattsson Sydner, Ylva; Hjälmeskog, Karin

    2018-01-01

    Food and health have long had dominant position within the subject of Home Economics (HE) in Sweden. However, what constitutes a proper diet, and how it is associated with a healthy lifestyle changes over time. In this article, a discourse analytic approach combined with a didactic perspective are used as the theoretical frame. The aim is to…

  10. Identifying and clarifying values and reason statements that promote effective food parenting practices, using intensive interviews

    Science.gov (United States)

    The objective was to generate and test parents' understanding of values and associated reason statements to encourage effective food parenting practices. This study was cross-sectional. Sixteen parents from different ethnic groups (African American, white, and Hispanic) living with their 3- to 5-yea...

  11. Identifying pregnant women who would adhere to food taboos in a ...

    African Journals Online (AJOL)

    Poor maternal nutrition, especially in rural settings, adversely affects pregnancy and birth outcomes. In many local communities, pregnant women have food taboos with consequent depletion of vital nutrients. To facilitate early identification and prompt counseling, this study aimed at describing pregnant women who are ...

  12. Towards ecosystem-based management: Identifying operational food-web indicators for marine ecosystems

    DEFF Research Database (Denmark)

    Tam, Jamie C.; Link, Jason S.; Rossberg, Axel G.

    2017-01-01

    Modern approaches to Ecosystem-Based Management and sustainable use of marine resources must account for the myriad of pressures (interspecies, human and environmental) affecting marine ecosystems. The network of feeding interactions between co-existing species and populations (food webs) are an ...

  13. Identifying and Clarifying Values and Reason Statements that Promote Effective Food Parenting Practices, Using Intensive Interviews

    Science.gov (United States)

    Beltran, Alicia; Hingle, Melanie D.; Knesek, Jessica; O'Connor, Teresia; Baranowski, Janice; Thompson, Debbe; Baranowski, Tom

    2011-01-01

    Objective: Generate and test parents' understanding of values and associated reason statements to encourage effective food parenting practices. Methods: This study was cross-sectional. Sixteen parents from different ethnic groups (African American, white, and Hispanic) living with their 3- to 5-year-old child were recruited. Interested parents…

  14. Consumer understanding of food labels: toward a generic tool for identifying the average consumer

    DEFF Research Database (Denmark)

    Sørensen, Henrik Selsøe; Holm, Lotte; Møgelvang-Hansen, Peter

    2013-01-01

    The ‘average consumer’ is referred to as a standard in regulatory contexts when attempts are made to benchmark how consumers are expected to reason while decoding food labels. An attempt is made to operationalize this hypothetical ‘average consumer’ by proposing a tool for measuring the level of ...... that independent future studies of consumer behavior and decision making in relation to food products in different contexts could benefit from this type of benchmarking tool.......The ‘average consumer’ is referred to as a standard in regulatory contexts when attempts are made to benchmark how consumers are expected to reason while decoding food labels. An attempt is made to operationalize this hypothetical ‘average consumer’ by proposing a tool for measuring the level...... of informedness of an individual consumer against the national median at any time. Informedness, i.e. the individual consumer's ability to interpret correctly the meaning of the words and signs on a food label is isolated as one essential dimension for dividing consumers into three groups: less-informed, informed...

  15. The radiation chemistry of amino acids, peptides and proteins in relation to the radiation sterilization of high-protein foods

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1981-01-01

    An important source of information on the question of whether or not toxic or other deleterious substances are formed in the radiation sterilization of foods is the chemical study of reaction products and reaction mechanisms in the radiolysis of individual food components. The present evaluation of the radiation chemistry of amino acids, peptides and proteins outlines the various radiation-induced processes which lead to amino acid degradation and to the synthesis of amino acid derivatives of higher molecular weight. Among the latter are the α,α'-diamino dicarboxylic acids which are formed as major products in the radiolysis of peptides both in aqueous solution and in the solid state. The α,α'-diamino acids are of particular interest as irradiation products because they represent a class of compounds not normally encountered in plant and animal protein sources. Such compounds have, however, been isolated from certain types of bacteria and bacterial products. All of the available data strongly suggest that the α,α'-diamino acids are produced in significant yield in the radiation sterilization of high protein foods. The importance of initiating extensive chemical and biological studies of these and of other high molecular weight products in irradiated food is emphasised. (author)

  16. Radiation chemistry of amino acids, peptides and proteins in relation to the radiation sterilization of high-protein foods

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1979-03-01

    An important source of information on the question of whether or not toxic or other deleterious substances are formed in the radiation sterilization of foods is the chemical study of reaction products and reaction mechanisms in the radiolysis of individual food components. The present evaluation of the radiation chemistry of amino acids, peptides and proteins outlines the various radiation-induced processes which lead to amino acid degradation and to the synthesis of amino acid derivatives of higher molecular weight. Among the latter are the α,α'-diamino dicarboxylic acids which are formed as major products in the radiolysis of peptides both in aqueous solution and in the solid state. The α,α'-diamino acids are of particular interest as irradiation products because they represent a class of compounds not normally encountered in plant and animal protein sources. Such compounds have, however, been isolated from certain types of bacteria and pathogenic toxins. All of the available data strongly suggest that the α,α'-diamino acids are produced in significant yield in the radiation sterilization of high protein foods. The importance of initiating extensive chemical and biological studies of initiating extensive chemical and biological studies of these and of other high molecular weight products in irradiated food is emphasized

  17. Radiation chemistry of amino acids, peptides and proteins in relation to the radiation sterilization of high-protein foods

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1981-12-01

    An important source of information on the question of whether or not toxic or other deleterious substances are formed in the radiation sterilization of foods is the chemical study of reaction products and reaction mechanisms in the radiolysis of individual food components. The present evaluation of the radiation chemistry of amino acids, peptides, and proteins outlines the various radiation-induced processes which lead to amino acid degradation and to the synthesis of amino acid derivatives of higher molecular weight. Among the latter are the α,α'-diamino dicarboxylic acids which are formed as major products in the radiolysis of peptides both in aqueous solution and in the solid state. The α,α'-diamino acids are of particular interest as irradiation products because they represent a class of compounds not normally encountered in plant and animal protein sources. Such compounds have, however, been isolated from certain types of bacteria and bacterial products. All of the available data strongly suggest that the α,α'-diamino acids are produced in significant yield in the radiation sterilization of high protein foods. The importance of initiating extensive chemical and biological studies of these and of other high molecular weight products in irradiated food is emphasized

  18. A free sugars daily value (DV) identifies more "less healthy" prepackaged foods and beverages than a total sugars DV.

    Science.gov (United States)

    Bernstein, Jodi T; Labonté, Marie-Ève; Franco-Arellano, Beatriz; Schermel, Alyssa; L'Abbé, Mary R

    2018-04-01

    Regulatory changes in Canada will require food labels to have a benchmark [% Daily Value, %DV] for total sugars, based on 100 g/day, while US labels will require a %DV for added sugars, based on 50 g/day. The objective of this study was to compare two labelling policies, a total sugars DV (100 g/day) and a free sugars DV (50 g/day) on food labels. This cross-sectional analysis of the Food Label Information Program database focussed on top sources of total sugars intake in Canada (n = 6924 foods). Products were categorized as "less healthy" using two sets of criteria: a) free sugars levels exceeding the WHO guidelines (≥10% energy from free sugars); and b) exceeding healthfulness cut-offs of the Food Standards Australia New Zealand Nutrient Profiling Scoring Criterion (FSANZ-NPSC). The proportion of "less healthy" products with ≥15%DV (defined as "a lot" of sugars i.e. high in sugars, based on Health Canada's %DV labelling footnote and educational message for dietary guidance) were compared for each sugar labelling scenario. The free sugars DV showed better alignment with both methods for assessing "healthfulness" than the total sugars DV. The free sugars DV identified a greater proportion of "less healthy" foods with ≥15%DV, based on both the FSANZ-NPSC (70% vs. 45%, p chocolate bars, confectionery, and frozen desserts categories. Compared to total sugars DV labelling, using a free sugars DV identified more "less healthy" foods. Findings support the adoption of free sugars labelling. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Relative validity and reproducibility of a food frequency questionnaire for identifying the dietary patterns of toddlers in New Zealand.

    Science.gov (United States)

    Mills, Virginia C; Skidmore, Paula M L; Watson, Emily O; Taylor, Rachael W; Fleming, Elizabeth A; Heath, Anne-Louise M

    2015-04-01

    Dietary patterns provide insight into relationships between diet and disease. Food frequency questionnaires (FFQs) can identify dietary patterns in adults, but similar analyses have not been performed for toddlers. The aim of the Eating Assessment in Toddlers study was to evaluate the relative validity and reproducibility of dietary patterns from an FFQ developed for toddlers aged 12 to 24 months. Participants were 160 toddlers aged 12 to 24 months and their primary caregiver who completed an FFQ twice, approximately 5 weeks apart (FFQ1 and FFQ2). A 5-day weighed food record was collected on nonconsecutive days between FFQ administrations. Principal component analysis identified three major dietary patterns similar across FFQ1, FFQ2, and the 5-day weighted food record. The sweet foods and fries pattern was characterized by high intakes of sweet foods, fries and roast potato and kumara (sweet potato), butter and margarines, processed meat, sweet drinks, and fruit or milk drinks. The vegetables and meat pattern was characterized by high intakes of vegetables, meat, eggs and beans, and fruit. The milk and fruit pattern was characterized by high intakes of milk and milk products and fruit, and low intakes of breastmilk and infant and follow-up formula. The FFQ (FFQ1) correctly classified 43.1% to 51.0% of toddlers into the same quartile of pattern score as the 5-day weighted food record, and Pearson correlations ranged from 0.56 to 0.68 for the three patterns. Reliability coefficients ranged from 0.71 to 0.72 for all three dietary patterns. the Eating Assessment in Toddlers study FFQ shows acceptable relative validity and high reproducibility for identifying dietary patterns in toddlers. Copyright © 2015 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

  20. Interactions of vegetable proteins with other polymers: Structure-function relationships and applications in the food industry

    OpenAIRE

    Lin, Duanquan; Lu, Wei; Kelly, Alan L.; Zhang, Longtao; Zheng, Baodong; Miao, Song

    2017-01-01

    In recent years, there has been increasing interest in vegetable proteins, due to their various health beneficial functions and wide applications in the food industry. Vegetable proteins combined with other edible polymers can be used to improve the quality and nutritional value of food products. In these complex food systems, interactions between different components are inevitable, and these interactions have a significant influence on the structure and functions of food products. This stud...

  1. Bet v 1 homologues in strawberry identified as IgE-binding proteins and presumptive allergens.

    Science.gov (United States)

    Karlsson, A L; Alm, R; Ekstrand, B; Fjelkner-Modig, S; Schiött, A; Bengtsson, U; Björk, L; Hjernø, K; Roepstorff, P; Emanuelsson, C S

    2004-12-01

    No strawberry allergen has so far been identified and characterized. Serum samples were collected from patients with a suggestive case history of adverse reactions to strawberry and other fruits. Extracts from fresh and frozen strawberries were analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting and mass spectrometry. Patient blood samples were analysed for inhibition of IgE binding and basophil degranulation. Several IgE-binding proteins could be detected. In more than half of the patient sera, a 20/18-kDa doublet band was observed in Western blotting. These two bands were excised and analysed by mass spectrometry showing the presence of proteins belonging to the Bet v 1 family of allergens. Inhibition of the IgE binding to the 20/18-kDa doublet was obtained by addition of two recombinantly expressed allergens belonging to the Bet v 1 family (Bet v 1 and Mal d 1) and strawberry protein extract. In a cell-based assay of patient blood samples, basophil degranulation could be induced by strawberry protein extract and by Bet v 1 and Mal d 1. We conclude that strawberry homologues to Bet v 1 may be allergens of importance for adverse reactions to strawberry.

  2. Engineering nanoparticles surface for biosensing: "Chemical noses" to detect and identify proteins, bacteria and cancerous cells

    Science.gov (United States)

    Miranda-Sanchez, Oscar Ramon

    Rapid and sensitive detection of biomolecules is an important issue in nanomedicine. Many disorders are manifested by changes in protein levels of serum and other biofluids. Rapid and effective differentiation between normal and cancerous cells is an important challenge for the diagnosis and treatment of tumor. Likewise, rapid and effective identification of pathogens is a key target in both biomedical and environmental monitoring. Most biological recognition processes occur via specific interactions. Gold nanoparticles (AuNP s) feature sizes commensurate with biomacromolecules, coupled with useful physical and optical properties. A key issue in the use of nanomaterials is controlling the interfacial interactions of these complex systems. Modulation of these physicochemical properties can be readily achieved by engineering nanoparticles surface. Inspired by the idea of mimicking nature, a convenient, precise and rapid method for sensing proteins, cancerous cells and bacteria has been developed by overtaking the superb performance of biological olfactory systems in odor detection, identification, tracking, and location. On the fundamental side, an array-based/'chemical nose' sensor composed of cationic functionalized AuNPs as receptors and anionic fluorescent conjugated polymers or green fluorescent proteins or enzyme/substrates as transducers that can properly detect and identify proteins, bacteria, and cancerous cells has been successfully fabricated.

  3. Identifying the Location of a Single Protein along the DNA Strand Using Solid-State Nanopores.

    Science.gov (United States)

    Yu, Jae-Seok; Lim, Min-Cheol; Huynh, Duyen Thi Ngoc; Kim, Hyung-Jun; Kim, Hyun-Mi; Kim, Young-Rok; Kim, Ki-Bum

    2015-05-26

    Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.

  4. Genome-wide RNAi screen identifies novel host proteins required for alphavirus entry.

    Directory of Open Access Journals (Sweden)

    Yaw Shin Ooi

    Full Text Available The enveloped alphaviruses include important and emerging human pathogens such as Chikungunya virus and Eastern equine encephalitis virus. Alphaviruses enter cells by clathrin-mediated endocytosis, and exit by budding from the plasma membrane. While there has been considerable progress in defining the structure and function of the viral proteins, relatively little is known about the host factors involved in alphavirus infection. We used a genome-wide siRNA screen to identify host factors that promote or inhibit alphavirus infection in human cells. Fuzzy homologue (FUZ, a protein with reported roles in planar cell polarity and cilia biogenesis, was required for the clathrin-dependent internalization of both alphaviruses and the classical endocytic ligand transferrin. The tetraspanin membrane protein TSPAN9 was critical for the efficient fusion of low pH-triggered virus with the endosome membrane. FUZ and TSPAN9 were broadly required for infection by the alphaviruses Sindbis virus, Semliki Forest virus, and Chikungunya virus, but were not required by the structurally-related flavivirus Dengue virus. Our results highlight the unanticipated functions of FUZ and TSPAN9 in distinct steps of alphavirus entry and suggest novel host proteins that may serve as targets for antiviral therapy.

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

    Science.gov (United States)

    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

  6. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

    Science.gov (United States)

    Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

    2016-05-01

    A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

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

    Science.gov (United States)

    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.

  8. Protein C/S ratio, an accurate and simple tool to identify carriers of a protein C gene mutation

    NARCIS (Netherlands)

    Libourel, EJ; Meinardi, [No Value; de Kam, PJ; Ruiters, MHJ; van der Meer, J; van der Schaaf, W; Veenstra, R.

    Hereditary protein C deficiency is demonstrated by lowered protein C plasma levels in a patient and at least one first-degree relative. This approach is insufficient in some cases owing to overlapping protein C levels in carriers and non-carriers of a protein C gene mutation. The protein C/S ratio

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

    Science.gov (United States)

    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.

  10. Recent developments in identifying and quantifying emotions during food consumption.

    Science.gov (United States)

    Kenney, Erica; Adhikari, Koushik

    2016-08-01

    Emotions and the consumption of food and beverages are inextricably intertwined. As the fields of sensory and consumer science seek to better conceptualize the consumer experience, interest in emotion measurement is growing. Emotions can provide key information to differentiate between products and predict consumer choice as well as give more detail about product perception. There are several emotion measurement instruments, including physiological methods and facial recognition, self-reported verbal emotion measurement and self-reported visual emotion measurement. This review discusses the purpose of measuring emotions, what is the definition of an emotion, what different instruments are available, and touches upon some promising research to deepen the connection between food and emotions. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Burcza, Anna, E-mail: anna.burcza@mri.bund.de; Gräf, Volker; Walz, Elke; Greiner, Ralf [Max Rubner-Institute, Department of Food Technology and Bioprocess Engineering (Germany)

    2015-11-15

    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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  14. Identifying the role of different personality traits on the relationship between stress and food choice

    OpenAIRE

    Trew, Marissa

    2014-01-01

    Research shows that high levels of stress correlate with higher consumption of high- fat and high-sugar snack-type foods, particularly amongst women. However, it has been observed that not all individuals are vulnerable to this pattern of ‘stress-related’ eating. Both stress and dietary habits have been strongly correlated with specific personality traits but previous research has neglected to observe whether personality traits significantly affect correlations between perceived stress and ty...

  15. Optimalization of the protein content of canned baby-foods based on their nutritive value.

    Science.gov (United States)

    Dworschák, E; Molnár, L; Horváth, E D; Vukov, K

    1981-01-01

    When planning canned foods the protein value Net Dietary-protein Energy percent = 8% of a 5-month old infant's requirement was considered as constant. The nutritive value required for this purpose was calculated on the basis of amino acid composition, making use of the Morup-Olesen index. Canned foods were made of two protein-containing components, of sunflower-oil and (occasionally) of starch, by computer, keeping the energy value constant, i. e. 1250 kJ, which covers half of the infant's daily requirement. The optimalization based on the protein value is illustrated by the examples of egg-potato, beef-peas and flour-beans pairs, considering the practical requirements as well.

  16. Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.

    Science.gov (United States)

    Liu, Qian; Kwoh, Chee Keong; Hoi, Steven C H

    2013-01-01

    Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To empirically quantify the importance of β contacts, we design βACV, an SVM classifier with β contacts as input, to classify homodimers from crystal packing. We found that our βACV is able to achieve the state-of-the-art classification performance superior to SVM classifiers with distance-based contacts as input. Our βACV also outperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performance suggests that β contacts can truly identify critical specific contacts in protein binding interfaces. β contacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-based contacts.

  17. The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.

    Directory of Open Access Journals (Sweden)

    Kari A Dilley

    Full Text Available Ebola virus and Marburg virus are members of the Filovirdae family and causative agents of hemorrhagic fever with high fatality rates in humans. Filovirus virulence is partially attributed to the VP35 protein, a well-characterized inhibitor of the RIG-I-like receptor pathway that triggers the antiviral interferon (IFN response. Prior work demonstrates the ability of VP35 to block potent RIG-I activators, such as Sendai virus (SeV, and this IFN-antagonist activity is directly correlated with its ability to bind RNA. Several structural studies demonstrate that VP35 binds short synthetic dsRNAs; yet, there are no data that identify viral immunostimulatory RNAs (isRNA or host RNAs bound to VP35 in cells. Utilizing a SeV infection model, we demonstrate that both viral isRNA and host RNAs are bound to Ebola and Marburg VP35s in cells. By deep sequencing the purified VP35-bound RNA, we identified the SeV copy-back defective interfering (DI RNA, previously identified as a robust RIG-I activator, as the isRNA bound by multiple filovirus VP35 proteins, including the VP35 protein from the West African outbreak strain (Makona EBOV. Moreover, RNAs isolated from a VP35 RNA-binding mutant were not immunostimulatory and did not include the SeV DI RNA. Strikingly, an analysis of host RNAs bound by wild-type, but not mutant, VP35 revealed that select host RNAs are preferentially bound by VP35 in cell culture. Taken together, these data support a model in which VP35 sequesters isRNA in virus-infected cells to avert RIG-I like receptor (RLR activation.

  18. The challenge of protein crops as a sustainable source of food and feed for the future

    OpenAIRE

    2017-01-01

    Grain legumes, together with quinoa and amaranth (pseudocereals) and other crops are attractive candidates to satisfy the growing demand for plant protein production worldwide for food and feed. Despite their high value, many protein crops have not been adequately assessed and numerous species are underutilized. Special attention has to be paid to genetic diversity and landraces, and to the key limiting factors affecting yield, including water deficiency and other abiotic and biotic stresses,...

  19. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

    Directory of Open Access Journals (Sweden)

    Hanspers Kristina

    2010-01-01

    Full Text Available Abstract Background Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.

  20. Food choices, perceptions of healthiness, and eating motives of self-identified followers of a low-carbohydrate diet

    Directory of Open Access Journals (Sweden)

    Piia Jallinoja

    2014-12-01

    Full Text Available Background: Low-carbohydrate (LC diets have gained substantial media coverage in many Western countries. Little is, however, known about the characteristics of their followers. Objective: The article analyses how those who report following an LC diet differ from the rest of the population in their background, food choices, weight reduction status, as well as food-related perceptions and motives. The data are a part of the Health Behaviour and Health among the Finnish Adult Population survey collected in spring 2012 (n=2,601, covering 15- to 64-year-old Finns. Results: Seven per cent of the respondents identified themselves as followers of the LC diet. Gender and education were not associated with following an LC diet. The youngest respondents were the least likely to follow such a diet. The LC diet group preferred butter but also vegetables more commonly than the other respondents and were less likely to use vegetable bread spreads. The followers of the LC diet and the other respondents agreed about the healthiness of whole grain, vegetable oils, vegetables, and fruits and berries, and of the harmfulness of white wheat. Compared to the other respondents, the LC diet group was less likely to regard eating vegetable/low-fat products as important, more likely to regard eating healthy carbohydrates, and the health and weight-managing aspects of foods, as important and placed less value on sociability and pleasures connected to food. The results showed varying food choices among the followers of the LC diet: some even reported that they were not avoiding carbohydrates, sugars, and white wheat in their diet. Conclusions: Planners of nutrition policies should follow-up on new diets as they emerge and explore the food choices and motives of their followers and how these diets affect the food choices of the whole population.

  1. Food choices, perceptions of healthiness, and eating motives of self-identified followers of a low-carbohydrate diet.

    Science.gov (United States)

    Jallinoja, Piia; Niva, Mari; Helakorpi, Satu; Kahma, Nina

    2014-01-01

    Low-carbohydrate (LC) diets have gained substantial media coverage in many Western countries. Little is, however, known about the characteristics of their followers. The article analyses how those who report following an LC diet differ from the rest of the population in their background, food choices, weight reduction status, as well as food-related perceptions and motives. The data are a part of the Health Behaviour and Health among the Finnish Adult Population survey collected in spring 2012 (n=2,601), covering 15- to 64-year-old Finns. Seven per cent of the respondents identified themselves as followers of the LC diet. Gender and education were not associated with following an LC diet. The youngest respondents were the least likely to follow such a diet. The LC diet group preferred butter but also vegetables more commonly than the other respondents and were less likely to use vegetable bread spreads. The followers of the LC diet and the other respondents agreed about the healthiness of whole grain, vegetable oils, vegetables, and fruits and berries, and of the harmfulness of white wheat. Compared to the other respondents, the LC diet group was less likely to regard eating vegetable/low-fat products as important, more likely to regard eating healthy carbohydrates, and the health and weight-managing aspects of foods, as important and placed less value on sociability and pleasures connected to food. The results showed varying food choices among the followers of the LC diet: some even reported that they were not avoiding carbohydrates, sugars, and white wheat in their diet. Planners of nutrition policies should follow-up on new diets as they emerge and explore the food choices and motives of their followers and how these diets affect the food choices of the whole population.

  2. Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis.

    Science.gov (United States)

    Scholz, Roland; Imami, Koshi; Scott, Nichollas E; Trimble, William S; Foster, Leonard J; Finlay, B Brett

    2015-07-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation

  3. FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification.

    Science.gov (United States)

    Gattiker, Alexandre; Bienvenut, Willy V; Bairoch, Amos; Gasteiger, Elisabeth

    2002-10-01

    FindPept (http://www.expasy.org/tools/findpept.html) is a software tool designed to identify the origin of peptide masses obtained by peptide mass fingerprinting which are not matched by existing protein identification tools. It identifies masses resulting from unspecific proteolytic cleavage, missed cleavage, protease autolysis or keratin contaminants. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. Based on a number of experimental examples, we show that the commonly held rules for the specificity of tryptic cleavage are an oversimplification, mainly because of effects of neighboring residues, experimental conditions, and contaminants present in the enzyme sample.

  4. Combination of existing and alternative technologies to promote oilseeds and pulses proteins in food applications

    Directory of Open Access Journals (Sweden)

    Chéreau Denis

    2016-07-01

    Full Text Available The continuous world population growth induces a total protein demand increase based mainly on plant sources. To meet these global nutritional challenges, existing and innovative dry and wet fractionation processes will have to be combined to better valorise plant protein fraction from pulses and oilseeds. The worldwide success of soy protein isolates originate from the intrinsic qualities of soybean proteins but also from a continuous R&D effort since mid-twenty century. Therefore, the soy protein development model can be applied to protein isolates from diverse pulses and oilseeds meals as rapeseed which has already been recognised as novel food protein in Europe. To boost the delivery of plant proteins, agrofood-industries and academics must pool their respective expertise. Innovative and issue solving R&D projects have to be launched to better valorise pulses and oilseed proteins by (i creating oil extraction processes which preserve native proteins structure; (ii developing novel protein extraction processes from lab up to industrial pilot scale; (iii producing plant protein isolates having comparable foaming, emulsifying or gelling functionality than animal; and (iv generating hydrolysed proteins with high digestibility adapted to human nutrition. It is also essential to initiate research programs to innovate in wet and dry fractionations of plants or to design in vitro models to evaluate proteins digestibility and allergenicity. The increased awareness regarding plant protein valorisation resulted in the creation by agro-industries and academics of the open platform IMPROVE which propose a combination of competencies and equipment to boost market uptake of Plant Based Proteins.

  5. Endogenous ribosomal protein L29 (RPL29: a newly identified regulator of angiogenesis in mice

    Directory of Open Access Journals (Sweden)

    Dylan T. Jones

    2013-01-01

    Cellular ribosomal protein L29 (RPL29 is known to be important in protein synthesis, but its function during angiogenesis has never been described before. We have shown previously that mice lacking β3-integrins support enhanced tumour angiogenesis and, therefore, deletion of endothelial αvβ3 can provide a method for discovery of novel regulators of tumour angiogenesis. Here, we describe significant upregulation of RPL29 in β3-null endothelial cells at both the mRNA and protein level. Ex vivo, we show that VEGF-stimulated microvessel sprouting was reduced significantly in Rpl29-heterozygous and Rpl29-null aortic ring assays compared with wild-type controls. Moreover, we provide in vivo evidence that RPL29 can regulate tumour angiogenesis. Tumour blood vessel density in subcutaneously grown Lewis lung carcinomas was reduced significantly in Rpl29-mutant mice. Additionally, depletion of Rpl29 using RNA interference inhibited VEGF-induced aortic ring sprouting, suggesting that anti-RPL29 strategies might have anti-angiogenic potential. Overall, our results identify that loss or depletion of RPL29 can reduce angiogenesis in vivo and ex vivo.

  6. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    Directory of Open Access Journals (Sweden)

    Wouter Boomsma

    2016-02-01

    Full Text Available The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work

  7. Computational mapping identifies the binding sites of organic solvents on proteins

    Science.gov (United States)

    Dennis, Sheldon; Kortvelyesi, Tamas; Vajda, Sandor

    2002-01-01

    Computational mapping places molecular probes—small molecules or functional groups—on a protein surface to identify the most favorable binding positions. Although x-ray crystallography and NMR show that organic solvents bind to a limited number of sites on a protein, current mapping methods result in hundreds of energy minima and do not reveal why some sites bind molecules with different sizes and polarities. We describe a mapping algorithm that explains the origin of this phenomenon. The algorithm has been applied to hen egg-white lysozyme and to thermolysin, interacting with eight and four different ligands, respectively. In both cases the search finds the consensus site to which all molecules bind, whereas other positions that bind only certain ligands are not necessarily found. The consensus sites are pockets of the active site, lined with partially exposed hydrophobic residues and with a number of polar residues toward the edge. These sites can accommodate each ligand in a number of rotational states, some with a hydrogen bond to one of the nearby donor/acceptor groups. Specific substrates and/or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations. PMID:11904374

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

    NARCIS (Netherlands)

    Koppelman, S.J.; Lakemond, C.M.M.; Vlooswijk, R.; Hefle, S.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,

  9. Effects of Protein Foods on the Nutritional Status of Adults with ...

    African Journals Online (AJOL)

    This study compares the efficacy of low- protein foods, from cooked beef (diet A), smoked cat fish (diet B), cooked beef and smoked cat fish (diet C) and cooked beef, smoked cat fish and hulled steamed red cowpea pudding (diet D) ) on the energy intake, anthropometric indices, body mass index (BMI) and serum albumin of ...

  10. An oral sensitization model in Brown Norway rats to screen for potential allergenicity of food proteins

    NARCIS (Netherlands)

    Knippels, L.M.J.; Houben, G.F.; Spanhaak, S.; Penninks, A.H.

    1999-01-01

    We developed an oral sensitization protocol for food proteins for the rat. Young Brown Norway (BN) rats were exposed to 1 mg ovalbumin (OVA) by daily gavage dosing for 42 days without the use of an adjuvant. OVA-specific IgE and IgG responses were determined by ELISA. On an oral challenge with OVA

  11. A model for consumers' preferences for Novel Protein Foods and environmental quality

    NARCIS (Netherlands)

    Ierland, van E.C.; Zhu, X.

    2005-01-01

    We develop an environmental Applied General Equilibrium (AGE) model, which includes the economic functions of the environment, to investigate the impacts of consumers' preference changes towards the enhanced consumption of Novel Protein Foods (NPFs) and towards a higher willingness to pay for

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

    Science.gov (United States)

    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  0.05) 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.

  13. The antibacterial protein lysozyme identified as the termite egg recognition pheromone.

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    Kenji Matsuura

    Full Text Available Social insects rely heavily on pheromone communication to maintain their sociality. Egg protection is one of the most fundamental social behaviours in social insects. The recent discovery of the termite-egg mimicking fungus 'termite-ball' and subsequent studies on termite egg protection behaviour have shown that termites can be manipulated by using the termite egg recognition pheromone (TERP, which strongly evokes the egg-carrying and -grooming behaviours of workers. Despite the great scientific and economic importance, TERP has not been identified because of practical difficulties. Herein we identified the antibacterial protein lysozyme as the TERP. We isolated the target protein using ion-exchange and hydrophobic interaction chromatography, and the MALDI-TOF MS analysis showed a molecular size of 14.5 kDa. We found that the TERP provided antibacterial activity against a gram-positive bacterium. Among the currently known antimicrobial proteins, the molecular size of 14.5 kDa limits the target to lysozyme. Termite lysozymes obtained from eggs and salivary glands, and even hen egg lysozyme, showed a strong termite egg recognition activity. Besides eggs themselves, workers also supply lysozyme to eggs through frequent egg-grooming, by which egg surfaces are coated with saliva containing lysozyme. Reverse transcript PCR analysis showed that mRNA of termite lysozyme was expressed in both salivary glands and eggs. Western blot analysis confirmed that lysozyme production begins in immature eggs in queen ovaries. This is the first identification of proteinaceous pheromone in social insects. Researchers have focused almost exclusively on hydrocarbons when searching for recognition pheromones in social insects. The present finding of a proteinaceous pheromone represents a major step forward in, and result in the broadening of, the search for recognition pheromones. This novel function of lysozyme as a termite pheromone illuminates the profound influence

  14. Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein.

    Science.gov (United States)

    Gal, Maayan; Bloch, Itai; Shechter, Nelia; Romanenko, Olga; Shir, Ofer M

    2016-01-01

    Protein-protein interactions (PPI) play a critical role in regulating many cellular processes. Finding novel PPI inhibitors that interfere with specific binding of two proteins is considered a great challenge, mainly due to the complexity involved in characterizing multi-molecular systems and limited understanding of the physical principles governing PPIs. Here we show that the combination of virtual screening techniques, which are capable of filtering a large library of potential small molecule inhibitors, and a unique secondary screening by isothermal titration calorimetry, a label-free method capable of observing direct interactions, is an efficient tool for finding such an inhibitor. In this study we applied this strategy in a search for a small molecule capable of interfering with the interaction of the tumor-suppressor p53 and the E3-ligase MDM2. We virtually screened a library of 15 million small molecules that were filtered to a final set of 80 virtual hits. Our in vitro experimental assay, designed to validate the activity of mixtures of compounds by isothermal titration calorimetry, was used to identify an active molecule against MDM2. At the end of the process the small molecule (4S,7R)-4-(4-chlorophenyl)-5-hydroxy-2,7-dimethyl-N-(6-methylpyridin-2-yl)-4,6,7,8 tetrahydrIoquinoline-3-carboxamide was found to bind MDM2 with a dissociation constant of ~2 µM. Following the identification of this single bioactive compound, spectroscopic measurements were used to further characterize the interaction of the small molecule with the target protein. 2D NMR spectroscopy was used to map the binding region of the small molecule, and fluorescence polarization measurement confirmed that it indeed competes with p53.

  15. Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins

    Science.gov (United States)

    Hassan, Karl A.; Jackson, Scott M.; Penesyan, Anahit; Patching, Simon G.; Tetu, Sasha G.; Eijkelkamp, Bart A.; Brown, Melissa H.; Henderson, Peter J. F.; Paulsen, Ian. T.

    2013-01-01

    Chlorhexidine is widely used as an antiseptic or disinfectant in both hospital and community settings. A number of bacterial species display resistance to this membrane-active biocide. We examined the transcriptomic response of a representative nosocomial human pathogen, Acinetobacter baumannii, to chlorhexidine to identify the primary chlorhexidine resistance elements. The most highly up-regulated genes encoded components of a major multidrug efflux system, AdeAB. The next most highly overexpressed gene under chlorhexidine stress was annotated as encoding a hypothetical protein, named here as AceI. Orthologs of the aceI gene are conserved within the genomes of a broad range of proteobacterial species. Expression of aceI or its orthologs from several other γ- or β-proteobacterial species in Escherichia coli resulted in significant increases in resistance to chlorhexidine. Additionally, disruption of the aceI ortholog in Acinetobacter baylyi rendered it more susceptible to chlorhexidine. The AceI protein was localized to the membrane after overexpression in E. coli. This protein was purified, and binding assays demonstrated direct and specific interactions between AceI and chlorhexidine. Transport assays using [14C]-chlorhexidine determined that AceI was able to mediate the energy-dependent efflux of chlorhexidine. An E15Q AceI mutant with a mutation in a conserved acidic residue, although unable to mediate chlorhexidine resistance and transport, was still able to bind chlorhexidine. Taken together, these data are consistent with AceI being an active chlorhexidine efflux protein and the founding member of a family of bacterial drug efflux transporters. PMID:24277845

  16. Chemical Screens Identify Drugs that Enhance or Mitigate Cellular Responses to Antibody-Toxin Fusion Proteins.

    Directory of Open Access Journals (Sweden)

    Antonella Antignani

    Full Text Available The intersection of small molecular weight drugs and antibody-based therapeutics is rarely studied in large scale. Both types of agents are currently part of the cancer armamentarium. However, very little is known about how to combine them in optimal ways. Immunotoxins are antibody-toxin gene fusion proteins engineered to target cancer cells via antibody binding to surface antigens. For fusion proteins derived from Pseudomonas exotoxin (PE, potency relies on the enzymatic domain of the toxin which catalyzes the ADP-ribosylation of EF2 causing inhibition of protein synthesis leading to cell death. Candidate immunotoxins have demonstrated clear value in clinical trials but generally have not been curative as single agents. Therefore we undertook three screens to discover effective combinations that could act synergistically. From the MIPE-3 library of compounds we identified various enhancers of immunotoxin action and at least one major class of inhibitor. Follow-up experiments confirmed the screening data and suggested that immunotoxins when administered with everolimus or nilotinib exhibit favorable combinatory activity and would be candidates for preclinical development. Mechanistic studies revealed that everolimus-immunotoxin combinations acted synergistically on elements of the protein synthetic machinery, including S61 kinase and 4E-BP1 of the mTORC1 pathway. Conversely, PARP inhibitors antagonized immunotoxins and also blocked the toxicity due to native ADP-ribosylating toxins. Thus, our goal of investigating a chemical library was justified based on the identification of several approved compounds that could be developed preclinically as 'enhancers' and at least one class of mitigator to be avoided.

  17. A novel protein tyrosine kinase Tec identified in lamprey, Lampetra japonica.

    Science.gov (United States)

    Li, Ranran; Su, Peng; Liu, Chang; Zhang, Qiong; Zhu, Ting; Pang, Yue; Liu, Xin; Li, Qingwei

    2015-08-01

    Protein tyrosine kinase Tec, a kind of non-receptor tyrosine kinase, is primarily found to be expressed in T cells, B cells, hematopoietic cells, and liver cells as a cytoplasmic protein. Tec has been proved to be a critical modulator of T cell receptor signaling pathway. In the present study, a homolog of Tec was identified in the lamprey, Lampetra japonica. The full-length Tec cDNA of L. japonica (Lja-Tec) contains a 1923 bp open reading frame that encodes a 641-amino acid protein. The multi-alignment of the deduced amino acid sequence of Lja-Tec with typical vertebrate Tecs showed that it possesses all conserved domains of the Tec family proteins, indicating that an ortholog of Tec exists in the extant jawless vertebrate. In the phylogenetic tree that was reconstructed with 24 homologs of jawless and jawed vertebrates, the Tecs from lampreys and hagfish were clustered as a single clade. The genetic distance between the outgroup and agnathan Tecs' group is closer than that between outgroup and gnathostome Tecs' group, indicating that its origin was far earlier than any of the jawed vertebrates. The mRNA levels of Lja-Tec in lymphocyte-like cells and gills were detected by real-time quantitative polymerase chain reaction. Results showed that it was significantly upregulated under stimulation with mixed pathogens. This result was further confirmed by western blot analysis. All these results indicated that Lja-Tec plays an important role in immune response. Our data will provide a reference for the further study of lamprey Tec and its immunological function in jawless vertebrates. © The Author 2015. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

  18. The protein efficiency ratios of 30:70 mixtures of animal:vegetable protein are similar or higher than those of the animal foods alone.

    Science.gov (United States)

    Hernández, M; Montalvo, I; Sousa, V; Sotelo, A

    1996-02-01

    Animal foods in general are considered to be foods with high protein qualities, although their qualities are not always similar because of differences in essential amino acids. The purpose of this study was to compare the protein quality of different animal foods and of their mixtures with vegetable foods, mainly cereals, at the 30:70 animal:vegetable protein proportion with experiments performed under the same conditions. The animal foods were eggs, beef, pork, barbecued lamb, chicken, ham, sausage and milk powder. The vegetable foods used in the mixtures were rice, lime-treated corn flour, wheat flour and cooked black beans. The protein concentrations in the raw and cooked materials were analyzed. The protein efficiency ratios (PER) and digestibilities were determined in Fisher 344 weanling rats. Based on the corrected PER, the foods with the best protein quality were egg (3.24), sirloin beef (3.16), lamb (3.11) and chicken breast (3.07), which were significantly different (P < 0.05) from milk powder (2.88) and beef liver and beef round (2.81 and 2.70, respectively). The ham (2.63) and the pork loin (2.57) had a similar protein quality to that of casein (2.50). The lowest protein quality was found in sausages (2.14). In most of the mixtures of animal and vegetable protein (30:70), the PER was similar to or higher than that of the animal food alone. Beans were the vegetable food that showed the lowest response to the addition of animal food. The conclusion of the study is that some 30:70 mixtures of animal:vegetable protein, such as chicken, beef round and pork with cereals could be utilized for regular meals because of their high PER and low cost.

  19. Using exploratory factor analysis of food frequency questionnaires to identify dietary patterns among Yup’ik People

    Science.gov (United States)

    Ryman, Tove K.; Austin, Melissa A.; Hopkins, Scarlett; Philip, Jacques; O’Brien, Diane; Thummel, Kenneth; Boyer, Bert B.

    2012-01-01

    Objective A food frequency questionnaire (FFQ) developed by the Center for Alaska Native Health Research for studies in Yup’ik people includes market foods and subsistence foods such as moose, seal, waterfowl and salmon that may be related to disease risk. Because the FFQ contains >100 food items, we sought to characterize dietary patterns more simply for use in ongoing pharmacogenomics studies. Design Exploratory factor analysis was used to derive a small number of “factors” that explain a substantial amount of the variation in the Yup’ik diet. We estimated factor scores and measured associations with demographic characteristics and biomarkers. Setting Southwest Alaska, US Subjects 358 Yup’ik people, ≥ 18 years Results We identified 3 factors that each accounted for ≥10% of the common variance: the first characterized by “processed foods” (e.g., salty snacks, sweetened cereals); the second by “fruits and vegetables” (e.g., fresh citrus, potato salad); and the third by “subsistence foods” (seal or walrus soup, non-oily fish). Participants from coastal communities had higher values for the “subsistence” factor, whereas participants from inland communities had higher values for the “fruits and vegetables” factor. A biomarker of marine intake, δ 15N, was correlated with the “subsistence” factor, whereas a biomarker of corn and sugar-cane based market food intake, δ 13C, was correlated with “processed foods”. Conclusions This exploratory factor analysis identified 3 factors that appear to reflect dietary patterns among Yup’ik based on associations with participant characteristics and biomarkers. These factors will be useful for chronic disease studies in this population. PMID:23290469

  20. The use of functional chemical-protein associations to identify multi-pathway renoprotectants.

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    Jia Xu

    Full Text Available Typically, most nephropathies can be categorized as complex human diseases in which the cumulative effect of multiple minor genes, combined with environmental and lifestyle factors, determines the disease phenotype. Thus, multi-target drugs would be more likely to facilitate comprehensive renoprotection than single-target agents. In this study, functional chemical-protein association analysis was performed to retrieve multi-target drugs of high pathway wideness from the STITCH 3.1 database. Pathway wideness of a drug evaluated the efficiency of regulation of Kyoto Encyclopedia of Genes and Genomes (KEGG pathways in quantity. We identified nine experimentally validated renoprotectants that exerted remarkable impact on KEGG pathways by targeting a limited number of proteins. We selected curcumin as an illustrative compound to display the advantage of multi-pathway drugs on renoprotection. We compared curcumin with hemin, an agonist of heme oxygenase-1 (HO-1, which significantly affects only one KEGG pathway, porphyrin and chlorophyll metabolism (adjusted p = 1.5×10-5. At the same concentration (10 µM, both curcumin and hemin equivalently mitigated oxidative stress in H2O2-treated glomerular mesangial cells. The benefit of using hemin was derived from its agonistic effect on HO-1, providing relief from oxidative stress. Selective inhibition of HO-1 completely blocked the action of hemin but not that of curcumin, suggesting simultaneous multi-pathway intervention by curcumin. Curcumin also increased cellular autophagy levels, enhancing its protective effect; however, hemin had no effects. Based on the fact that the dysregulation of multiple pathways is implicated in the etiology of complex diseases, we proposed a feasible method for identifying multi-pathway drugs from compounds with validated targets. Our efforts will help identify multi-pathway agents capable of providing comprehensive protection against renal injuries.

  1. Design of whey protein nanostructures for incorporation and release of nutraceutical compounds in food.

    Science.gov (United States)

    Ramos, Oscar L; Pereira, Ricardo N; Martins, Artur; Rodrigues, Rui; Fuciños, Clara; Teixeira, José A; Pastrana, Lorenzo; Malcata, F Xavier; Vicente, António A

    2017-05-03

    Whey proteins are widely used as nutritional and functional ingredients in formulated foods because they are relatively inexpensive, generally recognized as safe (GRAS) ingredient, and possess important biological, physical, and chemical functionalities. Denaturation and aggregation behavior of these proteins is of particular relevance toward manufacture of novel nanostructures with a number of potential uses. When these processes are properly engineered and controlled, whey proteins may be formed into nanohydrogels, nanofibrils, or nanotubes and be used as carrier of bioactive compounds. This review intends to discuss the latest understandings of nanoscale phenomena of whey protein denaturation and aggregation that may contribute for the design of protein nanostructures. Whey protein aggregation and gelation pathways under different processing and environmental conditions such as microwave heating, high voltage, and moderate electrical fields, high pressure, temperature, pH, and ionic strength were critically assessed. Moreover, several potential applications of nanohydrogels, nanofibrils, and nanotubes for controlled release of nutraceutical compounds (e.g. probiotics, vitamins, antioxidants, and peptides) were also included. Controlling the size of protein networks at nanoscale through application of different processing and environmental conditions can open perspectives for development of nanostructures with new or improved functionalities for incorporation and release of nutraceuticals in food matrices.

  2. Unique device identifiers for coronary stent postmarket surveillance and research: a report from the Food and Drug Administration Medical Device Epidemiology Network Unique Device Identifier demonstration.

    Science.gov (United States)

    Tcheng, James E; Crowley, Jay; Tomes, Madris; Reed, Terrie L; Dudas, Joseph M; Thompson, Kweli P; Garratt, Kirk N; Drozda, Joseph P

    2014-10-01

    Although electronic product identification in the consumer sector is ubiquitous, unique identification of medical devices is just being implemented in 2014. To evaluate unique device identifiers (UDIs) in health care, the US Food and Drug Administration (FDA) funded the Medical Device Epidemiology Network initiative, including a demonstration of the implementation of coronary stent UDI data in the information systems of a multihospital system (Mercy Health). This report describes the first phase of the demonstration. An expert panel of interventional cardiologists nominated by the American College of Cardiology and the Society for Cardiovascular Angiography and Interventions was convened with representatives of industry, health system members of the Healthcare Transformation Group, the American College of Cardiology National Cardiovascular Data Registry, and FDA to articulate concepts needed to best use UDI-associated data. The expert panel identified 3: (1) use cases for UDI-associated data (eg, research), (2) a supplemental data set of clinically relevant attributes (eg, stent dimensions), and (3) governance and administrative principles for the authoritative management of these data. Eighteen use cases were identified, encompassing clinical care, supply chain management, consumer information, research, regulatory, and surveillance domains. In addition to the attributes of the FDA Global Unique Device Identification Database, 9 additional coronary stent-specific attributes were required to address use case requirements. Recommendations regarding governance were elucidated as foundational principles for UDI-associated data management. This process for identifying requisite extensions to support the effective use of UDI-associated data should be generalizable. Implementation of a UDI system for medical devices must anticipate both global and device-specific information. Copyright © 2014 Mosby, Inc. All rights reserved.

  3. Review: Amino acid concentration of high protein food products and an overview of the current methods used to determine protein quality.

    Science.gov (United States)

    Huang, Shiqi; Wang, Lydia M; Sivendiran, Thakshi; Bohrer, Benjamin M

    2017-12-04

    Quality of the dietary protein in foods rather than amount of dietary protein may be of greater importance from a human health and wellness standpoint. Various systems are in place to determine the value of dietary protein. Protein digestibility-corrected amino acid score (PDCAAS) and digestible indispensable amino acid score (DIAAS) are the two major protein standards used to determine the completeness of proteins by their unique concentration and digestibility of indispensable amino acids. The purpose of this review was to provide a comprehensive comparison of the amino acid concentration of high protein foods and provide the current status of the use and practicality of the PDCAAS and DIAAS system. This review builds upon previous research analyzing the total nutrient density of protein-rich foods and expands scientific research investigating the quality of proteins. In summary, the average sum of indispensable amino acids for meat and fish products is much more consistent than that of non-meat and plant-based food products. However, some non-meat products have relatively similar amounts of indispensable amino acids on a similar serving size basis. The overwhelming aspect of determining protein quality is that greater research is needed to determine protein digestibility of food products.

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

    Science.gov (United States)

    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...

  5. Comparison of antibody responses to hen's egg and cow's milk proteins in orally sensitized rats and food-allergic patients

    NARCIS (Netherlands)

    Knippels, L.M.J.; Kleij, H.P.M. van der; Koppelman, S.J.; Houben, G.F.; Penninks, A.H.; Felius, A.A.

    2000-01-01

    Background: No adequate enteral sensitization models are available to study food allergy and the allergenicity of food proteins. To further validate an enteral brown Norway (BN) rat sensitization model under development, we studied specific protein recognition to determine whether a comparable

  6. Allergenic risks of mealworm and other insects : An approach to assess the risks of new food proteins in allergic patients

    NARCIS (Netherlands)

    Hustinx-Broekman, H.C.H.P.

    2017-01-01

    Assessment of cross-reactivity and primary sensitization and allergy by new food proteins: the goal and contents of this thesis. Allergies to new food proteins can result from cross-reactivity in existing sensitized or allergic individuals and thereby thus immediately manifest themselves in

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

    Science.gov (United States)

    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.

  8. Sufficient Protein Quality of Food Aid Varies with the Physiologic Status of Recipients.

    Science.gov (United States)

    Callaghan, Meghan; Oyama, Momo; Manary, Mark

    2017-03-01

    Protein quality scores use the amino acid (AA) requirements of a healthy North American child. AA requirements vary with physiologic status. We estimated AA requirements for healthy North American children, children with environmental enteric dysfunction, children recovering from wasting, and children with an acute infection. The protein quality of food aid products was then calculated to determine whether it was sufficient in all these groups, and we found that it may not be adequate for all of them. Physiologic status is important when assessing the protein quality of food aid. Rates of weight gain from 8 published trials treating children with moderate acute malnutrition were abstracted, and protein quality scores from the corresponding food aid products were calculated with the use of the digestible indispensable amino acid score (DIAAS). Two DIAAS values were calculated, one in healthy children aged 1-3 y as a reference population and the other in malnourished children aged 1-3 y as a reference population. These data were used to calculate the best fit regression line between weight gain and protein quality. The slope of the regression line was greater when malnourished children were used as a reference population than when healthy children were used (0.128; 95% CI: 0.118, 0.138 compared with 0.097; 95% CI: 0.090, 0.105 measured in g · kg -1 · d -1 · DIASS U -1 ). These findings suggest that adjusting AA requirements for physiologic status may more accurately estimate the minimum protein quality of food aid products. © 2017 American Society for Nutrition.

  9. Interlaboratory tests to identify irradiation treatment of various foods via gas chromatographic detection of hydrocarbons, ESR spectroscopy and TL analysis

    International Nuclear Information System (INIS)

    Schreiber, G.A.; Helle, N.; Schulzki, G.; Linke, B.; Spiegelberg, A.; Mager, M.; Boegl, K.W.

    1996-01-01

    The gas chromatographic (GC) analysis of radiation-induced volatile hydrocarbons (HC) and 2-alkylcyclobutanones, the ESR spectroscopic detection of radiation-specific radicals and the thermoluminescence (TL) analysis of silicate mineral are the most important methods for identification of irradiated foods. After successful performance in interlaboratory studies on meat products, fish, spices, herbs and shells of nuts, all or some of these methods have been approved by national authorities in Germany and the United Kingdom. Recently, draft European Standards have been elaborated for approval by member states of the European Committee for Standardization (CEN). Several research laboratories have shown that these methods can be applied to various foods not yet tested in collaborative studies. However, for an effective application in food control it is necessary to prove their suitability in interlaboratory studies. Therefore, in 1993/94, various interlaboratory tests were organised by the BgVV. In an ESR spectroscopic test, shrimps and paprika powder were examined. Shrimps were also the subject of examination in a TL test. Finally, GC detection of radiation-induced hydrocarbons in the fat fraction of foods was used in another test to identify irradiated Camembert, avocado, papaya and mango. In the following paper, results of the interlaboratory tests are summarised. Detailed reports are published by this institute. (author)

  10. Interlaboratory tests to identify irradiation treatment of various foods via gas chromatographic detection of hydrocarbons, ESR spectroscopy and TL analysis

    Energy Technology Data Exchange (ETDEWEB)

    Schreiber, G.A.; Helle, N.; Schulzki, G.; Linke, B.; Spiegelberg, A.; Mager, M.; Boegl, K.W. [BgVV - Federal Inst. for Health Protection of Consumers and Veterinary Medicine, Berlin (Germany)

    1996-12-31

    The gas chromatographic (GC) analysis of radiation-induced volatile hydrocarbons (HC) and 2-alkylcyclobutanones, the ESR spectroscopic detection of radiation-specific radicals and the thermoluminescence (TL) analysis of silicate mineral are the most important methods for identification of irradiated foods. After successful performance in interlaboratory studies on meat products, fish, spices, herbs and shells of nuts, all or some of these methods have been approved by national authorities in Germany and the United Kingdom. Recently, draft European Standards have been elaborated for approval by member states of the European Committee for Standardization (CEN). Several research laboratories have shown that these methods can be applied to various foods not yet tested in collaborative studies. However, for an effective application in food control it is necessary to prove their suitability in interlaboratory studies. Therefore, in 1993/94, various interlaboratory tests were organised by the BgVV. In an ESR spectroscopic test, shrimps and paprika powder were examined. Shrimps were also the subject of examination in a TL test. Finally, GC detection of radiation-induced hydrocarbons in the fat fraction of foods was used in another test to identify irradiated Camembert, avocado, papaya and mango. In the following paper, results of the interlaboratory tests are summarised. Detailed reports are published by this institute. (author).

  11. Are suppressors of cytokine signaling proteins recently identified in atherosclerosis possible therapeutic targets?

    Science.gov (United States)

    Tang, Jingjing; Raines, Elaine W

    2005-10-01

    Atherosclerosis is a slowly progressing chronic inflammatory disease characterized by focal arterial lesions that can ultimately occlude the entire blood vessel and lead to sudden death. Lesions associated with cardiovascular events are those enriched in macrophages and other inflammatory cells. Activation of inflammatory cells within lesions induces the release of cytokines which promotes more inflammation and associated tissue damage if cytokine signaling pathways remain unregulated. Thus, pathways capable of suppressing proinflammatory cytokine signaling hold the potential to limit life-threatening cardiovascular events caused by atherogenesis. This review focuses on suppressors of cytokine signaling proteins recently identified in the atherosclerosis-prone ApoE(-/-) mouse and provides perspectives of their potential for intervention in atherosclerotic lesion progression.

  12. An All-Recombinant Protein-Based Culture System Specifically Identifies Hematopoietic Stem Cell Maintenance Factors.

    Science.gov (United States)

    Ieyasu, Aki; Ishida, Reiko; Kimura, Takaharu; Morita, Maiko; Wilkinson, Adam C; Sudo, Kazuhiro; Nishimura, Toshinobu; Ohehara, Jun; Tajima, Yoko; Lai, Chen-Yi; Otsu, Makoto; Nakamura, Yukio; Ema, Hideo; Nakauchi, Hiromitsu; Yamazaki, Satoshi

    2017-03-14

    Hematopoietic stem cells (HSCs) are considered one of the most promising therapeutic targets for the treatment of various blood disorders. However, due to difficulties in establishing stable maintenance and expansion of HSCs in vitro, their insufficient supply is a major constraint to transplantation studies. To solve these problems we have developed a fully defined, all-recombinant protein-based culture system. Through this system, we have identified hemopexin (HPX) and interleukin-1α as responsible for HSC maintenance in vitro. Subsequent molecular analysis revealed that HPX reduces intracellular reactive oxygen species levels within cultured HSCs. Furthermore, bone marrow immunostaining and 3D immunohistochemistry revealed that HPX is expressed in non-myelinating Schwann cells, known HSC niche constituents. These results highlight the utility of this fully defined all-recombinant protein-based culture system for reproducible in vitro HSC culture and its potential to contribute to the identification of factors responsible for in vitro maintenance, expansion, and differentiation of stem cell populations. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. An All-Recombinant Protein-Based Culture System Specifically Identifies Hematopoietic Stem Cell Maintenance Factors

    Directory of Open Access Journals (Sweden)

    Aki Ieyasu

    2017-03-01

    Full Text Available Hematopoietic stem cells (HSCs are considered one of the most promising therapeutic targets for the treatment of various blood disorders. However, due to difficulties in establishing stable maintenance and expansion of HSCs in vitro, their insufficient supply is a major constraint to transplantation studies. To solve these problems we have developed a fully defined, all-recombinant protein-based culture system. Through this system, we have identified hemopexin (HPX and interleukin-1α as responsible for HSC maintenance in vitro. Subsequent molecular analysis revealed that HPX reduces intracellular reactive oxygen species levels within cultured HSCs. Furthermore, bone marrow immunostaining and 3D immunohistochemistry revealed that HPX is expressed in non-myelinating Schwann cells, known HSC niche constituents. These results highlight the utility of this fully defined all-recombinant protein-based culture system for reproducible in vitro HSC culture and its potential to contribute to the identification of factors responsible for in vitro maintenance, expansion, and differentiation of stem cell populations.

  14. A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii.

    Science.gov (United States)

    Li, Enhu; Reich, Claudia I; Olsen, Gary J

    2008-12-01

    We have adapted an electrophoretic mobility shift assay (EMSA) to isolate genomic DNA fragments that bind the archaeal transcription initiation factors TATA-binding protein (TBP) and transcription factor B (TFB) to perform a genome-wide search for promoters. Mobility-shifted fragments were cloned, tested for their ability to compete with known promoter-containing fragments for a limited concentration of transcription factors, and sequenced. We applied the method to search for promoters in the genome of Methanocaldococcus jannaschii. Selection was most efficient for promoters of tRNA genes and genes for several presumed small non-coding RNAs (ncRNA). Protein-coding gene promoters were dramatically underrepresented relative to their frequency in the genome. The repeated isolation of these genomic regions was partially rectified by including a hybridization-based screening. Sequence alignment of the affinity-selected promoters revealed previously identified TATA box, BRE, and the putative initiator element. In addition, the conserved bases immediately upstream and downstream of the BRE and TATA box suggest that the composition and structure of archaeal natural promoters are more complicated.

  15. Evolutionary and molecular analysis of Dof transcription factors identified a conserved motif for intercellular protein trafficking.

    Science.gov (United States)

    Chen, Huan; Ahmad, Munawar; Rim, Yeonggil; Lucas, William J; Kim, Jae-Yean

    2013-06-01

    · Cell-to-cell trafficking of transcription factors (TFs) has been shown to play an important role in the regulation of plant developmental events, but the evolutionary relationship between cell-autonomous and noncell-autonomous (NCA) TFs remains elusive. · AtDof4.1, named INTERCELLULAR TRAFFICKING DOF 1 (ITD1), was chosen as a representative NCA member to explore this evolutionary relationship. Using domain structure-function analyses and swapping studies, we examined the cell-to-cell trafficking of plant-specific Dof TF family members across Arabidopsis and other species. · We identified a conserved intercellular trafficking motif (ITM) that is necessary and sufficient for selective cell-to-cell trafficking and can impart gain-of-function cell-to-cell movement capacity to an otherwise cell-autonomous TF. The functionality of related motifs from Dof members across the plant kingdom extended, surprisingly, to a unicellular alga that lacked plasmodesmata. By contrast, the algal homeodomain related to the NCA KNOX homeodomain was either inefficient or unable to impart such cell-to-cell movement function. · The Dof ITM appears to predate the evolution of selective plasmodesmal trafficking in the plant kingdom, which may well have acted as a molecular template for the evolution of Dof proteins as NCA TFs. However, the ability to efficiently traffic for KNOX homeodomain (HD) proteins may have been acquired during the evolution of early nonvascular plants. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  18. Combining discrete and continuous mixing distributions to identify niche markets for food

    OpenAIRE

    Danny Campbell; Edel Doherty

    2013-01-01

    This paper explores the demand and willingness to pay (WTP) for value-added services to chicken. Since the demand for such services are likely to be highly segmented and often applies only to a market niche, models based on assumptions of homogeneity among consumers are likely to be inappropriate. For this reason, this paper combines discrete and continuous mixing distributions to concurrently identify the size of the niche market and the heterogeneity among consumers within the market niche....

  19. Adolescents in the United States can identify familiar foods at the time of consumption and when prompted with an image 14 h postprandial, but poorly estimate portions.

    Science.gov (United States)

    Schap, TusaRebecca E; Six, Bethany L; Delp, Edward J; Ebert, David S; Kerr, Deborah A; Boushey, Carol J

    2011-07-01

    To evaluate adolescents' abilities to identify foods and estimate the portion size of foods consumed in order to inform development of the mobile telephone food record (mpFR). Data were collected from two samples of adolescents (11-18 years). Adolescents in sample 1 participated in one lunch (n 63) and fifty-five of the sixty-three adolescents (87 %) returned for breakfast the next morning. Sample 2 volunteers received all meals and snacks for a 24 h period. At mealtime, sample 1 participants were asked to write down the names of the foods. Sample 2 participants identified foods in an image of their meal 10-14 h postprandial. Adolescents in sample 2 also estimated portion sizes of their breakfast foods and snacks. Sample 1 identified thirty of the thirty-eight food items correctly, and of the misidentified foods all were identified within the correct major food group. For sample 2, eleven of the thirteen food items were identified correctly 100 % of the time. Half of the breakfast and snack foods had at least one portion size estimate within 10 % of the true amount using a variety of measurement descriptors. The results provide evidence that adolescents can correctly identify familiar foods and they can look at an image of their meal and identify the foods in the image up to 14·5 h postprandial. The results of the present study not only inform the development of the mpFR but also provide strong evidence of the use of digital images of eating occasions in research and clinical settings.

  20. Dairy foods and dairy proteins in the management of type 2 diabetes: a systematic review of the clinical evidence.

    Science.gov (United States)

    Pasin, Gonca; Comerford, Kevin B

    2015-05-01

    Type 2 diabetes mellitus (T2DM) is a growing public health concern affecting hundreds of millions of people worldwide and costing the global economy hundreds of billions of dollars annually. This chronic disease damages the blood vessels and increases the risk of other cardiometabolic ailments such as cardiovascular disease and stroke. If left unmanaged it can also lead to nerve damage, kidney damage, blindness, and amputation. For the most part, many of these symptoms can be prevented or reduced through simple dietary modifications and proper nutrition. Therefore, identifying relatively inexpensive and easily implementable dietary modifications for the prevention and management of T2DM is of considerable value to human health and healthcare modalities around the globe. Protein-rich dairy products have consistently been shown in epidemiologic studies to be beneficial for reducing the risk of developing T2DM. The clinical evidence regarding both dairy foods and dairy proteins (i.e., casein and whey protein) have shown promise for improving insulin secretion in individuals with T2DM. However, the clinical research on dairy protein supplementation in subjects with T2DM has been limited to acute studies. These studies have been mostly descriptive and have not been focused on important T2DM endpoints such as prevention, management, or treatment. Long-term studies are clearly needed to help researchers and medical professionals better understand the effects of consistent dairy protein intake on the metabolic health of humans with T2DM. © 2015 American Society for Nutrition.

  1. Y-box protein-1/p18 fragment identifies malignancies in patients with chronic liver disease

    International Nuclear Information System (INIS)

    Tacke, Frank; Kanig, Nicolas; En-Nia, Abdelaziz; Kaehne, Thilo; Eberhardt, Christiane S; Shpacovitch, Victoria; Trautwein, Christian; Mertens, Peter R

    2011-01-01

    Immunohistochemical detection of cold shock proteins is predictive for deleterious outcome in various malignant diseases. We recently described active secretion of a family member, denoted Y-box (YB) protein-1. We tested the clinical and diagnostic value of YB-1 protein fragment p18 (YB-1/p18) detection in blood for malignant diseases. We used a novel monoclonal anti-YB-1 antibody to detect YB-1/p18 by immunoblotting in plasma samples of healthy volunteers (n = 33), patients with non-cancerous, mostly inflammatory diseases (n = 60), hepatocellular carcinoma (HCC; n = 25) and advanced solid tumors (n = 20). YB-1/p18 was then tested in 111 patients with chronic liver diseases, alongside established tumor markers and various diagnostic measures, during evaluation for potential liver transplantation. We developed a novel immunoblot to detect the 18 kD fragment of secreted YB-1 in human plasma (YB-1/p18) that contains the cold-shock domains (CSD) 1-3 of the full-length protein. YB-1/p18 was detected in 11/25 HCC and 16/20 advanced carcinomas compared to 0/33 healthy volunteers and 10/60 patients with non-cancerous diseases. In 111 patients with chronic liver disease, YB-1/p18 was detected in 20 samples. Its occurrence was not associated with advanced Child stages of liver cirrhosis or liver function. In this cohort, YB-1/p18 was not a good marker for HCC, but proved most powerful in detecting malignancies other than HCC (60% positive) with a lower rate of false-positive results compared to established tumor markers. Alpha-fetoprotein (AFP) was most sensitive in detecting HCC, but simultaneous assessment of AFP, CA19-9 and YB-1/p18 improved overall identification of HCC patients. Plasma YB-1/p18 can identify patients with malignancies, independent of acute inflammation, renal impairment or liver dysfunction. The detection of YB-1/p18 in human plasma may have potential as a tumor marker for screening of high-risk populations, e.g. before organ transplantation, and should

  2. IL-1beta induced protein changes in diabetes prone BB rat islets of Langerhans identified by proteome analysis

    DEFF Research Database (Denmark)

    Sparre, T; Bjerre-Christensen, Ulla; Mose Larsen, P

    2002-01-01

    of 82 out of 1 815 protein spots detected by two dimensional gel electrophoresis in IL-1beta exposed diabetes prone Bio Breeding (BB-DP) rat islets of Langerhans in vitro. The aim of this study was to identify the proteins in these 82 spots by mass spectrometry and compare these changes with those seen...

  3. Functionality of lipids and lipid-protein interactions in cereal-derived food products

    Directory of Open Access Journals (Sweden)

    Marion Didier

    2003-01-01

    Full Text Available Lipids and especially cereal lipids play a significant role in the processing and quality of cereals and baked cereal foods (bread, biscuits and beverages (beer. Most of the physico-chemical mechanisms responsible for the lipid functionality has been investigated and recently the specific role of lipid-binding proteins, e.g. lipid transfer proteins and puroindolines, has been highlighted. The state of the researches performed in this field are briefly presented in this review and the data obtained until now show that new perspectives are opened in cereal breeding and processing for improving the quality of cereals and cereal products.

  4. An integrated transcriptomic and proteomic analysis of sea star epidermal secretions identifies proteins involved in defense and adhesion.

    Science.gov (United States)

    Hennebert, Elise; Leroy, Baptiste; Wattiez, Ruddy; Ladurner, Peter

    2015-10-14

    Sea stars rely on epidermal secretions to cope with their benthic life. Their integument produces a mucus, which represents the first barrier against invaders; and their tube feet produce adhesive secretions to pry open mussels and attach strongly but temporarily to rocks. In this study, we combined high-throughput sequencing of expressed mRNA and mass-spectrometry-based identification of proteins to establish the first proteome of mucous and adhesive secretions from the sea star Asterias rubens. We show that the two secretions differ significantly, the major adhesive proteins being only present in trace amounts in the mucus secretion. Except for 41 proteins which were present in both secretions, a total of 34 and 244 proteins were identified as specific of adhesive secretions and mucus, respectively. We discuss the role of some of these proteins in the adhesion of sea stars as well as in their protection against oxygen reactive species and microorganisms. In addition, 58% of the proteins identified in adhesive secretions did not present significant similarity to other known proteins, revealing a list of potential novel sea star adhesive proteins uncharacterized so far. The panel of proteins identified in this study offers unprecedented opportunities for the development of sea star-inspired biomimetic materials. Copyright © 2015. Published by Elsevier B.V.

  5. A multiplexed analysis approach identifies new association of inflammatory proteins in patients with overactive bladder.

    Science.gov (United States)

    Ma, Emily; Vetter, Joel; Bliss, Laura; Lai, H Henry; Mysorekar, Indira U; Jain, Sanjay

    2016-07-01

    Overactive bladder (OAB) is a common debilitating bladder condition with unknown etiology and limited diagnostic modalities. Here, we explored a novel high-throughput and unbiased multiplex approach with cellular and molecular components in a well-characterized patient cohort to identify biomarkers that could be reliably used to distinguish OAB from controls or provide insights into underlying etiology. As a secondary analysis, we determined whether this method could discriminate between OAB and other chronic bladder conditions. We analyzed plasma samples from healthy volunteers (n = 19) and patients diagnosed with OAB, interstitial cystitis/bladder pain syndrome (IC/BPS), or urinary tract infections (UTI; n = 51) for proinflammatory, chemokine, cytokine, angiogenesis, and vascular injury factors using Meso Scale Discovery (MSD) analysis and urinary cytological analysis. Wilcoxon rank-sum tests were used to perform univariate and multivariate comparisons between patient groups (controls, OAB, IC/BPS, and UTI). Multivariate logistic regression models were fit for each MSD analyte on 1) OAB patients and controls, 2) OAB and IC/BPS patients, and 3) OAB and UTI patients. Age, race, and sex were included as independent variables in all multivariate analysis. Receiver operating characteristic (ROC) curves were generated to determine the diagnostic potential of a given analyte. Our findings demonstrate that five analytes, i.e., interleukin 4, TNF-α, macrophage inflammatory protein-1β, serum amyloid A, and Tie2 can reliably differentiate OAB relative to controls and can be used to distinguish OAB from the other conditions. Together, our pilot study suggests a molecular imbalance in inflammatory proteins may contribute to OAB pathogenesis. Copyright © 2016 the American Physiological Society.

  6. Breast cancer resistance protein identifies clonogenic keratinocytes in human interfollicular epidermis.

    Science.gov (United States)

    Ma, Dongrui; Chua, Alvin Wen Choong; Yang, Ennan; Teo, Peiyun; Ting, Yixin; Song, Colin; Lane, Ellen Birgitte; Lee, Seng Teik

    2015-03-24

    There is a practical need for the identification of robust cell-surface markers that can be used to enrich for living keratinocyte progenitor cells. Breast cancer resistance protein (ABCG2), a member of the ATP binding cassette (ABC) transporter family, is known to be a marker for stem/progenitor cells in many tissues and organs. We investigated the expression of ABCG2 protein in normal human epidermis to evaluate its potential as a cell surface marker for identifying and enriching for clonogenic epidermal keratinocytes outside the pilosebaceous tract. Immunofluorescence and immunoblotting studies of human skin showed that ABCG2 is expressed in a subset of basal layer cells in the epidermis. Flow cytometry analysis showed approximately 2-3% of keratinocytes in non-hair-bearing epidermis expressing ABCG2; this population also expresses p63, β1 and α6 integrins and keratin 14, but not CD34, CD71, C-kit or involucrin. The ABCG2-positive keratinocytes showed significantly higher colony forming efficiency when co-cultured with mouse 3T3 feeder cells, and more extensive long-term proliferation capacity in vitro, than did ABCG2-negative keratinocytes. Upon clonal analysis, most of the freshly isolated ABCG2-positive keratinocytes formed holoclones and were capable of generating a stratified differentiating epidermis in organotypic culture models. These data indicate that in skin, expression of the ABCG2 transporter is a characteristic of interfollicular keratinocyte progentior cells and suggest that ABCG2 may be useful for enriching keratinocyte stem cells in human interfollicular epidermis.

  7. Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic Tardigrade improve osmotic tolerance of human cells.

    Directory of Open Access Journals (Sweden)

    Sae Tanaka

    Full Text Available Tardigrades are able to tolerate almost complete dehydration through transition to a metabolically inactive state, called "anhydrobiosis". Late Embryogenesis Abundant (LEA proteins are heat-soluble proteins involved in the desiccation tolerance of many anhydrobiotic organisms. Tardigrades, Ramazzottius varieornatus, however, express predominantly tardigrade-unique heat-soluble proteins: CAHS (Cytoplasmic Abundant Heat Soluble and SAHS (Secretory Abundant Heat Soluble proteins, which are secreted or localized in most intracellular compartments, except the mitochondria. Although mitochondrial integrity is crucial to ensure cellular survival, protective molecules for mitochondria have remained elusive. Here, we identified two novel mitochondrial heat-soluble proteins, RvLEAM and MAHS (Mitochondrial Abundant Heat Soluble, as potent mitochondrial protectants from Ramazzottius varieornatus. RvLEAM is a group3 LEA protein and immunohistochemistry confirmed its mitochondrial localization in tardigrade cells. MAHS-green fluorescent protein fusion protein localized in human mitochondria and was heat-soluble in vitro, though no sequence similarity with other known proteins was found, and one region was conserved among tardigrades. Furthermore, we demonstrated that RvLEAM protein as well as MAHS protein improved the hyperosmotic tolerance of human cells. The findings of the present study revealed that tardigrade mitochondria contain at least two types of heat-soluble proteins that might have protective roles in water-deficient environments.

  8. Ankle brachial index, C-reactive protein, and central augmentation index to identify individuals with severe atherosclerosis

    DEFF Research Database (Denmark)

    Eldrup, Nikolaj; Sillesen, Henrik; Prescott, Eva

    2006-01-01

    We examined the ability of ankle brachial index, C-reactive protein and central augmentation index to identify individuals in the general population with severe atherosclerosis, diagnosed as those with ischaemic cardiovascular disease.......We examined the ability of ankle brachial index, C-reactive protein and central augmentation index to identify individuals in the general population with severe atherosclerosis, diagnosed as those with ischaemic cardiovascular disease....

  9. Feeding proteins to livestock: Global land use and food vs. feed competition

    Directory of Open Access Journals (Sweden)

    Manceron Stéphane

    2014-07-01

    Full Text Available Competition between direct consumption of plant production and the feeding of livestock is key to global food availability. This is because livestock consume edible commodities that could be available for (food insecure populations but also because it diverts arable land from food production. The share of total plant production redirected towards feeding livestock is (roughly known but estimations of land surfaces virtually occupied by livestock production are scarce. In this study, following up on the Agrimonde Terra** project, we estimate areas devoted to the feeding livestock. First, we estimate the protein composition of an averaged feed basket at the global scale in 2005 and detail the evolution of the protein-source feed component during the period 1961–2009. We focus on protein-rich crops such as oil crops and show its proportion in the global livestock diets has tripled since 1960, though only accounting for about one fourth of total proteins. Then, we estimate land virtually occupied by crop feed at the global scale using a set of straightforward hypotheses. Our estimates suggest that, although livestock and feed production has continuously increased and despite uncertainties in available data, competition for land between feed and food uses has decreased over the last two decades. The share of areas cultivated for feed requirements decreased from about 50% in the 1970s to 37% nowadays. This trend is attributable to the increase of crop yields and to a decrease of the share of cereals in livestock diets to the benefit of oilseeds by-products. However, estimating the share of total areas used for feed is complicated by the significant role played by by-products.

  10. Guideline for making application dossiers for novel proteins; Novel food dossiers: from black box to tool box

    NARCIS (Netherlands)

    Wagenberg, van C.P.A.; Janssens, B.; Kalk, C.; Sluis, van der A.; Noordam, M.Y.; Spiegel, van der M.

    2014-01-01

    This document describes when a new protein intended to market for human consumption is considered to be a novel food protein (novel protein) and when it is not, when an application dossier for authorisation must be made and when, in general, an application dossier for notification might be

  11. Geochemistry and mercury contamination in receiving environments of artisanal mining wastes and identified concerns for food safety.

    Science.gov (United States)

    Reichelt-Brushett, Amanda J; Stone, Jane; Howe, Pelli; Thomas, Bernard; Clark, Malcolm; Male, Yusthinus; Nanlohy, Albert; Butcher, Paul

    2017-01-01

    Artisanal small-scale gold mining (ASGM) using mercury (Hg) amalgamation has been occurring on Buru Island, Indonesia since early 2012, and has caused rapid accumulation of high Hg concentrations in river, estuary and marine sediments. In this study, sediment samples were collected from several sites downstream of the Mount Botak ASGM site, as well as in the vicinity of the more recently established site at Gogrea where no sampling had previously been completed. All sediment samples had total Hg (THg) concentrations exceeding Indonesian sediment quality guidelines and were up to 82 times this limit at one estuary site. The geochemistry of sediments in receiving environments indicates the potential for Hg-methylation to form highly bioavailable Hg species. To assess the current contamination threat from consumption of local seafood, samples of fish, molluscs and crustaceans were collected from the Namlea fish market and analysed for THg concentrations. The majority of edible tissue samples had elevated THg concentrations, which raises concerns for food safety. This study shows that river, estuary and marine ecosystems downstream of ASGM operations on Buru Island are exposed to dangerously high Hg concentrations, which are impacting aquatic food chains, and fisheries resources. Considering the high dietary dependence on marine protein in the associated community and across the Mollucas Province, and the short time period since ASGM operations commenced in this region, the results warrant urgent further investigation, risk mitigation, and community education. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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.

  13. 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

    Directory of Open Access Journals (Sweden)

    Kevin B. Comerford

    2016-07-01

    Full Text Available 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.

  14. 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

    Science.gov (United States)

    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

  15. Protein quality of insects as potential ingredients for dog and cat foods.

    Science.gov (United States)

    Bosch, Guido; Zhang, Sheng; Oonincx, Dennis G A B; Hendriks, Wouter H

    2014-01-01

    Insects have been proposed as a high-quality, efficient and sustainable dietary protein source. The present study evaluated the protein quality of a selection of insect species. Insect substrates were housefly pupae, adult house cricket, yellow mealworm larvae, lesser mealworm larvae, Morio worm larvae, black soldier fly larvae and pupae, six spot roach, death's head cockroach and Argentinean cockroach. Reference substrates were poultry meat meal, fish meal and soyabean meal. Substrates were analysed for DM, N, crude fat, ash and amino acid (AA) contents and for in vitro digestibility of organic matter (OM) and N. The nutrient composition, AA scores as well as in vitro OM and N digestibility varied considerably between insect substrates. For the AA score, the first limiting AA for most substrates was the combined requirement for Met and Cys. The pupae of the housefly and black soldier fly were high in protein and had high AA scores but were less digestible than other insect substrates. The protein content and AA score of house crickets were high and similar to that of fish meal; however, in vitro N digestibility was higher. The cockroaches were relatively high in protein but the indispensable AA contents, AA scores and the in vitro digestibility values were relatively low. In addition to the indices of protein quality, other aspects such as efficiency of conversion of organic side streams, feasibility of mass-production, product safety and pet owner perception are important for future dog and cat food application of insects as alternative protein source.

  16. Fibroblast activation protein alpha expression identifies activated fibroblasts after myocardial infarction.

    Science.gov (United States)

    Tillmanns, Jochen; Hoffmann, Daniel; Habbaba, Yasmin; Schmitto, Jan D; Sedding, Daniel; Fraccarollo, Daniela; Galuppo, Paolo; Bauersachs, Johann

    2015-10-01

    Fibroblast activation protein α (FAP) is a membrane-bound serine protease expressed by activated fibroblasts during wound healing in the skin. Expression of FAP after myocardial infarction (MI) and potential effects on cardiac wound healing are largely unknown. MI was induced in rats and FAP expression was analyzed at 3, 7 and 28 days post-MI by microarray, Western blot and immunohistochemistry. In human hearts after MI, a FAP(+) fibroblast population was identified, and characterized by immunohistochemistry for prolyl-4-hydroxylase β, α-smooth muscle actin, Thy-1 and vimentin. Signaling pathways leading to FAP expression were studied in human cardiac fibroblasts by Western blot and ELISA using TGFβ1, TGF-beta type I-receptor (TGFbR1)-inhibitor SB431542 or the MAPK-inhibitor U0126 as well as siRNA targeting SMAD2 and SMAD3. Finally, fibroblasts were assayed for FAP-dependent migration (modified Boyden-chamber), proliferation (BrdU-assay) and gelatinolytic activity by gelatin zymography. In rats, FAP expression was increased after MI especially in the peri-infarct area peaking at 7 days post-MI. Co-localization analysis identified the majority of FAP(+) cells as activated proto-myofibroblasts and myofibroblasts. Concordantly, FAP(+) fibroblasts were abundant in ischemic tissue of human hearts after MI, but not in healthy control hearts. In vitro, FAP was induced by TGFβ1 via the canonical SMAD2/SMAD3 pathway. Depletion of FAP in fibroblasts reduced migratory capacity, while proliferation was not affected. Gelatin zymography revealed gelatinase activity by fibroblast-derived FAP. In this study, we show for the first time the expression of FAP in activated fibroblasts after MI and its activation by TGFβ1. Effects of FAP on fibroblast migration and gelatinolytic activity indicate a potential role in cardiac wound healing and remodeling. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Identifying inhibitors/enhancers of quantitative real-time PCR in food samples using a newly developed synthetic plasmid.

    Science.gov (United States)

    Sovová, Tereza; Křížová, Barbora; Hodek, Jan; Ovesná, Jaroslava

    2016-02-01

    Polymerase chain reaction (PCR) has become a common technique offering fast and sensitive analysis of DNA in food/feed samples. However, many substances, either already present in the sample or introduced during sample processing, inhibit PCR and thus underestimate the DNA content. It is therefore necessary to identify PCR inhibition in order to correctly evaluate the sample. We designed and validated a synthetic plasmid DNA that can be used to detect and quantify PCR inhibition. The DNA sequence, appropriate primers and probe, were designed in silico, synthesized and the sequence was inserted into a plasmid vector. The performance of the plasmid was verified via calibration curves and by performing the assay in the presence of various DNAs (crops, fungus, bacterium). The detection of PCR inhibition was assessed using six inhibiting substances with different modes of action, substances used in sample processing (EDTA, ethanol, NaCl, SDS) and food additives (sodium glutamate, tartrazine). The plasmid performance proved to be reproducible and there were no interactions with other DNAs. The plasmid was able to identify the presence of the inhibitors in a wide range of concentrations. The presented plasmid DNA is a suitable and inexpensive possibility for evaluating PCR inhibition. © 2015 Society of Chemical Industry.

  18. Sequence Analysis of Hypothetical Proteins from 26695 to Identify Potential Virulence Factors

    Directory of Open Access Journals (Sweden)

    Ahmad Abu Turab Naqvi

    2016-09-01

    Full Text Available Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP. This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

  19. Chagas disease vector blood meal sources identified by protein mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Judith I Keller

    Full Text Available Chagas disease is a complex vector borne parasitic disease involving blood feeding Triatominae (Hemiptera: Reduviidae insects, also known as kissing bugs, and the vertebrates they feed on. This disease has tremendous impacts on millions of people and is a global health problem. The etiological agent of Chagas disease, Trypanosoma cruzi (Kinetoplastea: Trypanosomatida: Trypanosomatidae, is deposited on the mammalian host in the insect's feces during a blood meal, and enters the host's blood stream through mucous membranes or a break in the skin. Identifying the blood meal sources of triatomine vectors is critical in understanding Chagas disease transmission dynamics, can lead to identification of other vertebrates important in the transmission cycle, and aids management decisions. The latter is particularly important as there is little in the way of effective therapeutics for Chagas disease. Several techniques, mostly DNA-based, are available for blood meal identification. However, further methods are needed, particularly when sample conditions lead to low-quality DNA or to assess the risk of human cross-contamination. We demonstrate a proteomics-based approach, using liquid chromatography tandem mass spectrometry (LC-MS/MS to identify host-specific hemoglobin peptides for blood meal identification in mouse blood control samples and apply LC-MS/MS for the first time to Triatoma dimidiata insect vectors, tracing blood sources to species. In contrast to most proteins, hemoglobin, stabilized by iron, is incredibly stable even being preserved through geologic time. We compared blood stored with and without an anticoagulant and examined field-collected insect specimens stored in suboptimal conditions such as at room temperature for long periods of time. To our knowledge, this is the first study using LC-MS/MS on field-collected arthropod disease vectors to identify blood meal composition, and where blood meal identification was confirmed with more

  20. Chagas disease vector blood meal sources identified by protein mass spectrometry.

    Science.gov (United States)

    Keller, Judith I; Ballif, Bryan A; St Clair, Riley M; Vincent, James J; Monroy, M Carlota; Stevens, Lori

    2017-01-01

    Chagas disease is a complex vector borne parasitic disease involving blood feeding Triatominae (Hemiptera: Reduviidae) insects, also known as kissing bugs, and the vertebrates they feed on. This disease has tremendous impacts on millions of people and is a global health problem. The etiological agent of Chagas disease, Trypanosoma cruzi (Kinetoplastea: Trypanosomatida: Trypanosomatidae), is deposited on the mammalian host in the insect's feces during a blood meal, and enters the host's blood stream through mucous membranes or a break in the skin. Identifying the blood meal sources of triatomine vectors is critical in understanding Chagas disease transmission dynamics, can lead to identification of other vertebrates important in the transmission cycle, and aids management decisions. The latter is particularly important as there is little in the way of effective therapeutics for Chagas disease. Several techniques, mostly DNA-based, are available for blood meal identification. However, further methods are needed, particularly when sample conditions lead to low-quality DNA or to assess the risk of human cross-contamination. We demonstrate a proteomics-based approach, using liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify host-specific hemoglobin peptides for blood meal identification in mouse blood control samples and apply LC-MS/MS for the first time to Triatoma dimidiata insect vectors, tracing blood sources to species. In contrast to most proteins, hemoglobin, stabilized by iron, is incredibly stable even being preserved through geologic time. We compared blood stored with and without an anticoagulant and examined field-collected insect specimens stored in suboptimal conditions such as at room temperature for long periods of time. To our knowledge, this is the first study using LC-MS/MS on field-collected arthropod disease vectors to identify blood meal composition, and where blood meal identification was confirmed with more traditional DNA

  1. Development of an energy-protein for animal food based crop residues pear (Pyrus communis

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    Néstor Julián Pulido-Suárez,

    2016-01-01

    Full Text Available Pear (Pyrus communis is a fruit from the species of deciduous, widely consumed worldwide for its high quality energ y. However, pear itself does not provide the amount of protein required for cattle feeding, so alternatives to improve its nutritional quality have been studied. On these grounds, the objective of this study was to evaluate the parameters of solid state fermentation, and compositional energ y value of a protein food based on pears (Pyrus communis with apparent physical damage. A completely random design was used to evaluate three treatments; these correspond to percentages of inclusion of calcium carbonate (0.25, 0.50, 0.75 formulation based on already established (40 % pear, 25 % rice flour, 25 % wheat bran and 10 % urea, the parameters evaluated were: pH, ashes (CZ, crude protein (CP and crude fiber (CF, and they were recorded at 0, 24, 48 and 72 hours. As a result, it was found that the pH dropped gradually for each treatment and at each sampling period; however, there were no significant differences. The lower value at the end of the process is recorded T2 (0.25 with 4.66, followed by T3 (0.50 with 4.50, the ash reached values of up to 6 % with T3, and T2 (0.50 reached the highest percentages in fiber and crude protein. Finally, decreasing the fermentation variables ensures a food with no presence of undesirable microorganisms and stable over time.

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

    Directory of Open Access Journals (Sweden)

    Kathryn E. Bradbury

    2017-12-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Graeme D. Coles

    2016-07-01

    Full Text Available 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.

  6. Comparative analysis of human reproductive proteomes identifies candidate proteins of sperm maturation.

    Science.gov (United States)

    Fu-Jun, Liu; Xiao-Fang, Shen

    2012-12-01

    Male reproductive proteomes provide basis for studying gene products and its involvement or regulation in sperm physiology. Here, a comparative study between these proteomes was performed to find potential proteins and functions associated with human sperm maturation. Seven reproductive proteomes associated with human sperm physiology were integrated. Gene ontology analysis were performed using DAVID and Panther tools to determine enriched functions. Total of 270 proteins overlapped between epididymal, prostatic milieu and sperm proteome were thought to be candidate proteins involved in sperm maturation, and they showed enriched functions of proteasomal protein catabolic process and protein folding. 34 epididymal milieu proteins and 274 prostatic milieu proteins were contributed to the composition of seminal fluids proteome. Literatures have confirmed the involvements in sperm maturation of many of these proteins The spatial expressions of 24 epididymal milieu proteins involved in chaperone and antioxidant activity were authenticated by real-time RT-PCR. These proteins may serve as candidate molecules for future studies of sperm maturation and male infertility.

  7. Comparison of Protein Value of Commercial Baby Food with Homemade Baby Food and Casein Standard in Rats as the Refference point

    Directory of Open Access Journals (Sweden)

    Z. Asemi

    2008-10-01

    Full Text Available Background and ObjectivesEvaluation of protein quality in food is of great importance due to the biological and economical impacts of food proteins. This study has been conducted with the aim of comparing the protein quality of homemade food (mixture of macaroni and soy bean with commercial baby food (Cerelac Wheat using Casein as the refference point.MethodsThis study was conducted on 64 twenty one day old male Wistar rats. The rats were divided into 8 groups, and each group was put on a different diet regiments. The diet regiments were as follow: 2 homemade food+Cerelac test diet, 1 Ccasein+Methionine standard diet, 1 protien-free basal diet, 2 test diet, 1 standard diet and 1 basal diet. The purpose of protien-free diet was to evaluate True Protien Digestability (TPD. Net Protein Ratio (NPR and Protien Efficiency Ratios (PER were investigated by the basal diet. Protein intake and increasing of weight were determined for NPR and PER calculating. Nitrogen intake and fecal Nitrogen were determined to calculate TPD. Comparison of TPD, NPR and PER among the groups were analyzed by ANOVA and Tukey methods.ResultsTPD values of Standard, Cerelac and homemade food diets were 92.8±4, 87±8 and 85.4±3.2; NPR values were 4.3±0.4, 4.3±0.9, 3.8±0.6; and PER values were 3±0.2, 2.5±0.4, 1.7±0.1 respectively. The statistical difference between TPD and PER values were significant (p 0.05. ConclusionThese results shows that TPD and PER of homemade foods are lower than Cerelac while their NPR are acceptable.Keywords: Protein; Cerelac; Macaroni; Soybeens.

  8. INFLUENCE OF DIFFERENT FOOD ADDITIVES AND INGREDIENTS ON THE TECHNOLOGICAL CHARACTERISTICS OF ANIMAL PROTEINS

    Directory of Open Access Journals (Sweden)

    N. A. Drozdova

    2016-01-01

    Full Text Available In the present review, we focus on the features of the collagen structure. In particular, we report the correlation between the amount of proline and hydroxyproline and the temperature of denaturation, as well as the changes of collagen structure after thermal treatment. After cooling, denaturated collagen forms dense jellies which may absorb a large amount of water. The influence of pH on the denaturalion temperature, solubility andthe strength characteristics of collagen-containing proteins are described. The review also describes the data on the influence of various food additives and chemicals (acids, alkalis, salts i.a. phosphates, hydrocolloids on the collagen protein structure and technological properties. The effect of acids, alkalis, salts on the properties of collagen dependson the nature and strength of the ions and their affinity for the collagen ions. The interactions between the collagen proteins and hydrocolloids result in the synergetic effect. Phosphates and collagen form solid structures.

  9. Uses of Phage Display in Agriculture: A Review of Food-Related Protein-Protein Interactions Discovered by Biopanning over Diverse Baits

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

  10. Impact of fried foods on macronutrient intake, with special reference to fat and protein.

    Directory of Open Access Journals (Sweden)

    Henry, CJ K.

    1998-08-01

    Full Text Available Thermal treatment of protein is known to reduce protein quality and the destruction of certain amino acids. Fish and chips still remain a popular food source in Britain. Little work has been done on the changes in protein quality during fish frying. The paper will present results obtained from the assessment of protein quality using net protein utilisation (NPU in fried and steamed fish. Weanling male Sprague-Dawley rats were given stock diet {RM1 expanded, SDS Ltd., Witham, Essex for 7 days at 30 days of age, groups of four were offered one of four diets that differed only in the type of fish and processing used. Diets contained 200g of fish protein, 550g carbohydrate (400g sucrose and 150g corn-meal, 50g mineral and vitamin mix and 200g fat/kg diet. The different fish species used were Cod and Plaice and the processing used was either steaming or frying. Although a fall in NPU was noted in fried fish compared to the steamed fish these changes in NPU could be reduced if the fish was covered with batter prior to frying.

  11. Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes.

    Science.gov (United States)

    McVeigh, Paul; McCammick, Erin; McCusker, Paul; Wells, Duncan; Hodgkinson, Jane; Paterson, Steve; Mousley, Angela; Marks, Nikki J; Maule, Aaron G

    2018-02-05

    G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc) of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and

  12. Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes

    Directory of Open Access Journals (Sweden)

    Paul McVeigh

    2018-04-01

    Full Text Available G protein-coupled receptors (GPCRs are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in

  13. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    Directory of Open Access Journals (Sweden)

    Boucher Charles AB

    2010-07-01

    Full Text Available Abstract Background The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics. Results Our analyses show that human proteins interacting with HIV form a densely connected and central sub-network within the total human protein interaction network. The evaluation of this sub-network for connectivity and centrality resulted in a set of proteins essential for the HIV life-cycle. Remarkably, we were able to associate proteins involved in RNA polymerase II transcription with hubs and proteasome formation with bottlenecks. Inferred network motifs show significant over-representation of positive and negative feedback patterns between virus and host. Strikingly, such patterns have never been reported in combined virus-host systems. Conclusions HIV infection results in a reprioritization of cellular processes reflected by an increase in the relative importance of transcriptional machinery and proteasome formation. We conclude that during the evolution of HIV, some patterns of interaction have been selected for resulting in a system where virus proteins preferably interact with central human proteins for direct control and with proteasomal proteins for indirect control over the cellular processes. Finally, the patterns described by network motifs illustrate how virus and host interact with one another.

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

    DEFF Research Database (Denmark)

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

    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...... 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....... 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...

  15. A set of descriptors for identifying the protein-drug interaction in cellular networking.

    Science.gov (United States)

    Nanni, Loris; Lumini, Alessandra; Brahnam, Sheryl

    2014-10-21

    The study of protein-drug interactions is a significant issue for drug development. Unfortunately, it is both expensive and time-consuming to perform physical experiments to determine whether a drug and a protein are interacting with each other. Some previous attempts to design an automated system to perform this task were based on the knowledge of the 3D structure of a protein, which is not always available in practice. With the availability of protein sequences generated in the post-genomic age, however, a sequence-based solution to deal with this problem is necessary. Following other works in this area, we propose a new machine learning system based on several protein descriptors extracted from several protein representations, such as, variants of the position specific scoring matrix (PSSM) of proteins, the amino-acid sequence, and a matrix representation of a protein. The prediction engine is operated by an ensemble of support vector machines (SVMs), with each SVM trained on a specific descriptor and the results of each SVM combined by sum rule. The overall success rate achieved by our final ensemble is notably higher than previous results obtained on the same datasets using the same testing protocols reported in the literature. MATLAB code and the datasets used in our experiments are freely available for future comparison at http://www.dei.unipd.it/node/2357. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Identifying the Proteins that Mediate the Ionizing Radiation Resistance of Deinococcus Radiodurans R1

    Energy Technology Data Exchange (ETDEWEB)

    Battista, John R

    2010-02-22

    The primary objectives of this proposal was to define the subset of proteins required for the ionizing radiation (IR) resistance of Deinococcus radiodurans R1, characterize the activities of those proteins, and apply what was learned to problems of interest to the Department of Energy.

  17. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    NARCIS (Netherlands)

    D. van Dijk (David); G. Ertaylan (Gokhan); C.A.B. Boucher (Charles); P.M.A. Sloot (Peter)

    2010-01-01

    textabstractBackground: The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally

  18. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    NARCIS (Netherlands)

    van Dijk, D.; Ertaylan, G.; Boucher, C.A.B.; Sloot, P.M.A.

    2010-01-01

    Background: The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and

  19. An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates.

    Science.gov (United States)

    Hawley, Robert G; Chen, Yuzhong; Riz, Irene; Zeng, Chen

    2012-05-04

    In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

  20. Central site monitoring: results from a test of accuracy in identifying trials and sites failing Food and Drug Administration inspection.

    Science.gov (United States)

    Lindblad, Anne S; Manukyan, Zorayr; Purohit-Sheth, Tejashri; Gensler, Gary; Okwesili, Paul; Meeker-O'Connell, Ann; Ball, Leslie; Marler, John R

    2014-04-01

    Site monitoring and source document verification account for 15%-30% of clinical trial costs. An alternative is to streamline site monitoring to focus on correcting trial-specific risks identified by central data monitoring. This risk-based approach could preserve or even improve the quality of clinical trial data and human subject protection compared to site monitoring focused primarily on source document verification. To determine whether a central review by statisticians using data submitted to the Food and Drug Administration (FDA) by clinical trial sponsors can identify problem sites and trials that failed FDA site inspections. An independent Analysis Center (AC) analyzed data from four anonymous new drug applications (NDAs) where FDA had performed site inspections overseen by FDA's Office of Scientific Investigations (OSI). FDA team members in the OSI chose the four NDAs from among all NDAs with data in Study Data Tabulation Model (SDTM) format. Two of the NDAs had data that OSI had deemed unreliable in support of the application after FDA site inspections identified serious data integrity problems. The other two NDAs had clinical data that OSI deemed reliable after site inspections. At the outset, the AC knew only that the experimental design specified two NDAs with significant problems. FDA gave the AC no information about which NDAs had problems, how many sites were inspected, or how many were found to have problems until after the AC analysis was complete. The AC evaluated randomization balance, enrollment patterns, study visit scheduling, variability of reported data, and last digit reference. The AC classified sites as 'High Concern', 'Moderate Concern', 'Mild Concern', or 'No Concern'. The AC correctly identified the two NDAs with data deemed unreliable by OSI. In addition, central data analysis correctly identified 5 of 6 (83%) sites for which FDA recommended rejection of data and 13 of 15 sites (87%) for which any regulatory deviations were

  1. Release of skeletal muscle peptide fragments identifies individual proteins degraded during insulin deprivation in type 1 diabetic humans and mice.

    Science.gov (United States)

    Robinson, Matthew M; Dasari, Surendra; Karakelides, Helen; Bergen, H Robert; Nair, K Sreekumaran

    2016-09-01

    Insulin regulates skeletal muscle protein degradation, but the types of proteins being degraded in vivo remain to be determined due to methodological limitations. We present a method to assess the types of skeletal muscle proteins that are degraded by extracting their degradation products as low-molecular weight (LMW) peptides from muscle samples. High-resolution mass spectrometry was used to identify the original intact proteins that generated the LMW peptides, which we validated in rodents and then applied to humans. We deprived insulin from insulin-treated streptozotocin (STZ) diabetic mice for 6 and 96 h and for 8 h in type 1 diabetic humans (T1D) for comparison with insulin-treated conditions. Protein degradation was measured using activation of autophagy and proteasome pathways, stable isotope tracers, and LMW approaches. In mice, insulin deprivation activated proteasome pathways and autophagy in muscle homogenates and isolated mitochondria. Reproducibility analysis of LMW extracts revealed that ∼80% of proteins were detected consistently. As expected, insulin deprivation increased whole body protein turnover in T1D. Individual protein degradation increased with insulin deprivation, including those involved in mitochondrial function, proteome homeostasis, nDNA support, and contractile/cytoskeleton. Individual mitochondrial proteins that generated more LMW fragment with insulin deprivation included ATP synthase subunit-γ (+0.5-fold, P = 0.007) and cytochrome c oxidase subunit 6 (+0.305-fold, P = 0.03). In conclusion, identifying LMW peptide fragments offers an approach to determine the degradation of individual proteins. Insulin deprivation increases degradation of select proteins and provides insight into the regulatory role of insulin in maintaining proteome homeostasis, especially of mitochondria. Copyright © 2016 the American Physiological Society.

  2. Immunological analysis of food proteins using high-performance thin-layer chromatography-immunostaining.

    Science.gov (United States)

    Morschheuser, Lena; Mink, Kathrin; Horst, Ramona; Kallinich, Constanze; Rohn, Sascha

    2017-12-01

    The chromatographic analysis of intact proteins is still challenging, especially when biological functions as antigenicity of proteins or peptides are in the focus. Traditional immunoassays provide information about the entirety of antigenic proteins/peptides, e.g., in ELISA assays. On the other hand, when focusing on the investigation of (cross) reactivity of antibodies, Western blot following gel-electrophoresis represents the method of choice. However, gel-electrophoresis is limited by the molecular weight and therefore, not suitable for peptides ≤3kDa or proteins ≥250kDa. Furthermore, for gaining detailed information about the protein sequence (e.g., via mass spectrometric analysis), a so called in-gel digest needs to be performed following electrophoretic separation and is therefore elaborate and accompanied by a significant loss of structural, and even more severe, conformational information. Here, protein analysis using HPTLC seems to be a promising alternative due to the high level of variability regarding the chromatographic system (multiple mobile and stationary phases, even mixed) and manifold detection as well as hyphenation possibilities. This study exemplarily focused on the immunological investigation of proteins in milk following thin-layer chromatographic separation. The detection of these antigens is mandatory, as they might trigger allergenic reactions in sensitized people. Besides the proof of its applicability on different stationary phase materials, the newly developed immunoassay can be used as an approach for semi-quantitative estimation of antigenic proteins. In addition to the analysis of intact food allergens, also analyzing peptides thereof is worth considering which can be realized using HPTLC-immunostaining as well. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells.

    Directory of Open Access Journals (Sweden)

    Carina Banning

    2010-02-01

    Full Text Available Försters resonance energy transfer (FRET microscopy is widely used for the analysis of protein interactions in intact cells. However, FRET microscopy is technically challenging and does not allow assessing interactions in large cell numbers. To overcome these limitations we developed a flow cytometry-based FRET assay and analysed interactions of human and simian immunodeficiency virus (HIV and SIV Nef and Vpu proteins with cellular factors, as well as HIV Rev multimer-formation.Amongst others, we characterize the interaction of Vpu with CD317 (also termed Bst-2 or tetherin, a host restriction factor that inhibits HIV release from infected cells and demonstrate that the direct binding of both is mediated by the Vpu membrane-spanning region. Furthermore, we adapted our assay to allow the identification of novel protein interaction partners in a high-throughput format.The presented combination of FRET and FACS offers the precious possibility to discover and define protein interactions in living cells and is expected to contribute to the identification of novel therapeutic targets for treatment of human diseases.

  4. Identifying the ICT challenges of the Agri-Food sector to define the Architectural Requirements for a Future Internet Core Platform

    NARCIS (Netherlands)

    Brewster, C.A.; Wolfert, J.; Sundmaeker, H.

    2012-01-01

    This paper discusses the specific challenges of the agri-food sector in the light of research carried out in the SmartAgriFood project. Using questionnaires and focus groups, our research identifies a number of business needs and drivers which enable the identification of suitable Future Internet

  5. The development of a preference for cocaine over food identifies individual rats with addiction-like behaviors.

    Science.gov (United States)

    Perry, Adam N; Westenbroek, Christel; Becker, Jill B

    2013-01-01

    Cocaine dependence is characterized by compulsive drug taking that supercedes other recreational, occupational or social pursuits. We hypothesized that rats vulnerable to addiction could be identified within the larger population based on their preference for cocaine over palatable food rewards. To validate the choice self-administration paradigm as a preclinical model of addiction, we examined changes in motivation for cocaine and recidivism to drug seeking in cocaine-preferring and pellet-preferring rats. We also examined behavior in males and females to identify sex differences in this "addicted" phenotype. Preferences were identified during self-administration on a fixed-ratio schedule with cocaine-only, pellet-only and choice sessions. Motivation for each reward was probed early and late during self-administration using a progressive-ratio schedule. Reinstatement of cocaine- and pellet-seeking was examined following exposure to their cues and non-contingent delivery of each reward. Cocaine preferring rats increased their drug intake at the expense of pellets, displayed increased motivation for cocaine, attenuated motivation for pellets and greater cocaine and cue-induced reinstatement of drug seeking. Females were more likely to develop cocaine preferences and recidivism of cocaine- and pellet-seeking was sexually dimorphic. The choice self-administration paradigm is a valid preclinical model of addiction. The unbiased selection criteria also revealed sex-specific vulnerability factors that could be differentiated from generalized sex differences in behavior, which has implications for the neurobiology of addiction and effective treatments in each sex.

  6. High-Protein Foods and Physical Activity Protect Against Age-Related Muscle Loss and Functional Decline.

    Science.gov (United States)

    Bradlee, M Loring; Mustafa, Jabed; Singer, Martha R; Moore, Lynn L

    2017-12-12

    Some clinical trials suggest that protein supplementation enhances the effects of resistance exercise on skeletal muscle mass (SMM); fewer studies examine the effects of diets rich in protein-source foods on SMM and functional status among community-dwelling adults. Data from the Framingham Offspring study including diet (three-day records, exams 3 and 5), physical activity (exams 2 and 4), percent SMM (%SMM) (exams 6 and 7), and functional performance (exams 5 through 8) were used to evaluate independent and combined effects of physical activity and high-protein foods on adjusted mean %SMM (using analysis of covariance) and risk of functional decline (using Cox proportional hazard's models). Analyses were adjusted for such factors as age, education, height, smoking, and fruit and grain consumption). Higher intakes of protein-source foods (red meat, poultry, fish, dairy, and soy, nuts, seeds and legumes) were associated with higher %SMM over 9 years, particularly among women. Men and women with higher intakes of foods from animal sources had a higher % SMM regardless of activity; beneficial effects of plant-based protein foods were only evident in physically active adults. Active subjects with higher intakes of animal or plant protein-source foods had 35% lowest risks of functional decline. Among less active individuals, only those consuming more animal protein-source foods had reduced risks of functional decline (HR: 0.7l; 95% CI: 0.50-1.01). Higher intake of animal-protein foods, alone and especially in combination with a physically active lifestyle, was associated with preservation of muscle mass and functional performance in older adults. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. [Functional analysis of cancer-derived immunoglobulin G whole molecule-interacting proteins identified by LC-MS/MS].

    Science.gov (United States)

    Wang, Ju-Ping; Chen, Han-Ying; Peng, Hui

    2015-01-01

    To identify cancer-derived immunoglobulin G (IgG) whole molecule-interacting proteins to provide important clues for studying IgG biological functions. HeLa cell lysate was immunoprecipitated with rabbit antihuman IgG whole molecule antibody and normal rabbit IgG. The immunocomplex underwent sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and was detected with silver staining. Three prominently enhanced bands were subjected to protein identification with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the MS data were analyzed with Swiss-Prot database. Cancer-derived IgG whole molecule-interacting proteins were screened and functionally annotated. We identified 6 potential cancer-derived IgG whole molecule-interacting proteins with co-immunoprecipitation combined with LC-MS/MS, which provides valuable clues for studying the function of cancer-derived IgG.

  8. A protein-binding domain, EH, identified in the receptor tyrosine kinase substrate Eps15 and conserved in evolution

    DEFF Research Database (Denmark)

    Wong, W T; Schumacher, C; Salcini, A E

    1995-01-01

    In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several heteroge......In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several...... heterogeneous proteins of yeast and nematode. The EH domain spans about 70 amino acids and shows approximately 60% overall amino acid conservation. We demonstrated the ability of the EH domain to specifically bind cytosolic proteins in normal and malignant cells of mesenchymal, epithelial, and hematopoietic...

  9. FORAGING BY THE STOPLIGHT-PARROTFISH SPARISOMA-VIRIDE .2. INTAKE AND ASSIMILATION OF FOOD, PROTEIN AND ENERGY

    NARCIS (Netherlands)

    BRUGGEMANN, JH; BEGEMAN, J; BOSMA, EM; VERBURG, P; BREEMAN, AM

    Daily food intake by the herbivorous parrotfish Sparisoma viride, as well as assimilation efficiencies of algal food, protein and energy, were quantified through a combination of laboratory feeding trials and field observations. The intake of algal ash-free dry wt (AFDW) per bite increases linearly

  10. Detection of genetically modified organisms in foods by protein- and DNA-based techniques : bridging the methods

    NARCIS (Netherlands)

    Duijn, G. van; Biert, R. van; Bleeker-Marcelis, H.; Boeijen, I. van; Adan, A.J.; Jhakrie, S.; Hessing, M.

    2002-01-01

    According to European Commission (EC) Regulation 1139/98, foods and food ingredients that are to be delivered to the final consumer in which either protein or DNA resulting from genetic modification is present, shall be subject to additional specific labeling requirements. Since 1994, genetically

  11. Feeding difficulties in children with food protein-induced gastrointestinal allergies.

    Science.gov (United States)

    Meyer, Rosan; Rommel, Nathalie; Van Oudenhove, Lukas; Fleming, Catharine; Dziubak, Robert; Shah, Neil

    2014-10-01

    There is paucity of data on the prevalence of feeding difficulties in Food Protein-Induced Gastrointestinal Allergies (FPIGA) and their clinical characteristics. However, it is a commonly reported problem by clinicians. We set out to establish the occurrence of feeding difficulties in children with FPIGA, the association with gastrointestinal and extra-intestinal symptoms and number of foods eliminated from the diet. This retrospective observational analysis was performed in patients seen between 2002 and 2009 at Great Ormond Street Children's Hospital, Gastroenterology Department, London. Medical records where FPIGA was documented using the terms from the National Institute of Allergy and Infectious Disease and National Institute of Clinical Excellence and confirmed using an elimination diet, followed by a challenge were included. Feeding difficulties were assessed using a criteria previously used in healthy toddlers in the UK. Data from 437 children (203 female) were collected. Significantly more children with feeding difficulties presented with abdominal distention and bloating (P = 0.002), vomiting (P foods eliminated from the diet in the children with/without feeding difficulties (P = 0.028). Clinical manifestations like vomiting, constipation, rectal bleeding, weight loss, and the presence of extra-intestinal manifestations in addition to the number of foods avoided are in our FPIGA population linked to feeding difficulties. © 2014 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  12. A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

    OpenAIRE

    Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena; Dahl, Christiane

    2014-01-01

    In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altere...

  13. Mem-ADSVM: A two-layer multi-label predictor for identifying multi-functional types of membrane proteins.

    Science.gov (United States)

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

    2016-06-07

    Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. However, most of the existing membrane-protein predictors have the following problems: (1) they do not predict whether a given protein is a membrane protein or not; (2) they are limited to predicting membrane proteins with single-label functional types but ignore those with multi-functional types; and (3) there is still much room for improvement for their performance. To address these problems, this paper proposes a two-layer multi-label predictor, namely Mem-ADSVM, which can identify membrane proteins (Layer I) and their multi-functional types (Layer II). Specifically, given a query protein, its associated gene ontology (GO) information is retrieved by searching a compact GO-term database with its homologous accession number. Subsequently, the GO information is classified by a binary support vector machine (SVM) classifier to determine whether it is a membrane protein or not. If yes, it will be further classified by a multi-label multi-class SVM classifier equipped with an adaptive-decision (AD) scheme to determine to which functional type(s) it belongs. Experimental results show that Mem-ADSVM significantly outperforms state-of-the-art predictors in terms of identifying both membrane proteins and their multi-functional types. This paper also suggests that the two-layer prediction architecture is better than the one-layer for prediction performance. For reader׳s convenience, the Mem-ADSVM server is available online at http://bioinfo.eie.polyu.edu.hk/MemADSVMServer/. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Quality evaluation of rice bran protein isolate-based weaning food for preschoolers.

    Science.gov (United States)

    Khan, Saima H; Butt, Masood S; Anjum, Faqir M; Sameen, Ayesha

    2011-05-01

    Agro-industrial waste 'rice bran' was stabilized and the extracted protein isolates were used as ingredients to make nutritive complimentary food for the growing infants. The formulation processed through drum drying and the starchy ingredients were pregelatinized to reduce bulk in the prepared meal and facilitate spoon-feeding. The formulations had uniform texture, light golden color and good paste consistency. Nutrient composition was good enough to meet standards for supplementary infant foods. Caloric value remained up to 416 kcal/100 g with spoonable viscosity and 80.90-84.45% in vitro digestibility. A single meal could substantially contribute to the daily essential amino acid requirement. The formulation had good acceptability during a short-term infant-feeding trial. The present study can provide practical guideline for manufacturers as well as the nutritionist for the use of an economical and nutritive formulation for young children.

  15. Identifying and engineering promoters for high level and sustainable therapeutic recombinant protein production in cultured mammalian cells.

    Science.gov (United States)

    Ho, Steven C L; Yang, Yuansheng

    2014-08-01

    Promoters are essential on plasmid vectors to initiate transcription of the transgenes when generating therapeutic recombinant proteins expressing mammalian cell lines. High and sustained levels of gene expression are desired during therapeutic protein production while gene expression is useful for cell engineering. As many finely controlled promoters exhibit cell and product specificity, new promoters need to be identified, optimized and carefully evaluated before use. Suitable promoters can be identified using techniques ranging from simple molecular biology methods to modern high-throughput omics screenings. Promoter engineering is often required after identification to either obtain high and sustained expression or to provide a wider range of gene expression. This review discusses some of the available methods to identify and engineer promoters for therapeutic recombinant protein expression in mammalian cells.

  16. A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum.

    Science.gov (United States)

    Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena; Dahl, Christiane

    2014-04-01

    In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515).

  17. Molecular Characterization and Functional Analysis of PR-1-Like Proteins Identified from the Wheat Head Blight Fungus Fusarium graminearum.

    Science.gov (United States)

    Lu, Shunwen; Edwards, Michael C

    2018-04-01

    The group 1 pathogenesis-related (PR-1) proteins originally identified from plants and their homologs are also found in other eukaryotic kingdoms. Studies on nonplant PR-1-like (PR-1L) proteins have been pursued widely in humans and animals but rarely in filamentous ascomycetes. Here, we report the characterization of four PR-1L proteins identified from the ascomycete fungus Fusarium graminearum, the primary cause of Fusarium head blight of wheat and barley (designated FgPR-1L). Molecular cloning revealed that the four FgPR-1L proteins are all encoded by small open reading frames (612 to 909 bp) that are often interrupted by introns, in contrast to plant PR-1 genes that lack introns. Sequence analysis indicated that all FgPR-1L proteins contain the PR-1-specific three-dimensional structure, and one of them features a C-terminal transmembrane (TM) domain that has not been reported for any stand-alone PR-1 proteins. Transcriptional analysis revealed that the four FgPR-1L genes are expressed in axenic cultures and in planta with different spatial or temporal expression patterns. Phylogenetic analysis indicated that fungal PR-1L proteins fall into three major groups, one of which harbors FgPR-1L-2-related TM-containing proteins from both phytopathogenic and human-pathogenic ascomycetes. Low-temperature sodium dodecyl sulfate polyacrylamide gel electrophoresis and proteolytic assays indicated that the recombinant FgPR-1L-4 protein exists as a monomer and is resistant to subtilisin of the serine protease family. Functional analysis confirmed that deletion of the FgPR-1L-4 gene from the fungal genome results in significantly reduced virulence on susceptible wheat. This study provides the first example that the F. graminearum-wheat interaction involves a pathogen-derived PR-1L protein that affects fungal virulence on the host.

  18. A Novel Feature Extraction Method with Feature Selection to Identify Golgi-Resident Protein Types from Imbalanced Data.

    Science.gov (United States)

    Yang, Runtao; Zhang, Chengjin; Gao, Rui; Zhang, Lina

    2016-02-06

    The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew's Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions.

  19. Comparative genome analysis to identify SNPs associated with high oleic acid and elevated protein content in soybean.

    Science.gov (United States)

    Kulkarni, Krishnanand P; Patil, Gunvant; Valliyodan, Babu; Vuong, Tri D; Shannon, J Grover; Nguyen, Henry T; Lee, Jeong-Dong

    2018-03-01

    The objective of this study was to determine the genetic relationship between the oleic acid and protein content. The genotypes having high oleic acid and elevated protein (HOEP) content were crossed with five elite lines having normal oleic acid and average protein (NOAP) content. The selected accessions were grown at six environments in three different locations and phenotyped for protein, oil, and fatty acid components. The mean protein content of parents, HOEP, and NOAP lines was 34.6%, 38%, and 34.9%, respectively. The oleic acid concentration of parents, HOEP, and NOAP lines was 21.7%, 80.5%, and 20.8%, respectively. The HOEP plants carried both FAD2-1A (S117N) and FAD2-1B (P137R) mutant alleles contributing to the high oleic acid phenotype. Comparative genome analysis using whole-genome resequencing data identified six genes having single nucleotide polymorphism (SNP) significantly associated with the traits analyzed. A single SNP in the putative gene Glyma.10G275800 was associated with the elevated protein content, and palmitic, oleic, and linoleic acids. The genes from the marker intervals of previously identified QTL did not carry SNPs associated with protein content and fatty acid composition in the lines used in this study, indicating that all the genes except Glyma.10G278000 may be the new genes associated with the respective traits.

  20. In-frame cDNA library combined with protein complementation assay identifies ARL11-binding partners.

    Directory of Open Access Journals (Sweden)

    Sangkyou Lee

    Full Text Available The cDNA expression libraries that produce correct proteins are essential in facilitating the identification of protein-protein interactions. The 5'-untranslated regions (UTRs that are present in the majority of mammalian and non-mammalian genes are predicted to alter the expression of correct proteins from cDNA libraries. We developed a novel cDNA expression library from which 5'-UTRs were removed using a mixture of polymerase chain reaction primers that complement the Kozak sequences we refer to as an "in-frame cDNA library." We used this library with the protein complementation assay to identify two novel binding partners for ras-related ADP-ribosylation factor-like 11 (ARL11, cellular retinoic acid binding protein 2 (CRABP2, and phosphoglycerate mutase 1 (PGAM1. Thus, the in-frame cDNA library without 5'-UTRs we describe here increases the chance of correctly identifying protein interactions and will have wide applications in both mammalian and non-mammalian detection systems.

  1. Use of protein-engineered fabrics to identify design rules for integrin ligand clustering in biomaterials.

    Science.gov (United States)

    Benitez, Patrick L; Mascharak, Shamik; Proctor, Amy C; Heilshorn, Sarah C

    2016-01-01

    While ligand clustering is known to enhance integrin activation, this insight has been difficult to apply to the design of implantable biomaterials because the local and global ligand densities that enable clustering-enhanced integrin signaling were unpredictable. Here, two general design principles for biomaterial ligand clustering are elucidated. First, clustering ligands enhances integrin-dependent signals when the global ligand density, i.e., the ligand density across the cellular length scale, is near the ligand's effective dissociation constant (KD,eff). Second, clustering ligands enhances integrin activation when the local ligand density, i.e., the ligand density across the length scale of individual focal adhesions, is less than an overcrowding threshold. To identify these principles, we fabricated a series of elastin-like, electrospun fabrics with independent control over the local (0 to 122 000 ligands μm(-2)) and global (0 to 71 000 ligand μm(-2)) densities of an arginine-glycine-aspartate (RGD) ligand. Antibody blocking studies confirmed that human umbilical vein endothelial cell adhesion to these protein-engineered biomaterials was primarily due to αVβ3 integrin binding. Clustering ligands enhanced cell proliferation, focal adhesion number, and focal adhesion kinase expression near the ligand's KD,eff of 12 000 RGD μm(-2). Near this global ligand density, cells on ligand-clustered fabrics behaved similarly to cells grown on fabrics with significantly larger global ligand densities but without clustering. However, this enhanced ligand-clustering effect was not observed above a threshold cut-off concentration. At a local ligand density of 122 000 RGD μm(-2), cell division, focal adhesion number, and focal adhesion kinase expression were significantly reduced relative to fabrics with identical global ligand density and lesser local ligand densities. Thus, when clustering results in overcrowding of ligands, integrin receptors are no longer

  2. A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins

    NARCIS (Netherlands)

    Soni, Siddarth; Raaijmakers, Antonia J A; Raaijmakers, Linsey M; Damen, J Mirjam A; van Stuijvenberg, Leonie; Vos, Marc A; Heck, Albert J R; van Veen, Toon A B; Scholten, Arjen

    2016-01-01

    AIMS: Synchronous beating of the heart is dependent on the efficient functioning of the cardiac intercalated disk (ID). The ID is composed of a complex protein network enabling electrical continuity and chemical communication between individual cardiomyocytes. Recently, several different studies

  3. College students identify university support for basic needs and life skills as key ingredient in addressing food insecurity on campus

    Directory of Open Access Journals (Sweden)

    Tyler D. Watson

    2017-09-01

    Full Text Available A recent University of California (UC systemwide survey showed that 42% of UC college students experience food insecurity, consistent with other studies among U.S. college students. As part of UC's efforts to understand and address student food insecurity, we conducted 11 focus group interviews across four student subpopulations at UC Los Angeles (n = 82. We explored student experiences, perceptions and concerns related to both food insecurity and food literacy, which may help protect students against food insecurity. Themes around food insecurity included student awareness about food insecurity, cost of university attendance, food insecurity consequences, and coping strategies. Themes around food literacy included existing knowledge and skills, enjoyment and social cohesion, and learning in the dining halls. Unifying themes included the campus food environment not meeting student needs, a desire for practical financial and food literacy “life skills” training, and skepticism about the university's commitment to adequately address student basic needs. The results of this study broadly suggest there is opportunity for the university to address student food insecurity through providing food literacy training, among other strategies.

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

    Science.gov (United States)

    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.

  5. iTRAQ-Based Quantitative Proteomics Identifies Potential Regulatory Proteins Involved in Chicken Eggshell Brownness.

    Directory of Open Access Journals (Sweden)

    Guangqi Li

    Full Text Available Brown eggs are popular in many countries and consumers regard eggshell brownness as an important indicator of egg quality. However, the potential regulatory proteins and detailed molecular mechanisms regulating eggshell brownness have yet to be clearly defined. In the present study, we performed quantitative proteomics analysis with iTRAQ technology in the shell gland epithelium of hens laying dark and light brown eggs to investigate the candidate proteins and molecular mechanisms underlying variation in chicken eggshell brownness. The results indicated 147 differentially expressed proteins between these two groups, among which 65 and 82 proteins were significantly up-regulated in the light and dark groups, respectively. Functional analysis indicated that in the light group, the down-regulated iron-sulfur cluster assembly protein (Iba57 would decrease the synthesis of protoporphyrin IX; furthermore, the up-regulated protein solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator, member 5 (SLC25A5 and down-regulated translocator protein (TSPO would lead to increased amounts of protoporphyrin IX transported into the mitochondria matrix to form heme with iron, which is supplied by ovotransferrin protein (TF. In other words, chickens from the light group produce less protoporphyrin IX, which is mainly used for heme synthesis. Therefore, the exported protoporphyrin IX available for eggshell deposition and brownness is reduced in the light group. The current study provides valuable information to elucidate variation of chicken eggshell brownness, and demonstrates the feasibility and sensitivity of iTRAQ-based quantitative proteomics analysis in providing useful insights into the molecular mechanisms underlying brown eggshell pigmentation.

  6. A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins.

    Directory of Open Access Journals (Sweden)

    Siddarth Soni

    Full Text Available Synchronous beating of the heart is dependent on the efficient functioning of the cardiac intercalated disk (ID. The ID is composed of a complex protein network enabling electrical continuity and chemical communication between individual cardiomyocytes. Recently, several different studies have shed light on increasingly prevalent cardiac diseases involving the ID. Insufficient knowledge of its composition makes it difficult to study these disease mechanisms in more detail and therefore here we aim expand the ID proteome. Here, using a combination of general membrane enrichment, in-depth quantitative proteomics and an intracellular location driven bioinformatics approach, we aim to discover new putative ID proteins in rat ventricular tissue.General membrane isolation, enriched amongst others also with ID proteins as based on presence of the established markers connexin-43 and n-cadherin, was performed using centrifugation. By mass spectrometry, we quantitatively evaluated the level of 3455 proteins in the enriched membrane fraction (EMF and its counterpart, the soluble cytoplasmic fraction. These data were stringently filtered to generate a final set of 97 enriched, putative ID proteins. These included Cx43 and n-cadherin, but also many interesting novel candidates. We selected 4 candidates (Flotillin-2 (FLOT2, Nexilin (NEXN, Popeye-domain-containg-protein 2 (POPDC2 and thioredoxin-related-transmembrane-protein 2 (TMX2 and confirmed their co-localization with n-cadherin in the ID of human and rat heart cryo-sections, and isolated dog cardiomyocytes.The presented proteomics dataset of putative new ID proteins is a valuable resource for future research into this important molecular intersection of the heart.

  7. Is eating science or common sense? Knowledge about "natural foods" among self-identified "natural food" consumers, vendors and producers in rural and urban Mexico.

    Science.gov (United States)

    Kooijmans, Anneke; Flores-Palacios, Fátima

    2014-10-01

    To explore the common sense knowledge that consumers, vendors and producers hold of "natural foods". The focus was on common knowledge because this is infrequently explored in social psychology where most studies focus on the implementation of scientific knowledge. The focus was on natural foods because the naturalness of foods seems to be one of the particular concerns that current consumers have about today's food market and because a specific natural food preference was observed in the contexts of study. Fifty-seven informants in a rural context and 58 informants in an urban context participated in either a free association study or an interview study. Data content were analyzed. In the urban context natural foods obtain their significance in the relationship between food and the self-concept; eating natural (or good) food is a task that requires effort and attitude, and foods obtain a moral value. In the rural context natural foods obtain their significance as an expression of a social and cultural system of interdependence that establishes practices and customs that have a long history in the community. It is suggested that these common knowledge systems are related to practical challenges that are particular to the informants' context and that the structure of their common sense knowledge systems depend on the mediation of the flow of scientific knowledge and technological knowledge in each context. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Using amino acid correlation and community detection algorithms to identify functional determinants in protein families.

    Directory of Open Access Journals (Sweden)

    Lucas Bleicher

    Full Text Available Correlated mutation analysis has a long history of interesting applications, mostly in the detection of contact pairs in protein structures. Based on previous observations that, if properly assessed, amino acid correlation data can also provide insights about functional sub-classes in a protein family, we provide a complete framework devoted to this purpose. An amino acid specific correlation measure is proposed, which can be used to build networks summarizing all correlation and anti-correlation patterns in a protein family. These networks can be submitted to community structure detection algorithms, resulting in subsets of correlated amino acids which can be further assessed by specific parameters and procedures that provide insight into the relationship between different communities, the individual importance of community members and the adherence of a given amino acid sequence to a given community. By applying this framework to three protein families with contrasting characteristics (the Fe/Mn-superoxide dismutases, the peroxidase-catalase family and the C-type lysozyme/α-lactalbumin family, we show how our method and the proposed parameters and procedures are related to biological characteristics observed in these protein families, highlighting their potential use in protein characterization and gene annotation.

  9. Principal components analysis of diet and alternatives for identifying the combination of foods that are associated with the risk of disease: a simulation study.

    Science.gov (United States)

    Bakolis, Ioannis; Burney, Peter; Hooper, Richard

    2014-07-14

    Dietary patterns derived empirically using principal components analysis (PCA) are widely employed for investigating diet-disease relationships. In the present study, we investigated whether PCA performed better at identifying such associations than an analysis of each food on a FFQ separately, referred to here as an exhaustive single food analysis (ESFA). Data on diet and disease were simulated using real FFQ data and by assuming a number of food intakes in combination that were associated with the risk of disease. In each simulation, ESFA and PCA were employed to identify the combinations of foods that are associated with the risk of disease using logistic regression, allowing for multiple testing and adjusting for energy intake. ESFA was also separately adjusted for principal components of diet, foods that were significant in the unadjusted ESFA and propensity scores. For each method, we investigated the power with which an association between diet and disease could be identified, and the power and false discovery rate (FDR) for identifying the specific combination of food intakes. In some scenarios, ESFA had greater power to detect a diet-disease association than PCA. ESFA also typically had a greater power and a lower FDR for identifying the combinations of food intakes that are associated with the risk of disease. The FDR of both methods increased with increasing sample size, but when ESFA was adjusted for foods that were significant in the unadjusted ESFA, FDR were controlled at the desired level. These results question the widespread use of PCA in nutritional epidemiology. The adjusted ESFA identifies the combinations of foods that are causally linked to the risk of disease with low FDR and surprisingly good power.

  10. On the value of seasonal mammals for identifying mechanisms underlying the control of food intake and body weight.

    Science.gov (United States)

    Ebling, Francis J P

    2014-06-01

    This article is part of a Special Issue "Energy Balance". Seasonal cycles of adiposity and body weight reflecting changes in both food intake and energy expenditure are the norm in mammals that have evolved in temperate and polar habitats. Innate circannual rhythmicity and direct responses to the annual change in photoperiod combine to ensure that behavior and energy metabolism are regulated in anticipation of altered energetic demands such as the energetically costly processes of hibernation, migration, and lactation. In the last decade, major progress has been made into identifying the central mechanisms that underlie these profound long-term changes in behavior and physiology. Surprisingly they are distinct from the peptidergic and aminergic systems in the hypothalamus that have been identified in studies of the laboratory mouse and rat and implicated in timing meal intervals and in short-term responses to caloric restriction. Comparative studies across rodents, ungulates and birds reveal that tanycytes embedded in the ependymal layer of the third ventricle play a critical role in seasonal changes because they regulate the local availability of thyroid hormone. Understanding how this altered hormonal environment might regulate neurogenesis and plasticity in the hypothalamus should provide new insight into development of strategies to manage appetite and body weight. Copyright © 2014 The Author. Published by Elsevier Inc. All rights reserved.

  11. An integrated approach to identifying and characterising resilient urban food systems to promote population health in a changing climate.

    Science.gov (United States)

    James, Sarah W; Friel, Sharon

    2015-09-01

    To determine key points of intervention in urban food systems to improve the climate resilience, equity and healthfulness of the whole system. The paper brings together evidence from a 3-year, Australia-based mixed-methods research project focused on climate change adaptation, cities, food systems and health. In an integrated analysis of the three research domains - encompassing the production, distribution and consumption sectors of the food chain - the paper examines the efficacy of various food subsystems (industrial, alternative commercial and civic) in achieving climate resilience and good nutrition. Greater Western Sydney, Australia. Primary producers, retailers and consumers in Western Sydney. This overarching analysis of the tripartite study found that: (i) industrial food production systems can be more environmentally sustainable than alternative systems, indicating the importance of multiple food subsystems for food security; (ii) a variety of food distributors stocking healthy and sustainable items is required to ensure that these items are accessible, affordable and available to all; and (iii) it is not enough that healthy and sustainable foods are produced or sold, consumers must also want to consume them. In summary, a resilient urban food system requires that healthy and sustainable food items are produced, that consumers can attain them and that they actually wish to purchase them. This capstone paper found that the interconnected nature of the different sectors in the food system means that to improve environmental sustainability, equity and population health outcomes, action should focus on the system as a whole and not just on any one sector.

  12. Utility of eButton images for identifying food preparation behaviors and meal-related tasks in adolescents

    Science.gov (United States)

    Food preparation skills may encourage healthy eating. Traditional assessment of child food preparation employs self- or parent proxy-reporting methods, which are prone to error. The eButton is a wearable all-day camera that has promise as an objective, passive method for measuring child food prepara...

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

    Science.gov (United States)

    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

  14. Research Approaches and Methods for Evaluating the Protein Quality of Human Foods Proposed by an FAO Expert Working Group in 2014.

    Science.gov (United States)

    Lee, Warren Tk; Weisell, Robert; Albert, Janice; Tomé, Daniel; Kurpad, Anura V; Uauy, Ricardo

    2016-05-01

    The Protein Digestibility Corrected Amino Acid Score (PDCAAS) has been adopted for assessing protein quality in human foods since 1991, and the shortcomings of using the PDCAAS have been recognized since its adoption. The 2011 FAO Expert Consultation recognized that the Digestible Indispensable Amino Acid Score (DIAAS) was superior to the PDCAAS for determining protein quality. However, there were insufficient human data on amino acid digestibility before adopting the DIAAS. More human data were needed before DIAAS could be implemented. In 2014, FAO convened an expert working group to propose and agree on research protocols using both human-based assays and animal models to study ileal amino acid digestibility (metabolic availability) of human foods. The working group identified 5 research protocols for further research and development. A robust database of protein digestibility of foods commonly consumed worldwide, including those consumed in low-income countries, is needed for an informed decision on adopting the DIAAS. A review on the impacts of using the DIAAS on public health policies is necessary. It would be advantageous to have a global coordinating effort to advance research and data collection. Collaboration with international and national agriculture institutes is desirable. Opportunities should be provided for young researchers, particularly those from developing countries, to engage in protein-quality research for sustainable implementation of DIAAS. To conclude, the DIAAS is a conceptually preferable method compared with the PDCAAS for protein and amino acid quality evaluation. However, the complete value of the DIAAS and its impact on public health nutrition cannot be realized until there are sufficient accumulated ileal amino acid digestibility data on human foods that are consumed in different nutritional and environmental conditions, measured by competent authorities. A future meeting may be needed to evaluate the size and quality of the data set

  15. Food Products Made With Glycomacropeptide, a Low Phenylalanine Whey Protein, Provide a New Alternative to Amino Acid-Based Medical Foods for Nutrition Management of Phenylketonuria

    Science.gov (United States)

    Van Calcar, Sandra C.; Ney, Denise M.

    2012-01-01

    Phenylketonuria (PKU), an inborn error in phenylalanine (phe) metabolism, requires lifelong nutrition management with a low-phe diet, which includes a phe-free amino acid-based medical formula to provide the majority of an individual’s protein needs. Compliance with this diet is often difficult for older children, adolescents and adults with PKU. The whey protein glycomacropeptide (GMP) is ideally suited for the PKU diet since it is naturally low in phe. Nutritionally complete, acceptable medical foods and beverages can be made with GMP to increase the variety of protein sources for the PKU diet. As an intact protein, GMP improves protein utilization and increases satiety compared with amino acids. Thus, GMP provides a new, more physiologic source of low-phe dietary protein for those with PKU. PMID:22818728

  16. A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

    Science.gov (United States)

    Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

    2015-02-01

    The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

  17. Detection of hidden hazelnut protein in food by IgY-based indirect competitive enzyme-immunoassay

    NARCIS (Netherlands)

    Baumgartner, S.; Bremer, M.G.E.G.; Kemmers - Voncken, A.E.M.; Smits, N.G.E.; Haasnoot, W.; Banks, J.; Reece, P.; Danks, C.; Tomkies, V.; Immer, U.; Schmitt, K.; Krska, R.

    2004-01-01

    The development of an indirect competitive enzyme-immunoassay for the detection of hidden hazelnut protein in complex food matrices is described. A sensitive and selective polyclonal antibody was raised by immunisation of laying hens with protein extracts from roasted hazelnuts. In contrast to

  18. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination.

    Science.gov (United States)

    Kegel, Linde; Jaegle, Martine; Driegen, Siska; Aunin, Eerik; Leslie, Kris; Fukata, Yuko; Watanabe, Masahiko; Fukata, Masaki; Meijer, Dies

    2014-04-01

    The cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been associated with epilepsy and amyelination. Their function involves interactions with ADAM22 and ADAM23 cell surface receptors, possibly in apposing membranes, thus attenuating cellular interactions. LGI4-ADAM22 interactions are required for axonal sorting and myelination in the developing peripheral nervous system (PNS). Functional analysis revealed that, despite their high homology and affinity for ADAM22, LGI proteins are functionally distinct. To dissect the key residues in LGI proteins required for coordinating axonal sorting and myelination in the developing PNS, we adopted a phylogenetic and computational approach and demonstrate that the mechanism of action of LGI4 depends on a cluster of three amino acids on the outer surface of the LGI4 protein, thus providing a structural basis for the mechanistic differences in LGI protein function in nervous system development and evolution.

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

    Science.gov (United States)

    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.

  20. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

    2017-09-05

    In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  1. Foods

    Science.gov (United States)

    Brennan, Charles

    2012-11-21

    There is one commodity the world over that unites mankind-food. In 2011 the United Nations claimed that the world's population had reached the seven billion mark, a number which is set to increase dramatically in the decades to come. Food security, supply and sustainability are of paramount concern to the future economic and social progress of humanity. It is the responsibility of the food industry, together with food scientists and technologists, to shoulder the burden of ensuring an adequate supply of nutritious, safe and sensorially acceptable foods for a range of demanding consumers. In responding to this challenge, we need to understand the link between agriculture, engineering, food processing, molecular biosciences, human nutrition, commercialisation and innovation. Access to information concerning the composition and quality of foods has never been so easy for consumers and technologists alike. A plethora of research publications are made available each month to scientists and associated interested parties. The outcomes of these research manuscripts are often distilled and disseminated into messages available to everyone through bulletin boards, forums and the popular press. Newspapers and new agencies constantly report on the latest pharma-medical finding, or news regarding food safety and security concerns. We live in an age where information is so readily available to everyone that the task of finding credible and reputable data can be difficult at times. Providing sound evidenced based research is where a peer-reviewed journal can provide clarity. [...].

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Bansal Amolak S

    2012-06-01

    Full Text Available Abstract Introduction 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 presentations 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. Conclusion 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.

  4. Hematochezia before the First Feeding in a Newborn with Food Protein-Induced Enterocolitis Syndrome

    Directory of Open Access Journals (Sweden)

    Masanori Mizuno

    2011-09-01

    Full Text Available The prevalence and incidence of food protein-induced enterocolitis syndrome (FPIES are clearly not known; its onset before first feeding at birth especially has been rarely reported. A female newborn was referred to our institution due to blood-stained diarrhea before her first feeding at birth. Examination of the stool with Wright-Giemsa staining on day 6 revealed numerous fecal eosinophils, including Charcot-Leyden crystals. Lymphocyte stimulation test (LST against cow's milk protein also showed positive values on day 12. The hematochezia resolved immediately after starting intravenous nutrition. She was fed with breast milk and extensively hydrolyzed formula and discharged from hospital on day 49. FPIES was diagnosed based on these symptoms and data. Our case was thought to have acquired allergic enterocolitis after sensitization in her fetal period, which caused severe FPIES triggered by the first intake of cow's milk soon after birth. The patient with FPIES presents atypical clinical findings, which is likely to cause misdiagnosis and delay of appropriate treatment. Heightened awareness and increased attention may be necessary to diagnose FPIES, even soon after birth. Evaluating fecal eosinophils and LST, which may be difficult to perform in every clinical hospital, is thought to be useful for the detection of FPIES without oral food challenge.

  5. Identifying interventions to help rural Kenyan mothers cope with food insecurity: results of a focused ethnographic study.

    Science.gov (United States)

    Pelto, Gretel H; Armar-Klemesu, Margaret

    2015-12-01

    An ethnographic study was conducted in two areas in southern and western Kenya to identify potential interventions to improve the quality, availability and affordability of foods consumed by infants and young children. A cultural-ecological model of determinants of nutrition identified the sectors of information for data collection related to infant and young child (IYC) diet and feeding-related behaviours, and the focused ethnographic study manual was used to guide the research. The results provide qualitative evidence about facilitators and constraints to IYC nutrition in the two geographical areas and document their inter-connections. We conclude with suggestions to consider 13 potential nutrition-sensitive interventions. The studies provide empirical ethnographic support for arguments concerning the importance of combining nutrition-specific and nutrition-sensitive interventions through a multi-sectoral, integrated approach to improve the nutrition of infants and young children in low-income, resource-constrained populations. They also document the value of ethnography as a component of landscape analysis in nutrition programme and policy planning. Key messages In addition to constraints on infant and young child diet that originate in environmental and technological conditions in both agro-ecological zones, other factors that affect feeding practices include features of social organisation, household access to social support, caregivers income-earning activities and their own health. The results of the ethnographies, which highlight the importance of obtaining the knowledge and perspectives of caregivers of infants and young children, reveal the interactions of the multiple factors that affect child nutrition and the need for simultaneous nutrition-sensitive interventions to complement nutrition-specific intervention actions. Most caregivers in both areas not only understood the importance of diet and food quality for child survival, they also regarded it as

  6. Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Lund, Rikke; Hansen, Helle V

    2009-01-01

    The spread of cancer cells from a primary tumor to form metastasis at distant sites is a complex multi-step process. The cancer cell proteins, and plasma membrane proteins in particular, involved in this process are poorly defined and a study of the very early events of the metastatic process using...... clinical samples or in vitro assays is not feasible. We have used a unique model system consisting of two isogenic human breast cancer cell lines that are equally tumorigenic in mice, but while one gives rise to metastasis, the other disseminates single cells that remain dormant at distant organs. Membrane......'-nucleotidase (ecto-5'-NT, CD73), Ndrg1, integrin beta1, CD44, CD74 and MHC class II proteins. The altered expression levels of proteins identified by LC-MS/MS were validated using flow cytometry, Western blotting, immunocyto- and immunohisto-chemistry. Analysis of clinical breast cancer biopsies demonstrated...

  7. A Rational Approach to Identify Inhibitors of Mycobacterium tuberculosis Enoyl Acyl Carrier Protein Reductase

    Czech Academy of Sciences Publication Activity Database

    Chhabria, M. T.; Parmar, K. B.; Brahmkshatriya, Pathik

    2013-01-01

    Roč. 19, č. 21 (2013), s. 3878-3883 ISSN 1381-6128 Institutional support: RVO:61388963 Keywords : mycobacterium tuberculosis * enoyl acyl carrier protein reductase * pharmacophore modeling * molecular docking * binding interactions Subject RIV: FR - Pharmacology ; Medidal Chemistry Impact factor: 3.288, year: 2013

  8. Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

    Science.gov (United States)

    Yilmaz, Lutfu Safak; Atilgan, Ali Rana

    2000-09-01

    A low-resolution structural model based on the packing geometry of α-carbons is utilized to establish a connection between the flexible and rigid parts of a folded protein. The former commonly recognizes a complementing molecule for making a complex, while the latter manipulates the necessary conformational change for binding. We attempt analytically to distinguish this control architecture that intrinsically exists in globular proteins. First with two-dimensional simple models, then for a native protein, bovine pancreatic trypsin inhibitor, we explicitly demonstrate that inserting fluctuations in tertiary contacts supported by the stable core, one can regulate the displacement of residues on loop regions. The positional fluctuations of the flexible regions are annihilated by the rest of the protein in conformity with the Le Chatelier-Braun principle. The results indicate that the distortion of the principal nonbonded contacts between highly packed residues is accompanied by that of the slavery fluctuations that are widely distributed over the native structure. These positional arrangements do not appear in a reciprocal relation between a perturbation and the associated response; the effect of a movement of residue i on residue j is not equal to that of the same movement of residue j on residue i.

  9. Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator

    DEFF Research Database (Denmark)

    Carayol, Jérôme; Chabert, Christian; Di Cara, Alessandro

    2017-01-01

    Thousands of genetic variants have been associated with complex traits through genomewide association studies. However, the functional variants or mechanistic consequences remain elusive. Intermediate traits such as gene expression or protein levels are good proxies of the metabolic state of an o...

  10. Abnormal SDS-PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding

    Science.gov (United States)

    Shi, Yunhua; Mowery, Richard A; Ashley, Jonathan; Hentz, Michelle; Ramirez, Alejandro J; Bilgicer, Basar; Slunt-Brown, Hilda; Borchelt, David R; Shaw, Bryan F

    2012-01-01

    The amino acid substitution or post-translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS-PAGE. This type of “gel shifting” has perplexed biochemists and biologists for decades. We identify a mechanism for “gel shifting” that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post-translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS-PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues ∼80–101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80–101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demonstrated that amino acid substitutions increase migration during SDS-PAGE by promoting the binding of three to four additional SDS molecules, without significantly altering the secondary structure or Stokes radius of hSOD1-SDS complexes. The high negative charge of domain 80–101 is required for SOD1 gel shifting: neutralizing the polyacidic domain (via chimeric mouse-human SOD1 fusion proteins) inhibited amino acid substitutions from causing gel shifting. These results demonstrate that the pattern of gel shifting for mutant cytosolic proteins can be used to: (i) identify domains in the primary structure that control interactions between denatured cytosolic proteins and SDS and (ii) identify a predominant chemical mechanism for the interaction (e.g., hydrophobic vs. electrostatic). PMID:22692797

  11. Use of the Operon Structure of the C. elegans Genome as a Tool to Identify Functionally Related Proteins

    Directory of Open Access Journals (Sweden)

    Silvia Dossena

    2013-12-01

    Full Text Available One of the most pressing challenges in the post genomic era is the identification and characterization of protein-protein interactions (PPIs, as these are essential in understanding the cellular physiology of health and disease. Experimental techniques suitable for characterizing PPIs (X-ray crystallography or nuclear magnetic resonance spectroscopy, among others are usually laborious, time-consuming and often difficult to apply to membrane proteins, and therefore require accurate prediction of the candidate interacting partners. High-throughput experimental methods (yeast two-hybrid and affinity purification succumb to the same shortcomings, and can also lead to high rates of false positive and negative results. Therefore, reliable tools for predicting PPIs are needed. The use of the operon structure in the eukaryote Caenorhabditis elegans genome is a valuable, though underserved, tool for identifying physically or functionally interacting proteins. Based on the concept that genes organized in the same operon may encode physically or functionally related proteins, this algorithm is easy to be applied and, importantly, gives a limited number of candidate partners of a given protein, allowing for focused experimental verification. Moreover, this approach can be successfully used to predict PPIs in the human system, including those of membrane proteins.

  12. Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae

    Directory of Open Access Journals (Sweden)

    Xiao-Yan eYang

    2016-02-01

    Full Text Available Streptococcus pneumoniae (S. pneumoniae is a major human pathogen causing morbidity and mortality worldwide. Efficiently acquiring iron from the environment is critical for S. pneumoniae to sustain growth and cause infection. There are only three known iron-uptake systems in Streptococcal species responsible for iron acquisition from the host, including ABC transporters PiaABC, PiuABC and PitABC. Besides, no other iron-transporting system has been suggested. In this work, we employed our newly established translating mRNA analysis integrated with proteomics to evaluate the possible existence of novel iron transporters in the bacterium. We simultaneously deleted the iron-binding protein genes of the three iron-uptake systems to construct a piaA/piuA/pitA triple mutant (Tri-Mut of S. pneumoniae D39, in which genes and proteins related to iron transport should be regulated in response to the deletion. With ribosome associated mRNA sequencing-based translatomics focusing on translating mRNA and iTRAQ quantitative proteomics based on the covalent labeling of peptides with tags of varying mass, we indeed observed a large number of genes and proteins representing various coordinated biological pathways with significantly altered expression levels in the Tri-Mut mutant. Highlighted in this observation is the identification of several new potential iron-uptake ABC transporters participating in iron metabolism of Streptococcus. In particular, putative protein SPD_1609 in operon 804 was verified to be a novel iron-binding protein with similar function to PitA in S. pneumoniae. These data derived from the integrative translatomics and proteomics analyses provided rich information and insightful clues for further investigations on iron-transporting mechanism in bacteria and the interplay between Streptococcal iron availability and the biological metabolic pathways.

  13. Identifying the substrate proteins of U-box E3s E4B and CHIP by orthogonal ubiquitin transfer.

    Science.gov (United States)

    Bhuripanyo, Karan; Wang, Yiyang; Liu, Xianpeng; Zhou, Li; Liu, Ruochuan; Duong, Duc; Zhao, Bo; Bi, Yingtao; Zhou, Han; Chen, Geng; Seyfried, Nicholas T; Chazin, Walter J; Kiyokawa, Hiroaki; Yin, Jun

    2018-01-01

    E3 ubiquitin (UB) ligases E4B and carboxyl terminus of Hsc70-interacting protein (CHIP) use a common U-box motif to transfer UB from E1 and E2 enzymes to their substrate proteins and regulate diverse cellular processes. To profile their ubiquitination targets in the cell, we used phage display to engineer E2-E4B and E2-CHIP pairs that were free of cross-reactivity with the native UB transfer cascades. We then used the engineered E2-E3 pairs to construct "orthogonal UB transfer (OUT)" cascades so that a mutant UB (xUB) could be exclusively used by the engineered E4B or CHIP to label their substrate proteins. Purification of xUB-conjugated proteins followed by proteomics analysis enabled the identification of hundreds of potential substrates of E4B and CHIP in human embryonic kidney 293 cells. Kinase MAPK3 (mitogen-activated protein kinase 3), methyltransferase PRMT1 (protein arginine N -methyltransferase 1), and phosphatase PPP3CA (protein phosphatase 3 catalytic subunit alpha) were identified as the shared substrates of the two E3s. Phosphatase PGAM5 (phosphoglycerate mutase 5) and deubiquitinase OTUB1 (ovarian tumor domain containing ubiquitin aldehyde binding protein 1) were confirmed as E4B substrates, and β-catenin and CDK4 (cyclin-dependent kinase 4) were confirmed as CHIP substrates. On the basis of the CHIP-CDK4 circuit identified by OUT, we revealed that CHIP signals CDK4 degradation in response to endoplasmic reticulum stress.

  14. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.

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    Rong Chen

    2010-09-01

    Full Text Available Serum proteins are routinely used to diagnose diseases, but are hard to find due to low sensitivity in screening the serum proteome. Public repositories of microarray data, such as the Gene Expression Omnibus (GEO, contain RNA expression profiles for more than 16,000 biological conditions, covering more than 30% of United States mortality. We hypothesized that genes coding for serum- and urine-detectable proteins, and showing differential expression of RNA in disease-damaged tissues would make ideal diagnostic protein biomarkers for those diseases. We showed that predicted protein biomarkers are significantly enriched for known diagnostic protein biomarkers in 22 diseases, with enrichment significantly higher in diseases for which at least three datasets are available. We then used this strategy to search for new biomarkers indicating acute rejection (AR across different types of transplanted solid organs. We integrated three biopsy-based microarray studies of AR from pediatric renal, adult renal and adult cardiac transplantation and identified 45 genes upregulated in all three. From this set, we chose 10 proteins for serum ELISA assays in 39 renal transplant patients, and discovered three that were significantly higher in AR. Interestingly, all three proteins were also significantly higher during AR in the 63 cardiac transplant recipients studied. Our best marker, serum PECAM1, identified renal AR with 89% sensitivity and 75% specificity, and also showed increased expression in AR by immunohistochemistry in renal, hepatic and cardiac transplant biopsies. Our results demonstrate that integrating gene expression microarray measurements from disease samples and even publicly-available data sets can be a powerful, fast, and cost-effective strategy for the discovery of new diagnostic serum protein biomarkers.

  15. Effects of natural peptides from food proteins on angiotensin converting enzyme activity and hypertension.

    Science.gov (United States)

    Martin, Melanie; Deussen, Andreas

    2017-12-15

    Cardiovascular diseases are the leading cause of death. The underlying pathophysiology is largely contributed by an overactivation of the renin-angiotensin-aldosterone-system (RAAS). Herein, angiotensin II (AngII) is a key mediator not only in blood pressure control and vascular tone regulation, but also involved in inflammation, endothelial dysfunction, atherosclerosis, hypertension and congestive heart failure. Since more than three decades suppression of AngII generation by inhibition of the angiotensin-converting enzyme (ACE) or blockade of the AngII-receptor has shown clinical benefit by reducing hypertension, atherosclerosis and other inflammation-associated cardiovascular diseases. Besides pharmaceutical ACE-inhibitors some natural peptides derived from food proteins reduce in vitro ACE activity. Several animal studies and a few human clinical trials have shown antihypertensive effects of such peptides, which might be attractive as food additives to prevent age-related RAAS activation. However, their inhibitory potency on in vitro ACE activity does not always correlate with an antihypertensive impact. While some peptides with high inhibitory activity on ACE-activity in vitro show no antihypertensive effect in vivo, other peptides with only a moderate ACE inhibitory activity in vitro cause such effects. The explanation for this conflicting phenomenon between inhibitory activity and antihypertensive effect remains unclear to date. This review shall critically address the effects of natural peptides derived from different food proteins on the cardiovascular system and the possible underlying mechanisms. A central aspect will be to point to conceptual gaps in the current understanding of the action of these peptides with respect to in vivo blood pressure lowering effects.

  16. Protein-Pacing from Food or Supplementation Improves Physical Performance in Overweight Men and Women: The PRISE 2 Study.

    Science.gov (United States)

    Arciero, Paul J; Edmonds, Rohan C; Bunsawat, Kanokwan; Gentile, Christopher L; Ketcham, Caitlin; Darin, Christopher; Renna, Mariale; Zheng, Qian; Zhang, Jun Zhu; Ormsbee, Michael J

    2016-05-11

    We recently reported that protein-pacing (P; six meals/day @ 1.4 g/kg body weight (BW), three of which included whey protein (WP) supplementation) combined with a multi-mode fitness program consisting of resistance, interval sprint, stretching, and endurance exercise training (RISE) improves body composition in overweight individuals. The purpose of this study was to extend these findings and determine whether protein-pacing with only food protein (FP) is comparable to WP supplementation during RISE training on physical performance outcomes in overweight/obese individuals. Thirty weight-matched volunteers were prescribed RISE training and a P diet derived from either whey protein supplementation (WP, n = 15) or food protein sources (FP, n = 15) for 16 weeks. Twenty-one participants completed the intervention (WP, n = 9; FP, n = 12). Measures of body composition and physical performance were significantly improved in both groups (p protein source. Likewise, markers of cardiometabolic disease risk (e.g., LDL (low-density lipoprotein) cholesterol, glucose, insulin, adiponectin, systolic blood pressure) were significantly improved (p protein and food protein sources combined with multimodal RISE training are equally effective at improving physical performance and cardiometabolic health in obese individuals.

  17. Protein-Pacing from Food or Supplementation Improves Physical Performance in Overweight Men and Women: The PRISE 2 Study

    Directory of Open Access Journals (Sweden)

    Paul J. Arciero

    2016-05-01

    Full Text Available We recently reported that protein-pacing (P; six meals/day @ 1.4 g/kg body weight (BW, three of which included whey protein (WP supplementation combined with a multi-mode fitness program consisting of resistance, interval sprint, stretching, and endurance exercise training (RISE improves body composition in overweight individuals. The purpose of this study was to extend these findings and determine whether protein-pacing with only food protein (FP is comparable to WP supplementation during RISE training on physical performance outcomes in overweight/obese individuals. Thirty weight-matched volunteers were prescribed RISE training and a P diet derived from either whey protein supplementation (WP, n = 15 or food protein sources (FP, n = 15 for 16 weeks. Twenty-one participants completed the intervention (WP, n = 9; FP, n = 12. Measures of body composition and physical performance were significantly improved in both groups (p < 0.05, with no effect of protein source. Likewise, markers of cardiometabolic disease risk (e.g., LDL (low-density lipoprotein cholesterol, glucose, insulin, adiponectin, systolic blood pressure were significantly improved (p < 0.05 to a similar extent in both groups. These results demonstrate that both whey protein and food protein sources combined with multimodal RISE training are equally effective at improving physical performance and cardiometabolic health in obese individuals.

  18. Food Sources of Protein and Risk of Incident Gout in the Singapore Chinese Health Study.

    Science.gov (United States)

    Teng, Gim Gee; Pan, An; Yuan, Jian-Min; Koh, Woon-Puay

    2015-07-01

    Prospective studies evaluating diet in relation to the risk of gout in Asian populations are lacking. The purpose of this study was to examine the relationship between the consumption of dietary protein from each of its major sources and the risk of gout in a Chinese population. We used data from the Singapore Chinese Health Study, a prospective cohort of 63,257 Chinese adults who were 45-74 years old at recruitment during the years 1993-1998. Habitual diet information was collected via a validated semiquantitative food frequency questionnaire, and physician-diagnosed gout was self-reported during 2 followup interviews up to the year 2010. Cox proportional hazards models were used to calculate the hazard ratios (HRs) and 95% confidence intervals (95% CIs), with adjustment for potential confounders, among 51,114 eligible study participants who were free of gout at baseline and responded to our followup interviews. A total of 2,167 participants reported physician-diagnosed gout during the followup period. The multivariate-adjusted HRs (with 95% CIs) of gout, comparing the first quartile with the fourth quartile, were as follows: 1.27 (1.12-1.44; P for trend food, and 0.83 (0.73-0.95; P for trend = 0.012) for nonsoy legumes. No statistically significant associations were found with protein intake from other sources (red meat, eggs, dairy products, grains, or nuts and seeds). In this Chinese population living in Singapore, higher total dietary protein intake from mainly poultry and fish/shellfish was associated with an increased risk of gout, while dietary intake of soy and nonsoy legumes was associated with a reduced risk of gout. © 2015, American College of Rheumatology.

  19. Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis

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    Jarred W. Rensvold

    2013-01-01

    Full Text Available Mitochondria are centers of metabolism and signaling whose content and function must adapt to changing cellular environments. The biological signals that initiate mitochondrial restructuring and the cellular processes that drive this adaptive response are largely obscure. To better define these systems, we performed matched quantitative genomic and proteomic analyses of mouse muscle cells as they performed mitochondrial biogenesis. We find that proteins involved in cellular iron homeostasis are highly coordinated with this process and that depletion of cellular iron results in a rapid, dose-dependent decrease of select mitochondrial protein levels and oxidative capacity. We further show that this process is universal across a broad range of cell types and fully reversed when iron is reintroduced. Collectively, our work reveals that cellular iron is a key regulator of mitochondrial biogenesis, and provides quantitative data sets that can be leveraged to explore posttranscriptional and posttranslational processes that are essential for mitochondrial adaptation.

  20. [Progress of methodology for identifying target protein of natural active small molecules].

    Science.gov (United States)

    Tu, Peng-Fei; Zeng, Ke-Wu; Liao, Li-Xi; Song, Xiao-Min

    2016-01-01

    Drug targets are special molecules that can interact with drugs and exert pharmacological functions in human body. The natural active small molecules are the bioactive basis of traditional Chinese medicine, and the mechanism study is a hot topic now, especially for the identification of their target proteins. However, little progress has been made in this field until now. Here, we summarized the recent technologies and methods for the identification of target proteins of natural bioactive small molecules, and introduced the main research methods, principles and successful cases in this field. We also explored the applicability and discussed the advantages and disadvantages among different methods. We hope this review can be used as a reference for the researchers who engaged in natural pharmaceutical chemistry, pharmacology and chemical biology. Copyright© by the Chinese Pharmaceutical Association.

  1. Nucleotide and protein sequences for dog masticatory tropomyosin identify a novel Tpm4 gene product

    OpenAIRE

    Brundage, Elizabeth A.; Biesiadecki, Brandon J.; Reiser, Peter J.

    2015-01-01

    Jaw-closing muscles of several vertebrate species, including members of Carnivora, express a unique, “masticatory”, isoform of myosin heavy chain, along with isoforms of other myofibrillar proteins that are not expressed in most other muscles. It is generally believed that the complement of myofibrillar isoforms in these muscles serves high force generation for capturing live prey, breaking down tough plant material and defensive biting. A unique isoform of tropomyosin (Tpm) was reported to b...

  2. Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell.

    Science.gov (United States)

    Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

    2016-03-01

    The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. An Asymmetric Deuterium Labeling Strategy to Identify Interprotomer and Intraprotomer NOEs in Oligomeric Proteins

    International Nuclear Information System (INIS)

    Jasanoff, Alan

    1998-01-01

    A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a uniformly 13C-labeled trimer with the spectrum of the same trimer labeled with 13C in only one protomer, and with deuterium in the other two protomers. The spectrum of the unmixed trimer included both inter- and intraprotomer NOEs while the spectrum of the mixed trimer included only intraprotomer peaks. NOEs clearly absent from the spectrum of the mixed trimer could be confidently assigned to interprotomer interactions. Asymmetrically labeled trimers were isolated by refolding a 13C-labeled shorter form of the protein with a 2H-labeled longer form, chromatographically purifying trimers with only one short chain, and then processing with trypsin to yield only protomers with the desired N- and C-termini. In contrast to earlier studies, in which statistical mixtures of differently labeled protomers were analyzed, our procedure generated only a well-defined 1:2 oligomer, and no other mixed oligomers were present. This increased the maximum possible concentration of NMR-active protomers and thus the sensitivity of the experiments. Related methods should be applicable to many oligomeric proteins, particularly those with slow protomer exchange rates

  4. Synthesis and evaluation of radioactive and fluorescent residualizing labels for identifying sites of plasma protein catabolism

    International Nuclear Information System (INIS)

    Maxwell, J.L.; Baynes, J.W.; Thorpe, S.R.

    1986-01-01

    Inulin and lactose were each coupled to tyramine by reductive amination with NaBH 3 CN and the tyramine then labeled with 125 I. Dilactitol- 125 I-tyramine (DLT) and inulin- 125 I-tyramine (InTn) were coupled by reductive amination and cyanuric chloride, respectively, to asialofetuin (ASF), fetuin and rat serum albumin (RSA). Attachment of either label had no effect on the circulating half-lives of the proteins. Radioactivity from labeled ASF was recovered in rat liver (> 90%) by 1 h post-injection and remained in liver with half-lives of 2 and 6 days, respectively, for the DLT and InTn labels. Whole body recoveries of radioactivity from DLT- and InTn labels. Whole body recoveries of radioactivity from DLT- and InTn-labeled RSA were 5 and 6.5 days, respectively, again indicating that the larger glycoconjugate label residualized more efficiently in cells following protein degradation. (Lactitol) 2 -N-CH 2 -CH 2 -NH-fluroescein (DLF) was also coupled to ASF by reductive amination and recovered quantitatively in liver at 1 h post-injection. Native ASF was an effective competitor for clearance of DLF-ASF from the circulation. Fluorescent degradation products were retained in liver with a half-life of 1.2 days. Residualizing fluorescent labels should be useful for identification and sorting of cells active in the degradation of plasma proteins

  5. Epitope Sequences in Dengue Virus NS1 Protein Identified by Monoclonal Antibodies

    Directory of Open Access Journals (Sweden)

    Leticia Barboza Rocha

    2017-10-01

    Full Text Available Dengue nonstructural protein 1 (NS1 is a multi-functional glycoprotein with essential functions both in viral replication and modulation of host innate immune responses. NS1 has been established as a good surrogate marker for infection. In the present study, we generated four anti-NS1 monoclonal antibodies against recombinant NS1 protein from dengue virus serotype 2 (DENV2, which were used to map three NS1 epitopes. The sequence 193AVHADMGYWIESALNDT209 was recognized by monoclonal antibodies 2H5 and 4H1BC, which also cross-reacted with Zika virus (ZIKV protein. On the other hand, the sequence 25VHTWTEQYKFQPES38 was recognized by mAb 4F6 that did not cross react with ZIKV. Lastly, a previously unidentified DENV2 NS1-specific epitope, represented by the sequence 127ELHNQTFLIDGPETAEC143, is described in the present study after reaction with mAb 4H2, which also did not cross react with ZIKV. The selection and characterization of the epitope, specificity of anti-NS1 mAbs, may contribute to the development of diagnostic tools able to differentiate DENV and ZIKV infections.

  6. Antibodies in human serum and milk induced by enterobacteria and food proteins.

    Science.gov (United States)

    Ahlstedt, S; Carlsson, B; Fällström, S P; Hanson, L A; Holmgren, J; Lidin-Janson, G; Lindblad, B S; Jodal, U; Kaijser, B; Solh-Akerlund, A; Wadsworth, C

    Ingestion of Escherichia coli O83 bacteria by adults resulted in a transient irregular colonization leading to a serum antibody response in only four out of 14 cases examined. In all of three pregnant women, however, IgA antibodies against E. coli O83 antigen were released from colostral cells after similar bacterial ingestion although no serum antibody response was noted. The findings indicate a link between the antigenic exposure to the gut and secretory antibodies of the IgA class, presumably locally formed in the mammary gland. Antibodies of the secretory IgA class registered in colostrum may, at least partly, reflect the antigenic exposure of the gut. These antibodies are probably important in protecting against E. coli infections in the neonate, as suggested by the findings of antibodies in human milk against O and K antigens of non-enteropathogenic as well as enteropathogenic serotypes of E. coli. Furthermore, in milk of women from low socio-economic groups in Pakistan, neutralizing antibodies were present against enterotoxins of E. coli bacteria and occasionally against Vibrio cholerae enterotoxins. In addition, secretory IgA antibodies against food proteins were detected in human milk. This suggests that intestinal exposure to such antigens could stimulate a local immune response in the gut resulting in triggered lymphoid cells homing to the mammary gland. These human milk secretory IgA antibodies against bovine milk proteins may help to prevent cow's milk allergy in infants on mixed feeding, since these infants tend to have a lower serum antibody response to cow's milk proteins than infants fed mostly artificially. Furthermore, children suffering from cow's milk protein intolerance and gluten enteropathy may have higher serum levels of antibody to cow's milk protein antigens than normal children, possibly reflecting increased permeability of the intestinal mucosa for various antigens.

  7. Using Personal Water Footprints to Identify Consumer Food Choices that Influence the Conservation of Local Water Resources

    Science.gov (United States)

    Marrin, D. L.

    2015-12-01

    As the global demand for water and food escalates, the emphasis is on supply side factors rather than demand side factors such as consumers, whose personal water footprints are dominated (>90%) by food. Personal footprints include the water embedded in foods that are produced locally as well as those imported, raising the question of whether local shifts in people's food choices and habits could assist in addressing local water shortages. The current situation in California is interesting in that drought has affected an agriculturally productive region where a substantial portion of its food products are consumed by the state's large population. Unlike most agricultural regions where green water is the primary source of water for crops, California's arid climate demands an enormous volume of blue water as irrigation from its dwindling surface and ground water resources. Although California exports many of its food products, enough is consumed in-state so that residents making relatively minor shifts their food choices could save as much local blue water as their implementing more drastic reductions in household water use (comprising food group on both a caloric and gravimetric basis. Another change is wasting less food, which is a shared responsibility among consumers, producers and retailers; however, consumers' actions and preferences ultimately drive much of the waste. Personal water footprints suggest a role for individuals in conserving local water resources that is neither readily obvious nor a major focus of most conservation programs.

  8. Addressing the Knowledge Gaps in Agroecology and Identifying Guiding Principles for Transforming Conventional Agri-Food Systems

    Directory of Open Access Journals (Sweden)

    Angelina Sanderson Bellamy

    2017-02-01

    Full Text Available Today’s society faces many challenges when it comes to food production: producing food sustainably, producing enough of it, distributing food, consuming enough calories, consuming too many calories, consuming culturally-appropriate foods, and reducing the amount of food wasted. The distribution of power within the current mainstream agri-food system is dominated by multinational agri-businesses that control the flow of goods and wealth through the system. This hegemony has implemented a regime whose structures reinforce its control. A growing response to the current agri-food regime is the rise of agroecology, in both developed and developing country contexts. This is not a new phenomenon, but it has evolved over time from its Latin American origins. However, agroecology is not a monolithic block and represents many different perceptions of what it means to advance agroecology and ways in which it can help today’s society tackle the crisis of the agri-food system. This paper addresses these sometimes discordant view points, as well as the gaps in our knowledge regarding agroecology in an effort to lay out some guiding principles for how we can move forward in transforming the current agri-food system to achieve sustainability and a more equitable distribution of power and resources.

  9. Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein.

    Science.gov (United States)

    Li, Hui; Zhang, Dan-feng; Lin, Xiang-min; Peng, Xuan-xian

    2015-06-01

    Antibiotic-resistant bacteria are a great threat to human health and food safety and there is an urgent need to understand the mechanisms of resistance for combating these bacteria. In the current study, comparative proteomic methodologies were applied to identify Escherichia coli K-12 outer membrane (OM) proteins related to kanamycin resistance. Mass spectrometry and western blotting results revealed that OM proteins TolC, Tsx and OstA were up-regulated, whereas MipA, OmpA, FadL and OmpW were down-regulated in kanamycin-resistant E. coli K-12 strain. Genetic deletion of tolC (ΔtolC-Km) led to a 2-fold decrease in the minimum inhibitory concentration (MIC) of kanamycin and deletion of mipA (ΔmipA-Km) resulted in a 4-fold increase in the MIC of kanamycin. Changes in the MICs for genetically modified strains could be completely recovered by gene complementation. Compared with the wild-type strain, the survival capability of ΔompA-Km was significantly increased and that of Δtsx-Km was significantly decreased. We further evaluated the role and expression of MipA in response to four other antibiotics including nalidixic acid, streptomycin, chloramphenicol and aureomycin, which suggested that MipA was a novel OM protein related to antibiotic resistance. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. A new fluorescence-based method identifies protein phosphatases regulating lipid droplet metabolism.

    Directory of Open Access Journals (Sweden)

    Bruno L Bozaquel-Morais

    Full Text Available In virtually every cell, neutral lipids are stored in cytoplasmic structures called lipid droplets (LDs and also referred to as lipid bodies or lipid particles. We developed a rapid high-throughput assay based on the recovery of quenched BODIPY-fluorescence that allows to quantify lipid droplets. The method was validated by monitoring lipid droplet turnover during growth of a yeast culture and by screening a group of strains deleted in genes known to be involved in lipid metabolism. In both tests, the fluorimetric assay showed high sensitivity and good agreement with previously reported data using microscopy. We used this method for high-throughput identification of protein phosphatases involved in lipid droplet metabolism. From 65 yeast knockout strains encoding protein phosphatases and its regulatory subunits, 13 strains revealed to have abnormal levels of lipid droplets, 10 of them having high lipid droplet content. Strains deleted for type I protein phosphatases and related regulators (ppz2, gac1, bni4, type 2A phosphatase and its related regulator (pph21 and sap185, type 2C protein phosphatases (ptc1, ptc4, ptc7 and dual phosphatases (pps1, msg5 were catalogued as high-lipid droplet content strains. Only reg1, a targeting subunit of the type 1 phosphatase Glc7p, and members of the nutrient-sensitive TOR pathway (sit4 and the regulatory subunit sap190 were catalogued as low-lipid droplet content strains, which were studied further. We show that Snf1, the homologue of the mammalian AMP-activated kinase, is constitutively phosphorylated (hyperactive in sit4 and sap190 strains leading to a reduction of acetyl-CoA carboxylase activity. In conclusion, our fast and highly sensitive method permitted us to catalogue protein phosphatases involved in the regulation of LD metabolism and present evidence indicating that the TOR pathway and the SNF1/AMPK pathway are connected through the Sit4p-Sap190p pair in the control of lipid droplet biogenesis.

  11. Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans.

    Science.gov (United States)

    Kim, Sunhee; Lee, Hyoung-Joo; Hahm, Jeong-Hoon; Jeong, Seul-Ki; Park, Don-Ha; Hancock, William S; Paik, Young-Ki

    2016-02-05

    When Caenorhabditis elegans encounters unfavorable growth conditions, it enters the dauer stage, an alternative L3 developmental period. A dauer larva resumes larval development to the normal L4 stage by uncharacterized postdauer reprogramming (PDR) when growth conditions become more favorable. During this transition period, certain heterochronic genes involved in controlling the proper sequence of developmental events are known to act, with their mutations suppressing the Muv (multivulva) phenotype in C. elegans. To identify the specific proteins in which the Muv phenotype is highly suppressed, quantitative proteomic analysis with iTRAQ labeling of samples obtained from worms at L1 + 30 h (for continuous development [CD]) and dauer recovery +3 h (for postdauer development [PD]) was carried out to detect changes in protein abundance in the CD and PD states of both N2 and lin-28(n719). Of the 1661 unique proteins identified with a proteomic approach identifies and quantitates the regulatory proteins potentially involved in PDR in C. elegans, which safeguards the overall lifecycle in response to environmental changes.

  12. Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease

    Directory of Open Access Journals (Sweden)

    Mengqi Huo

    2017-06-01

    Full Text Available Salvia miltiorrhiza, known as Danshen, has attracted worldwide interest for its substantial effects on coronary heart disease (CHD. Danshensu (DSS is one of the main active ingredients of Danshen on CHD. Although it has been proven to have a good clinical effect on CHD, the action mechanisms remain elusive. In the current study, a coexpression network-based approach was used to illustrate the beneficial properties of DSS in the context of CHD. By integrating the gene expression profile data and protein-protein interactions (PPIs data, two coexpression protein interaction networks (CePIN in a CHD state (CHD CePIN and a non-CHD state (non-CHD CePIN were generated. Then, shared nodes and unique nodes in CHD CePIN were attained by conducting a comparison between CHD CePIN and non-CHD CePIN. By calculating the topological parameters of each shared node and unique node in the networks, and comparing the differentially expressed genes, target proteins involved in disease regulation were attained. Then, Gene Ontology (GO enrichment was utilized to identify biological processes associated to target proteins. Consequently, it turned out that the treatment of CHD with DSS may be partly attributed to the regulation of immunization and blood circulation. Also, it indicated that sodium/hydrogen exchanger 3 (SLC9A3, Prostaglandin G/H synthase 2 (PTGS2, Oxidized low-density lipoprotein receptor 1 (OLR1, and fibrinogen gamma chain (FGG may be potential therapeutic targets for CHD. In summary, this study provided a novel coexpression protein interaction network approach to provide an explanation of the mechanisms of DSS on CHD and identify key proteins which maybe the potential therapeutic targets for CHD.

  13. Identifying factors associated with fast food consumption among adolescents in Beijing China using a theory-based approach.

    Science.gov (United States)

    Ma, R; Castellanos, D C; Bachman, J

    2016-07-01

    China is in the midst of the nutrition transition with increasing rates of obesity and dietary changes. One contributor is the increase in fast food chains within the country. The purpose of this study was to develop a theory-based instrument that explores influencing factors of fast food consumption in adolescents residing in Beijing, China. Cross-sectional study. Value expectancy and theory of planned behaviour were utilised to explore influencing factors of fast food consumption in the target population. There were 201 Chinese adolescents between the ages of 12 and 18. Cronbach's alpha correlation coefficients were used to examine internal reliability of the theory-based questionnaire. Bivariate correlations and a MANOVA were utilised to determine the relationship between theory-based constructs, body mass index (BMI)-for-age and fast food intake frequency as well as to determine differences in theory-based scores among fast food consumption frequency groupings. The theory-based questionnaire showed good reliability. Furthermore, there was a significant difference in the theory-based subcategory scores between fast food frequency groups. A significant positive correlation was observed between times per week fast food was consumed and each theory-based subscale score. Using BMI-for-age of 176 participants, 81% were normal weight and 19% were considered overweight or obese. Results showed consumption of fast food to be on average 1.50 ± 1.33 per week. The relationship between BMI-for-age and times per week fast food was consumed was not significant. As the nutrition transition continues and fast food chains expand, it is important to explore factors effecting fast food consumption in China. Interventions targeting influencing factors can be developed to encourage healthy dietary choice in the midst of this transition. Copyright © 2016. Published by Elsevier Ltd.

  14. QuatIdent: a web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information.

    Science.gov (United States)

    Shen, Hong-Bin; Chou, Kuo-Chen

    2009-03-01

    Many proteins exist in vivo as oligomers with various different quaternary structural attributes rather than as single individual chains. They are the structural bases of various marvelous biological functions such as cooperative effects, allosteric mechanism, and ion-channel gating. Therefore, with the avalanche of protein sequences generated in the postgenomic era, it is very important for both basic research and drug discovery to identify their quaternary structural attributes in a timely manner. In view of this, a powerful ensemble identifier, called QuatIdent, is developed by fusing the functional domain and sequential evolution information. QuatIdent is a 2-layer predictor. The 1st layer is for identifying a query protein as belonging to which one of the following 10 main quaternary structural attributes: (1) monomer, (2) dimer, (3) trimer, (4) tetramer, (5) pentamer, (6) hexamer, (7) heptamer, (8) octamer, (9) decamer, and (10) dodecamer. If the result thus obtained turns out to be anything but monomer, the process will be automatically continued to further identify it as belonging to a homo-oligomer or hetero-oligomer. The overall success rate by QuatIdent for the 1st layer identification was 71.1% and that for the 2nd layer ranged from 84 to 96%. These rates were derived by the jackknife cross-validation tests on the stringent benchmark data sets where none of proteins has > or =60% pairwise sequence identity to any other in a same subset. QuatIdent is freely accessible to the public as a web server via the site at http://www.csbio.sjtu.edu.cn/bioinf/Quaternary/ , by which one can get the desired 2-level results for a query protein sequence in around 25 seconds. The longer the sequence is, the more time that is needed.

  15. IBT-based quantitative proteomics identifies potential regulatory proteins involved in pigmentation of purple sea cucumber, Apostichopus japonicus.

    Science.gov (United States)

    Xing, Lili; Sun, Lina; Liu, Shilin; Li, Xiaoni; Zhang, Libin; Yang, Hongsheng

    2017-09-01

    Sea cucumbers are an important economic species and exhibit high yield value among aquaculture animals. Purple sea cucumbers are very rare and beautiful and have stable hereditary patterns. In this study, isobaric tags (IBT) were first used to reveal the molecular mechanism of pigmentation in the body wall of the purple sea cucumber. We analyzed the proteomes of purple sea cucumber in early pigmentation stage (Pa), mid pigmentation stage (Pb) and late pigmentation stage (Pc), resulting in the identification of 5580 proteins, including 1099 differentially expressed proteins in Pb: Pa and 339 differentially expressed proteins in Pc: Pb. GO and KEGG analyses revealed possible differentially expressed proteins, including"melanogenesis", "melanosome", "melanoma", "pigment-biosynthetic process", "Epidermis development", "Ras-signaling pathway", "Wnt-signaling pathway", "response to UV light", and "tyrosine metabolism", involved in pigment synthesis and regulation in purple sea cucumbers. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying pigmentation in sea cucumbers. Furthermore, these results may also provide the base for further identification of proteins involved in resistance mechanisms against melanoma, albinism, UV damage, and other diseases in sea cucumbers. Copyright © 2017. Published by Elsevier Inc.

  16. An approach to including protein quality when assessing the net contribution of livestock to human food supply.

    Science.gov (United States)

    Ertl, P; Knaus, W; Zollitsch, W

    2016-11-01

    The production of protein from animal sources is often criticized because of the low efficiency of converting plant protein from feeds into protein in the animal products. However, this critique does not consider the fact that large portions of the plant-based proteins fed to animals may be human-inedible and that the quality of animal proteins is usually superior as compared with plant proteins. The aim of the present study was therefore to assess changes in protein quality in the course of the transformation of potentially human-edible plant proteins into animal products via livestock production; data from 30 Austrian dairy farms were used as a case study. A second aim was to develop an approach for combining these changes with quantitative aspects (e.g. with the human-edible feed conversion efficiency (heFCE), defined as kilogram protein in the animal product divided by kilogram potentially human-edible protein in the feeds). Protein quality of potentially human-edible inputs and outputs was assessed using the protein digestibility-corrected amino acid score and the digestible indispensable amino acid score, two methods proposed by the Food and Agriculture Organization of the United Nations to describe the nutritional value of proteins for humans. Depending on the method used, protein scores were between 1.40 and 1.87 times higher for the animal products than for the potentially human-edible plant protein input on a barn-gate level (=protein quality ratio (PQR)). Combining the PQR of 1.87 with the heFCE for the same farms resulted in heFCE×PQR of 2.15. Thus, considering both quantity and quality, the value of the proteins in the animal products for human consumption (in this case in milk and beef) is 2.15 times higher than that of proteins in the potentially human-edible plant protein inputs. The results of this study emphasize the necessity of including protein quality changes resulting from the transformation of plant proteins to animal proteins when

  17. Safety of Novel Protein Sources (Insects, Microalgae, Seaweed, Duckweed, and Rapeseed) and Legislative Aspects for Their Application in Food and Feed Production

    NARCIS (Netherlands)

    Spiegel, van der M.; Noordam, M.Y.; Fels-Klerx, van der H.J.

    2013-01-01

    Novel protein sources (like insects, algae, duckweed, and rapeseed) are expected to enter the European feed and food market as replacers for animal-derived proteins. However, food safety aspects of these novel protein sources are not well-known. The aim of this article is to review the state of the

  18. Structure modeling of all identified G protein-coupled receptors in the human genome.

    Directory of Open Access Journals (Sweden)

    Yang Zhang

    2006-02-01

    Full Text Available G protein-coupled receptors (GPCRs, encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness

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

    Science.gov (United States)

    2012-09-01

    library as C-terminal fusion to the capsid protein D of bacteriophage lambda,” J Mol Biol, 282(1), 125-35 (1998). [10] Z. Ren, and L. W. Black, “ Phage T4 ...alternatives using peptide display techniques such as bacterial display 1, 2, 3, 4, 5 , yeast display 6, 7 , phage display 4, 5, 8, 9, 10 , and synthetic...applications of phage and cell display,” Biotechnol Adv, 19(1), 1-33 (2001). [5] S. Y. Lee, J. H. Choi, and Z. H. Xu, “Microbial cell-surface

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

    International Nuclear Information System (INIS)

    Mezzenga, Raffaele; Fischer, Peter

    2013-01-01

    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. (review article)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Identification of a mitochondrial target of thiazolidinedione insulin sensitizers (mTOT--relationship to newly identified mitochondrial pyruvate carrier proteins.

    Directory of Open Access Journals (Sweden)

    Jerry R Colca

    Full Text Available Thiazolidinedione (TZD insulin sensitizers have the potential to effectively treat a number of human diseases, however the currently available agents have dose-limiting side effects that are mediated via activation of the transcription factor PPARγ. We have recently shown PPARγ-independent actions of TZD insulin sensitizers, but the molecular target of these molecules remained to be identified. Here we use a photo-catalyzable drug analog probe and mass spectrometry-based proteomics to identify a previously uncharacterized mitochondrial complex that specifically recognizes TZDs. These studies identify two well-conserved proteins previously known as brain protein 44 (BRP44 and BRP44 Like (BRP44L, which recently have been renamed Mpc2 and Mpc1 to signify their function as a mitochondrial pyruvate carrier complex. Knockdown of Mpc1 or Mpc2 in Drosophila melanogaster or pre-incubation with UK5099, an inhibitor of pyruvate transport, blocks the crosslinking of mitochondrial membranes by the TZD probe. Knockdown of these proteins in Drosophila also led to increased hemolymph glucose and blocked drug action. In isolated brown adipose tissue (BAT cells, MSDC-0602, a PPARγ-sparing TZD, altered the incorporation of (13C-labeled carbon from glucose into acetyl CoA. These results identify Mpc1 and Mpc2 as components of the mitochondrial target of TZDs (mTOT and suggest that understanding the modulation of this complex, which appears to regulate pyruvate entry into the mitochondria, may provide a viable target for insulin sensitizing pharmacology.

  4. Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects.

    Directory of Open Access Journals (Sweden)

    Anjali K Nath

    Full Text Available Cardiovascular development is vital for embryonic survival and growth. Early gestation embryo loss or malformation has been linked to yolk sac vasculopathy and congenital heart defects (CHDs. However, the molecular pathways that underlie these structural defects in humans remain largely unknown hindering the development of molecular-based diagnostic tools and novel therapies.Murine embryos were exposed to high glucose, a condition known to induce cardiovascular defects in both animal models and humans. We further employed a mass spectrometry-based proteomics approach to identify proteins differentially expressed in embryos with defects from those with normal cardiovascular development. The proteins detected by mass spectrometry (WNT16, ST14, Pcsk1, Jumonji, Morca2a, TRPC5, and others were validated by Western blotting and immunoflorescent staining of the yolk sac and heart. The proteins within the proteomic dataset clustered to adhesion/migration, differentiation, transport, and insulin signaling pathways. A functional role for several proteins (WNT16, ADAM15 and NOGO-A/B was demonstrated in an ex vivo model of heart development. Additionally, a successful application of a cluster of protein biomarkers (WNT16, ST14 and Pcsk1 as a prenatal screen for CHDs was confirmed in a study of human amniotic fluid (AF samples from women carrying normal fetuses and those with CHDs.The novel finding that WNT16, ST14 and Pcsk1 protein levels increase in fetuses with CHDs suggests that these proteins may play a role in the etiology of human CHDs. The information gained through this bed-side to bench translational approach contributes to a more complete understanding of the protein pathways dysregulated during cardiovascular development and provides novel avenues for diagnostic and therapeutic interventions, beneficial to fetuses at risk for CHDs.

  5. Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects.

    Science.gov (United States)

    Nath, Anjali K; Krauthammer, Michael; Li, Puyao; Davidov, Eugene; Butler, Lucas C; Copel, Joshua; Katajamaa, Mikko; Oresic, Matej; Buhimschi, Irina; Buhimschi, Catalin; Snyder, Michael; Madri, Joseph A

    2009-01-01

    Cardiovascular development is vital for embryonic survival and growth. Early gestation embryo loss or malformation has been linked to yolk sac vasculopathy and congenital heart defects (CHDs). However, the molecular pathways that underlie these structural defects in humans remain largely unknown hindering the development of molecular-based diagnostic tools and novel therapies. Murine embryos were exposed to high glucose, a condition known to induce cardiovascular defects in both animal models and humans. We further employed a mass spectrometry-based proteomics approach to identify proteins differentially expressed in embryos with defects from those with normal cardiovascular development. The proteins detected by mass spectrometry (WNT16, ST14, Pcsk1, Jumonji, Morca2a, TRPC5, and others) were validated by Western blotting and immunoflorescent staining of the yolk sac and heart. The proteins within the proteomic dataset clustered to adhesion/migration, differentiation, transport, and insulin signaling pathways. A functional role for several proteins (WNT16, ADAM15 and NOGO-A/B) was demonstrated in an ex vivo model of heart development. Additionally, a successful application of a cluster of protein biomarkers (WNT16, ST14 and Pcsk1) as a prenatal screen for CHDs was confirmed in a study of human amniotic fluid (AF) samples from women carrying normal fetuses and those with CHDs. The novel finding that WNT16, ST14 and Pcsk1 protein levels increase in fetuses with CHDs suggests that these proteins may play a role in the etiology of human CHDs. The information gained through this bed-side to bench translational approach contributes to a more complete understanding of the protein pathways dysregulated during cardiovascular development and provides novel avenues for diagnostic and therapeutic interventions, beneficial to fetuses at risk for CHDs.

  6. Quantitative Secretomic Analysis Identifies Extracellular Protein Factors That Modulate the Metastatic Phenotype of Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Hu, Rongkuan; Huffman, Kenneth E; Chu, Michael; Zhang, Yajie; Minna, John D; Yu, Yonghao

    2016-02-05

    Lung cancer is the leading cause of cancer-related deaths for men and women in the United States, with non-small cell lung cancer (NSCLC) representing 85% of all diagnoses. Late stage detection, metastatic disease and lack of actionable biomarkers contribute to the high mortality rate. Proteins in the extracellular space are known to be critically involved in regulating every stage of the pathogenesis of lung cancer. To investigate the mechanism by which secreted proteins contribute to the pathogenesis of NSCLC, we performed quantitative secretomic analysis of two isogenic NSCLC cell lines (NCI-H1993 and NCI-H2073) and an immortalized human bronchial epithelial cell line (HBEC3-KT) as control. H1993 was derived from a chemo-naïve metastatic tumor, while H2073 was derived from the primary tumor after etoposide/cisplatin therapy. From the conditioned media of these three cell lines, we identified and quantified 2713 proteins, including a series of proteins involved in regulating inflammatory response, programmed cell death and cell motion. Gene Ontology (GO) analysis indicates that a number of proteins overexpressed in H1993 media are involved in biological processes related to cancer metastasis, including cell motion, cell-cell adhesion and cell migration. RNA interference (RNAi)-mediated knock down of a number of these proteins, including SULT2B1, CEACAM5, SPRR3, AGR2, S100P, and S100A14, leads to dramatically reduced migration of these cells. In addition, meta-analysis of survival data indicates NSCLC patients whose tumors express higher levels of several of these secreted proteins, including SULT2B1, CEACAM5, SPRR3, S100P, and S100A14, have a worse prognosis. Collectively, our results provide a potential molecular link between deregulated secretome and NSCLC cell migration/metastasis. In addition, the identification of these aberrantly secreted proteins might facilitate the development of biomarkers for early detection of this devastating disease.

  7. Characterization of a variant of gap junction protein α8 identified in a family with hereditary cataract.

    Directory of Open Access Journals (Sweden)

    Debbie S Kuo

    Full Text Available Congenital cataracts occur in isolation in about 70% of cases or are associated with other abnormalities such as anterior segment dysgenesis and microphthalmia. We identified a three-generation family in the University of California San Francisco glaucoma clinic comprising three individuals with congenital cataracts and aphakic glaucoma, one of whom also had microphthalmia. The purpose of this study was to identify a possible causative mutation in this family and to investigate its pathogenesis.We performed exome sequencing and identified a putative mutation in gap junction protein α8 (GJA8. We used PCR and DNA sequencing of GJA8 in affected and unaffected members of the pedigree to test segregation of the variant with the phenotype. We tested cellular distribution and function of the variant protein by immunofluorescence and intercellular transfer of Neurobiotin in transiently transfected HeLa cells.Exome sequencing revealed a variant in GJA8 (c.658A>G encoding connexin50 (Cx50 that resulted in a missense change (p.N220D in transmembrane domain 4. The variant was present in all three affected family members, but was also present in the proband's grandfather who was reported to be unaffected. The mutant protein localized to the plasma membrane and supported intercellular Neurobiotin transfer in HeLa cells.We identified a variant in transmembrane domain 4 of Cx50 in a family with autosomal dominant congenital cataracts. This variant has been previously identified in other cataract cohorts, but it is also present in unaffected individuals. Our study demonstrates that the mutant protein localized to the plasma membrane and formed functional intercellular channels. These data suggest that GJA8 c.658A>G is most likely a benign rare variant.

  8. Intensified Protein Structuring for more sustainable foods : Development of the up-scaled Couette Cell for the production of meat replacers

    NARCIS (Netherlands)

    Krintiras, G.

    2016-01-01

    To meet the increasing need for protein-rich food of an ever growing population, plant-based proteins are being utilized in meat products as replacements for animal-based proteins. Legumes such as soy can serve as an alternative protein source, by featuring both high protein content (36%) and

  9. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

    Science.gov (United States)

    Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T; Texier, Yves; van Beersum, Sylvia E C; Horn, Nicola; Willer, Jason R; Mans, Dorus A; Dougherty, Gerard; Lamers, Ideke J C; Coene, Karlien L M; Arts, Heleen H; Betts, Matthew J; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J F; Marcelis, Carlo L; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A; Toedt, Grischa; van Dam, Teunis J P; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L; Blacque, Oliver E; Gibson, Toby J; Huynen, Martijn A; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E; Franco, Brunella; Giles, Rachel H; Ueffing, Marius; Russell, Robert B; Roepman, Ronald

    2016-05-13

    Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.

  10. Diagnostic utility of urine protein-to-creatinine ratio for identifying proteinuria in pregnancy.

    Science.gov (United States)

    Stout, Molly J; Scifres, Christina M; Stamilio, David M

    2013-01-01

    To evaluate urine protein-to-creatinine ratio (UPC) alone and with uric acid and clinical factors to predict or exclude significant proteinuria in preeclampsia evaluations. Retrospective cohort study patients undergoing evaluation for preeclampsia. Greater than 300 mg of protein in a 24-h collection was the gold standard defining proteinuria against which UPC performance was measured. Bivariable, multivariable, and Receiver Operating Characteristic Curve (ROC) analyses were performed. Sensitivity, specificity, predictive values, and likelihood ratios were calculated for multiple cut-points of UPC alone and with uric acid. In a cohort of 356 patients, the area under the curve for UPC in the diagnosis of proteinuria was 0.81. No single cut-point of UPC was diagnostic of preeclampsia. UPC values ≤0.08 or ≥1.19 have useful negative or positive predictive values of 86% and 96%. Uric acid and clinical factors did not improve the detection of significant proteinuria. Extreme values of UPC ratio ≤0.08 or ≥1.19 have favorable predictive values, which could enable the rapid diagnosis of preeclampsia without a 24-h urine collection.

  11. [Food protein-induced enterocolitis syndrome (FPIES) in 14 children].

    Science.gov (United States)

    Delahaye, C; Chauveau, A; Kiefer, S; Dumond, P

    2017-04-01

    Food protein-induced enterocolitis syndrome (FPIES) is a particular non-IgE-mediated food allergy, manifested by profuse and repetitive vomiting with hypotonia and lethargy in its acute form. A retrospective descriptive single-center study was conducted. Subjects included in this study were children with acute FPIES who consulted the allergy outpatient clinic of the Nancy Regional University Hospital between November 2013 and June 2016. Among the 14 patients (eight boys and six girls), nine had a history of atopy: a family history for six (42.8%) and a personal history for five (35.7%). Three had chronic FPIES turning into acute FPIES. Cow milk was the most common triggering food (50%), followed by fish (21.4%), mussels (14.3%), wheat (7.1%), egg (7.1%), and poultry (7.1%). The average time from ingestion to symptom onset was 90minutes. The symptoms were typical and diarrhea was not systematic (42.8%). Six children were hospitalized, some of them several times, including once in intensive care for one patient. The treatments established were, in order of frequency: oral or intravenous rehydration, corticosteroids, antihistamines, and antiemetics. Diagnosis time was 7.6 months on average; it was significantly shorter for milk than for solid foods (1.4 vs. 12 months, P-value=0.02), on average after two episodes. Another diagnosis than FPIES was raised at first for five patients (acute gastroenteritis, gastroesophageal reflux, and bowel obstruction caused by bowel volvulus). Allergy tests were initially negative. Two chronic FPIES cases (one milk FPIES and one milk and wheat FPIES) developed an acute FPIES to another food (fish and mussels); one patient changed from an acute fish FPIES to an IgE-mediated phenotype over time. FPIES resolved for four patients: three milk FPIES, on average 15.7 months after the first reaction, and one wheat FPIES, 2.5 years after the first reaction. A child with a white fish FPIES was able to introduce salmon and tuna. FPIES is a

  12. Comparison of Protein Value of Commercial Baby Food with Homemade Baby Food and Casein Standard in Rats as the Refference point

    Directory of Open Access Journals (Sweden)

    Z Asemi

    2012-05-01

    Full Text Available

    Background and Objectives

    Evaluation of protein quality in food is of great importance due to the  biological and economical impacts of food proteins. This study has been conducted with the aim of comparing the protein quality of  homemade food (mixture of macaroni and soy bean with commercial baby food (Cerelac Wheat using Casein as the refference point.

     

    Methods

    This study was conducted on 64 twenty one day old male Wistar rats. The rats were divided into 8 groups, and each group was put on a different diet regiments. The diet regiments were as follow: 2 homemade food+Cerelac test diet, 1 Ccasein+Methionine standard diet, 1 protien-free basal diet, 2 test diet, 1 standard diet and 1 basal diet. The purpose of protien-free diet was  to evaluate True Protien Digestability (TPD. Net Protein Ratio (NPR and Protien Efficiency Ratios (PER were investigated by the basal diet. Protein intake and increasing of weight were determined for NPR and PER calculating. Nitrogen intake and fecal Nitrogen were determined to calculate TPD. Comparison of TPD, NPR and PER among the groups were analyzed by ANOVA and Tukey methods.

     

    Results

    TPD values of Standard, Cerelac and homemade food diets were 92.8±4, 87±8 and 85.4±3.2; NPR values were 4.3±0.4, 4.3±0.9, 3.8±0.6; and PER values were 3±0.2, 2.5±0.4, 1.7±0.1 respectively. The statistical difference between TPD and PER values were significant (p < 0.05, whereas NPR differences were insignificant ( p > 0.05.

     

    Conclusion

    These results shows that TPD and PER of homemade foods are lower than Cerelac while their NPR are acceptable

  13. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    DEFF Research Database (Denmark)

    Boomsma, Wouter Krogh; Nielsen, Sofie Vincents; Lindorff-Larsen, Kresten

    2016-01-01

    conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology...

  14. TcTASV: a novel protein family in trypanosoma cruzi identified from a subtractive trypomastigote cDNA library.

    Science.gov (United States)

    García, Elizabeth A; Ziliani, María; Agüero, Fernán;