1
|
Goodman RE. Twenty-eight years of GM Food and feed without harm: why not accept them? GM CROPS & FOOD 2024; 15:40-50. [PMID: 38471133 PMCID: PMC10939142 DOI: 10.1080/21645698.2024.2305944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/11/2024] [Indexed: 03/14/2024]
Abstract
Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and anti-nutritional risks. They consider risks for non-target organisms and the environment. There are no cases where post-market surveillance has uncovered harm to consumers or the environment including potential transfer of DNA from the GMO to non-target organisms. In fact, many GMOs have helped improve production, yield and reduced risks from chemical insecticides or fungicides. Yet there are generic calls to label foods containing any genetic modification as a GMO and refusing to allow GM events to be labeled as organic. Many African countries have accepted the Cartagena Protocol as a tool to keep GM events out of their countries while facing food insecurity. The rationale for those restrictions are not rational. Other issues related to genetic diversity, seed production and environmental safety must be addressed. What can be done to increase acceptance of safe and nutritious foods as the population increases, land for cultivation is reduced and energy costs soar?
Collapse
Affiliation(s)
- Richard E. Goodman
- Food Allergy Research and Resource Program, Department of Food Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
2
|
McFarland C, Alkotaini B, Cowen CP, Edwards MG, Grein E, Hahn AD, Jennings JC, Patnaik R, Potter SM, Rael LT, Sharkey BP, Taylor SL, Totman R, Van Simaeys K, Vo P, Zhao D, Connors DE. Discovery, Expression, and In Silico Safety Evaluation of Honey Truffle Sweetener, a Sweet Protein Derived from Mattirolomyces terfezioides and Produced by Heterologous Expression in Komagataella phaffii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19470-19479. [PMID: 39126644 DOI: 10.1021/acs.jafc.4c04368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Honey truffle sweetener (HTS), a 121 amino acid protein is identified as a high-intensity sweetener found naturally occurring in the Hungarian Sweet Truffle Mattirolomyces terfezioides, an edible mushroom used in regional diets. The protein is intensely sweet, but the truffle is difficult to cultivate; therefore, the protein was systematically characterized, and the gene coding for the protein was expressed in a commonly used host yeast Komagataella phaffii. The heterologously expressed protein maintained the structural characteristics and sweet taste of the truffle. Preliminary safety evaluations for use as a food ingredient were performed on the protein including digestibility and in silico approaches for predicting the allergenicity and toxicity of the protein. HTS is predicted to be nonallergenic, nontoxic, and readily digestible. This protein is readily produced by precision fermentation of the host yeast, making it a potential replacement for both added sugars and small molecule high-intensity sweeteners in food.
Collapse
Affiliation(s)
- Chase McFarland
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Bassam Alkotaini
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Chloe P Cowen
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Michael G Edwards
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
- Bioinfo Solutions, LLC., Parker, Colorado 80138, United States
| | - Elizabeth Grein
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Alan D Hahn
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Justine C Jennings
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Ranjan Patnaik
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Susan M Potter
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Leonard T Rael
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Brendan P Sharkey
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Steve L Taylor
- University of Nebraska, Dept. of Food Science & Technology, 1901 N 21st St., Lincoln, Nebraska 68588-6205, United States
| | - Ryan Totman
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Karli Van Simaeys
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Phillip Vo
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Dan Zhao
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| | - Daniel E Connors
- MycoTechnology, Inc., 18250 E. 40th Ave, Ste. 50., Aurora, Colorado 80011, United States
| |
Collapse
|
3
|
Hasan M, Ahmed S, Imranuzzaman M, Bari R, Roy S, Hasan MM, Mia MM. Designing and development of efficient multi-epitope-based peptide vaccine candidate against emerging avian rotavirus strains: A vaccinomic approach. J Genet Eng Biotechnol 2024; 22:100398. [PMID: 39179326 PMCID: PMC11260576 DOI: 10.1016/j.jgeb.2024.100398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/17/2024] [Accepted: 06/19/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Enteric avian rotavirus (ARV) is the etiological agent of several health problems that pose a global threat to commercial chickens. Therefore, to avoid these widespread epidemics and high mortality rates, only vaccine and strict biosecurity are required. METHOD The present study employs computational techniques to design a unique multi-epitope-based vaccine candidate that successfully activates immune cells against the ARV by combining adjuvant, linker, and B and T-cell epitopes. Starting, homologous sequences in the various ARV serotypes were revealed in the NCBI BLAST database, and then the two surface proteins (VP4 and VP7) of the ARV were retrieved from the UniprotKB database. The Clustal Omega server was then used to identify the conserved regions among the homologous sequences, and the B and T-cell epitopes were predicted using IEDB servers. Then, superior epitopes-2 MHC-1 epitopes, 2 MHC-2 epitopes, and 3B-cell epitopes-were combined with various adjuvants to create a total of four unique vaccine candidates. Afterward, the designed vaccine candidates underwent computational validation to assess their antigenicity, allergenicity, and stability. The vaccine candidate (V2) that demonstrated non-antigenicity, a high VaxiJen score, and non-allergenicity was ultimately chosen for molecular docking and dynamic simulation. RESULTS Although the V2 and V4 vaccine candidates were highly immunogenic, V2 had a higher solubility rate. The predicted values of the aliphatic index and GRAVY value were 30.4 and 0.417, respectively. In terms of binding energy, V2 outperformed V4. Being successfully docked with TLRs, V2 was praised as the finest. After adaptation, the sequence's 50.73 % GC content outside of the BglII or ApaI restriction sites indicated that it was equivalently safe to clone. The chosen sequence was then inserted into the pET28a(+) vector within the BglII and ApaI restriction sites. This resulted in a final clone that was 4914 base pairs long, with the inserted sequence accounting for 478 bp and the vector accounting for the remainder. CONCLUSIONS The immune-mediated simulation results for the selected vaccine construct showed significant response; thus, the study confirmed that the selected V2 vaccine candidate could enhance the immune response against ARV.
Collapse
Affiliation(s)
- Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
| | - Shakil Ahmed
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
| | - Md Imranuzzaman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh; Department of Pharmacology and Toxicology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Rezaul Bari
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Shiplu Roy
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh; Department of Livestock Production and Management, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Mahadi Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Mukthar Mia
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh; Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| |
Collapse
|
4
|
Li T, Bu G, Chen Y, Zhao Q, Chang Y. Heat/non-heat treatment alleviates β-conglycinin-triggered food allergy reactions by modulating the Th1/Th2 immune balance in a BALB/c mouse model. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6531-6540. [PMID: 38517196 DOI: 10.1002/jsfa.13476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND With the increasing popularity of plant protein-based diets, soy proteins are favored as the most important source of plant protein worldwide. However, potential food allergy risks limit their use in the food industry. This work aims to reveal the mechanism of β-conglycinin-induced food allergy, and to explore the regulatory mechanism of heat treatment and high hydrostatic pressure (HHP) treatment in a BALB/c mouse model. RESULTS Our results showed that oral administration of β-conglycinin induced severe allergic symptoms in BALB/c mice, but these symptoms were effectively alleviated through heat treatment and HHP treatment. Moreover, β-conglycinin stimulated lymphocyte proliferation and differentiation; a large number of cytokines interleukin (IL)-4, IL-5, IL-10, IL-12 and IL-13 were released and interferon γ secretion was inhibited, which disrupted the Th1/Th2 immune balance and promoted the differentiation and proliferation of naive T cells into Th2-type cells. CONCLUSION Heat/non-heat treatment altered the conformation of soybean protein, which significantly reduced allergic reactions in mice. This regulatory mechanism may be associated with Th1/Th2 immune balance. Our results provide data support for understanding the changes in allergenicity of soybean protein within the food industry. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Tanghao Li
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
- Laboratory of Food Proteins and Colloids, School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Gaungzhou, China
| | - Guanhao Bu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Yixuan Chen
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Qingqing Zhao
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Yongfeng Chang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| |
Collapse
|
5
|
Liu X, Zhang L, Lai B, Li J, Zang J, Ma L. Harnessing Protein Hydrolysates and Peptides for Hyperuricemia Management: Insights into Sources, Mechanisms, Techniques, and Future Directions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18758-18773. [PMID: 39161084 DOI: 10.1021/acs.jafc.4c03605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Hyperuricemia (HUA) is a metabolic disorder characterized by an imbalance in uric acid production and excretion, frequently leading to gout and various chronic conditions. Novel bioactive compounds offer effective alternatives for managing HUA, reducing side effects of traditional medications. Recent studies have highlighted the therapeutic potential of protein hydrolysates and peptides in managing HUA. This review focuses on preparing and applying protein hydrolysates to treat HUA and explores peptides for xanthine oxidase inhibition. Particularly, we discuss their origins, enzymatic approaches, and mechanisms of action in detail. The review provides an updated understanding of HUA pathogenesis, current pharmacological interventions, and methodologies for the preparation, purification, identification, and assessment of these compounds. Furthermore, to explore the application of protein hydrolysates and peptides in the food industry, we also address challenges and propose solutions related to the safety, bitterness, oral delivery, and the integration of artificial intelligence in peptide discovery. Bridging traditional pharmacological approaches and innovative dietary interventions, this study paves the way for future research and development in HUA management, contributing to the utilization of proteins from different food sources. In conclusion, protein hydrolysates and peptides show significant promise as safe agents and dietary interventions for preventing and treating HUA.
Collapse
Affiliation(s)
- Xiaoyu Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Lei Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Boyin Lai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingming Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Liyan Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| |
Collapse
|
6
|
Lee YJ, Jung YJ, Kim JH, Jeong YS, Ku HK, Kim BH, Kim YJ, Kim JK, Kim YS, Kim JK, Ha SH. Molecular protocol to develop β-carotene-biofortified rice events via molecular optimization. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109051. [PMID: 39197421 DOI: 10.1016/j.plaphy.2024.109051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/29/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024]
Abstract
Providing food with nutrition and functionality is crucial for sustaining human life. Rice (Oryza sativa L.) is a representative staple crop with high carbohydrate content but low amounts of essential amino acids, micronutrients, and carotenoids such as provitamin A. To improve the nutritional quality, rice endosperm was biofortified to accumulate carotenoids such as β-carotene through genetic engineering (i.e., using synthetic carotenoid biosynthetic genes, a nonmammalian viral polycistronic sequence, and an optimized promoter and transit peptide) and high-throughput rice transformation (approximately 300 transgenic plants per construct). To facilitate the safety assessment of genetically modified food, molecular characterization was performed to select elite lines equipped with a single intergenic insertion of T-DNA, high transgene expression, in this case leading to high carotenoid content, and with phenotypic and compositional substantial equivalence. In this study, we present β-carotene-biofortified rice event candidate lines eligible for commercial use and a disclosed molecular protocol for the development of biotech rice crops.
Collapse
Affiliation(s)
- Yeo Jin Lee
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Young Joo Jung
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jin Hwa Kim
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ye Sol Jeong
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyung-Keun Ku
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Byeong-Hoon Kim
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ye Jin Kim
- Division of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Gyeongsang, 25354, Republic of Korea
| | - Ju-Kon Kim
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Gyeongsang, 25354, Republic of Korea
| | - Sun-Hwa Ha
- Graduate School of Green-Bio Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea.
| |
Collapse
|
7
|
Malinczak CA, Burns Naas LA, Clark A, Conze D, DiNovi M, Kaminski N, Kruger C, Lönnerdal B, Lukacs NW, Merker R, Peterson R. Workshop report: A study roadmap to evaluate the safety of recombinant human lactoferrin expressed in Komagataella phaffii intended as an ingredient in conventional foods - Recommendations of a scientific expert panel. Food Chem Toxicol 2024; 190:114817. [PMID: 38880466 DOI: 10.1016/j.fct.2024.114817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
Human milk lactoferrin (hmLF) is a glycoprotein with well-known effects on immune function. Helaina Inc. has used a glycoengineered yeast, Komatagaella phaffii, to produce recombinant human lactoferrin (Helaina rhLF, Effera™) that is structurally similar to hmLF with intended uses as a food ingredient. However, earlier FDA reviews of rhLF were withdrawn due to insufficient safety data and unanswered safety questions the experts and FDA raised about the immunogenicity/immunotoxicity risks of orally ingested rhLF. Helaina organized a panel of leading scientists to build and vet a safety study roadmap containing the studies and safety endpoints needed to address these questions. Panelists participated in a one-day virtual workshop in June 2023 and ensuing discussions through July 2023. Relevant workshop topics included physicochemical properties of LF, regulatory history of bovine LF and rhLF as food ingredients in the FDA's generally recognized as safe (GRAS) program, and synopses of publicly available studies on the immunogenicity/alloimmunization, immunotoxicology, iron homeostasis, and absorption, distribution, metabolism, and excretion of rhLF. Panelists concluded that the safety study roadmap addresses the unanswered safety questions and the intended safe use of rhLF as a food ingredient for adults and agreed on broad applications of the roadmap to assess the safety and support GRAS of other recombinant milk proteins with immunomodulatory functions.
Collapse
Affiliation(s)
| | | | | | | | | | - Norbert Kaminski
- Department of Pharmacology & Toxicology, Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | | | - Bo Lönnerdal
- Department of Internal Medicine, University of California, Davis, CA, USA.
| | - Nicholas W Lukacs
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, USA.
| | | | | |
Collapse
|
8
|
Anaya Y, Rosario Martinez R, Goodman RE, Johnson P, Vajpeyi S, Lu X, Peterson R, Weyers SM, Breen B, Newsham K, Scottoline B, Clark AJ, Malinczak CA. Evaluation of the potential food allergy risks of human lactoferrin expressed in Komagataella phaffii. Front Immunol 2024; 15:1380028. [PMID: 39114650 PMCID: PMC11303282 DOI: 10.3389/fimmu.2024.1380028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Prior to the introduction of novel food ingredients into the food supply, safety risk assessments are required, and numerous prediction models have been developed and validated to evaluate safety. Methods The allergenic risk potential of Helaina recombinant human lactoferrin (rhLF, Effera™), produced in Komagataella phaffii (K. phaffii) was assessed by literature search, bioinformatics sequence comparisons to known allergens, glycan allergenicity assessment, and a simulated pepsin digestion model. Results The literature search identified no allergenic risk for Helaina rhLF, K. phaffii, or its glycans. Bioinformatics search strategies showed no significant risk for cross-reactivity or allergenicity between rhLF or the 36 residual host proteins and known human allergens. Helaina rhLF was also rapidly digested in simulated gastric fluid and its digestibility profile was comparable to human milk lactoferrin (hmLF), further demonstrating a low allergenic risk and similarity to the hmLF protein. Conclusion Collectively, these results demonstrate a low allergenic risk potential of Helaina rhLF and do not indicate the need for further clinical testing or serum IgE binding to evaluate Helaina rhLF for risk of food allergy prior to introduction into the food supply.
Collapse
Affiliation(s)
- Yanisa Anaya
- Nutritional Biology & Safety, Helaina, Inc, New York, NY, United States
| | | | | | - Philip Johnson
- University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Xiaoning Lu
- Nutritional Biology & Safety, Helaina, Inc, New York, NY, United States
| | - Ross Peterson
- Regulatory Affairs, Helaina, Inc, New York, NY, United States
| | | | - Bella Breen
- Late Stage R&D, Helaina, Inc, New York, NY, United States
| | - Kahler Newsham
- Late Stage R&D, Helaina, Inc, New York, NY, United States
| | - Brian Scottoline
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, United States
| | - Anthony J. Clark
- Late Stage R&D, Helaina, Inc, New York, NY, United States
- Regulatory Affairs, Helaina, Inc, New York, NY, United States
| | | |
Collapse
|
9
|
Vukovic D, Gostimirovic S, Cvetanovic J, Gavric D, Aleksic Sabo V, Todorovic D, Medic D, Knezevic P. Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics. Curr Microbiol 2024; 81:215. [PMID: 38849666 DOI: 10.1007/s00284-024-03705-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 06/09/2024]
Abstract
Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.
Collapse
Affiliation(s)
- Darija Vukovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sonja Gostimirovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Cvetanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Verica Aleksic Sabo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | | | - Deana Medic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
| |
Collapse
|
10
|
Scaife K, Taylor SL, Pařenicová L, Goodman RE, Vo TD, Leune E, Abdelmoteleb M, Dommels Y. In silico evaluation of the potential allergenicity of a fungal biomass from Rhizomucor pusillus for use as a novel food ingredient. Regul Toxicol Pharmacol 2024; 150:105629. [PMID: 38657894 DOI: 10.1016/j.yrtph.2024.105629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
The world's hunger for novel food ingredients drives the development of safe, sustainable, and nutritious novel food products. For foods containing novel proteins, potential allergenicity of the proteins is a key safety consideration. One such product is a fungal biomass obtained from the fermentation of Rhizomucor pusillus. The annotated whole genome sequence of this strain was subjected to sequence homology searches against the AllergenOnline database (sliding 80-amino acid windows and full sequence searches). In a stepwise manner, proteins were designated as potentially allergenic and were further compared to proteins from commonly consumed foods and from humans. From the sliding 80-mer searches, 356 proteins met the conservative >35% Codex Alimentarius threshold, 72 of which shared ≥50% identity over the full sequence. Although matches were identified between R. pusillus proteins and proteins from allergenic food sources, the matches were limited to minor allergens from these sources, and they shared a greater degree of sequence homology with those from commonly consumed foods and human proteins. Based on the in silico analysis and a literature review for the source organism, the risk of allergenic cross-reactivity of R. pusillus is low.
Collapse
Affiliation(s)
- Kevin Scaife
- Intertek Health Sciences Inc., 2233 Argentia Road, Suite 201, Mississauga, ON, L5N 2X7, Canada.
| | - Steve L Taylor
- Taylor Consulting LLC, 941 Evergreen Drive, Lincoln, NE, 68510, USA
| | - Lucie Pařenicová
- The Protein Brewery B.V., Goeseelsstraat 10, 4817 MV, Breda, the Netherlands; BioXact B.V., Böttgerwater 44, 2497 ZJ, Den Haag, the Netherlands
| | - Richard E Goodman
- RE Goodman Consulting LLC, 8110 Dougan Circle, Lincoln, NE, 68516, USA
| | - Trung D Vo
- Intertek Health Sciences Inc., 2233 Argentia Road, Suite 201, Mississauga, ON, L5N 2X7, Canada
| | - Elisa Leune
- The Protein Brewery B.V., Goeseelsstraat 10, 4817 MV, Breda, the Netherlands
| | - Mohamed Abdelmoteleb
- Mohamed Abdelmoteleb, Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Yvonne Dommels
- The Protein Brewery B.V., Goeseelsstraat 10, 4817 MV, Breda, the Netherlands
| |
Collapse
|
11
|
Yang Y, He X, Li F, He S, Liu M, Li M, Xia F, Su W, Liu G. Animal-derived food allergen: A review on the available crystal structure and new insights into structural epitope. Compr Rev Food Sci Food Saf 2024; 23:e13340. [PMID: 38778570 DOI: 10.1111/1541-4337.13340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/19/2024] [Indexed: 05/25/2024]
Abstract
Immunoglobulin E (IgE)-mediated food allergy is a rapidly growing public health problem. The interaction between allergens and IgE is at the core of the allergic response. One of the best ways to understand this interaction is through structural characterization. This review focuses on animal-derived food allergens, overviews allergen structures determined by X-ray crystallography, presents an update on IgE conformational epitopes, and explores the structural features of these epitopes. The structural determinants of allergenicity and cross-reactivity are also discussed. Animal-derived food allergens are classified into limited protein families according to structural features, with the calcium-binding protein and actin-binding protein families dominating. Progress in epitope characterization has provided useful information on the structural properties of the IgE recognition region. The data reveals that epitopes are located in relatively protruding areas with negative surface electrostatic potential. Ligand binding and disulfide bonds are two intrinsic characteristics that influence protein structure and impact allergenicity. Shared structures, local motifs, and shared epitopes are factors that lead to cross-reactivity. The structural properties of epitope regions and structural determinants of allergenicity and cross-reactivity may provide directions for the prevention, diagnosis, and treatment of food allergies. Experimentally determined structure, especially that of antigen-antibody complexes, remains limited, and the identification of epitopes continues to be a bottleneck in the study of animal-derived food allergens. A combination of traditional immunological techniques and emerging bioinformatics technology will revolutionize how protein interactions are characterized.
Collapse
Affiliation(s)
- Yang Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, China
| | - Xinrong He
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Fajie Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Shaogui He
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen, Fujian, China
| | - Meng Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- College of Marine Biology, Xiamen Ocean Vocational College, Xiamen, Fujian, China
| | - Mengsi Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- School of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou, Fujian, China
| | - Fei Xia
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Wenjin Su
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| |
Collapse
|
12
|
Novoa J, Fernandez-Dumont A, Mills ENC, Moreno FJ, Pazos F. Advancing the allergenicity assessment of new proteins using a text mining resource. Food Chem Toxicol 2024; 187:114638. [PMID: 38582341 DOI: 10.1016/j.fct.2024.114638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/11/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
With a society increasingly demanding alternative protein food sources, new strategies for evaluating protein safety issues, such as allergenic potential, are needed. Large-scale and systemic studies on allergenic proteins are hindered by the limited and non-harmonized clinical information available for these substances in dedicated databases. A missing key information is that representing the symptomatology of the allergens, especially given in terms of standard vocabularies, that would allow connecting with other biomedical resources to carry out different studies related to human health. In this work, we have generated the first resource with a comprehensive annotation of allergens' symptomatology, using a text-mining approach that extracts significant co-mentions between these entities from the scientific literature (PubMed, ∼36 million abstracts). The method identifies statistically significant co-mentions between the textual descriptions of the two types of entities in the literature as indication of relationship. 1,180 clinical signs extracted from the Human Phenotype Ontology, the Medical Subject Heading terms of PubMed together with other allergen-specific symptoms, were linked to 1,036 unique allergens annotated in two main allergen-related public databases via 14,009 relationships. This novel resource, publicly available through an interactive web interface, could serve as a starting point for future manually curated compilation of allergen symptomatology.
Collapse
Affiliation(s)
- Jorge Novoa
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | | | - E N Clare Mills
- School of Biosciences and Medicine, The University of Surrey, Guildford, GU2 7XH, UK
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de La Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), 28049, Madrid, Spain.
| | - Florencio Pazos
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain.
| |
Collapse
|
13
|
Bruhn M, Spatz M, Kalinke U. MORITS: An improved method to predict peptides from heterologous proteins that are recognized by the same T-cell receptor. Sci Rep 2024; 14:8255. [PMID: 38589549 PMCID: PMC11002005 DOI: 10.1038/s41598-024-58350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
Antigen-specific priming of T cells results in the activation of T cells that exert effector functions by interaction of their T-cell receptor (TCR) with the corresponding self-MHC molecule presenting a peptide on the surface of a target cell. Such antigen-specific T cells potentially can also interact with peptide-MHC complexes that contain peptides from unrelated antigens, a phenomenon that often is referred to as heterologous immunity. For example, some individuals that were pre-immunized against an allergen, could subsequently mount better anti-viral T-cell responses than non-allergic individuals. So far only few peptide pairs that experimentally have been shown to provoke heterologous immunity were identified, and available prediction tools that can identify potential candidates are imprecise. We developed the MORITS algorithm to rapidly screen large lists of peptides for sequence similarities, while giving enhanced consideration to peptide residues presented by MHC that are particularly relevant for TCR interactions. In combination with established peptide-MHC binding prediction tools, the MORITS algorithm revealed peptide similarities between the SARS-CoV-2 proteome and certain allergens. The method outperformed previously published workflows and may help to identify novel pairs of peptides that mediate heterologous immune responses.
Collapse
Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Moritz Spatz
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| |
Collapse
|
14
|
Kedar O, Golberg A, Obolski U, Confino-Cohen R. Allergic to bureaucracy? Regulatory allergenicity assessments of novel food: Motivations, challenges, compromises, and possibilities. Compr Rev Food Sci Food Saf 2024; 23:e13300. [PMID: 38477215 DOI: 10.1111/1541-4337.13300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 03/14/2024]
Abstract
New sources of proteins are essential to meet the demands of the growing world population and evolving food trends. Assessing the allergenicity of proteins in novel food (NF) poses a significant food safety regulatory challenge. The Codex Alimentarius Commission presented an allergenicity assessment protocol for genetically modified (GM) foods, which can also be adapted for NF. Since no single laboratory test can adequately predict the allergenic potential of NF, the protocol follows a weight-of-evidence approach, evaluated by experts, as part of a risk management process. Regulatory bodies worldwide have adopted this safety protocol, which, among other things, promotes global harmonization. This review unravels the reliability and various motivations, terms, concepts, and approaches of allergenicity assessments, aiming to enhance understanding among manufacturers and the public. Health Canada, Food Safety Commission JAPAN, and Food Standards Australia New Zealand were surveyed, focusing on the European Food Safety Authority and the US Food Safety Administration for examples of scientific opinions regarding allergenicity assessments for novel and GM foods, from 2019 to 2023. According to our findings, current regulatory allergenicity assessments for NF approval primarily rely on literature reviews. Only a few of the NF assessments proactively presented additional tests. We recommend conducting bioinformatic analyses on NF when a panel of experts deems that there is insufficient prior scientific research.
Collapse
Affiliation(s)
- Odeya Kedar
- Faculty of Exact Sciences, Department of Environmental Studies, The Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Alexander Golberg
- Faculty of Exact Sciences, Department of Environmental Studies, The Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Uri Obolski
- Faculty of Exact Sciences, Department of Environmental Studies, The Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, School of Public Health, Department of Epidemiology and Preventive Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Confino-Cohen
- Allergy and Clinical Immunology Unit, Meir Medical Center, Kfar Saba, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
15
|
Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
Collapse
Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| |
Collapse
|
16
|
Du Z, Xu Y, Liu C, Li Y. pLM4Alg: Protein Language Model-Based Predictors for Allergenic Proteins and Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:752-760. [PMID: 38113537 DOI: 10.1021/acs.jafc.3c07143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The rising prevalence of allergy demands efficient and accurate bioinformatic tools to expedite allergen identification and risk assessment while also reducing wet experiment expenses and time. Recently, pretrained protein language models (pLMs) have successfully predicted protein structure and function. However, to our best knowledge, they have not been used for predicting allergenic proteins/peptides. Therefore, this study aims to develop robust models for allergenic protein/peptide prediction using five pLMs of varying sizes and systematically assess their performance through fine-tuning with a convolutional neural network. The developed pLM4Alg models have achieved state-of-the-art performance with accuracy, Matthews correlation coefficient, and area under the curve scoring 93.4-95.1%, 0.869-0.902, and 0.981-0.990, respectively. Moreover, pLM4Alg is the first model capable of handling prediction tasks involving residue-missed sequences and sequences containing nonstandard amino acid residues. To facilitate easy access, a user-friendly web server (https://f6wxpfd3sh.us-east-1.awsapprunner.com) has been established. pLM4Alg is expected to become the leading machine learning-based prediction model for allergenic peptides and proteins. Its collaboration with other predictors holds great promise for accelerating allergy research.
Collapse
Affiliation(s)
- Zhenjiao Du
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Yixiang Xu
- Healthy Processed Foods Research Unit, Western Regional Research Center, USDA-ARS, Albany, California 94710, United States
| | - Changqi Liu
- School of Exercise and Nutritional Sciences, San Diego State University, San Diego, California 92182, United States
| | - Yonghui Li
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas 66506, United States
| |
Collapse
|
17
|
Karnaneedi S, Limviphuvadh V, Maurer-Stroh S, Lopata AL. De Novo Transcriptomic Analyses to Identify and Compare Allergens in Foods. Methods Mol Biol 2024; 2717:351-365. [PMID: 37737997 DOI: 10.1007/978-1-0716-3453-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Food allergens have been traditionally identified using biomolecular and immunological approaches. However, the techniques used in extracting proteins from the food source to be analyzed may hinder the availability of all proteins when assessing immunological allergenicity. Additionally, depending on the number and pool of patient sera used to detect the IgE antibody-binding allergens, some allergens may not be detected if not all the patients in the pool are sensitized to all the allergens. To overcome these limitations, we describe an additional approach before the in vitro approaches, by analyzing the transcriptome in silico for all putative allergens within the analyzed food source.
Collapse
Affiliation(s)
- Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia.
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia.
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| |
Collapse
|
18
|
Singh P, Shaikh S, Gupta S, Gupta R. In-silico development of multi-epitope subunit vaccine against lymphatic filariasis. J Biomol Struct Dyn 2023:1-15. [PMID: 38117103 DOI: 10.1080/07391102.2023.2294838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
The World Health Organization in 2022 reported that more than 863 million people in 50 countries are at risk of developing lymphatic filariasis (LF), a disease caused by parasitic infection. Immune responses to parasites suggest that the development of a prophylactic vaccine against LF is possible. Using a reverse vaccinology approach, the current study identified Trehalose-6-phosphatase (TPP) as a potential vaccine candidate among 15 reported vaccine antigens for B. malayi. High-ranking B and T-cell epitopes in the Trehalose-6-phosphatase (TPP) were shortlisted using online servers for subsequent analysis. We selected these peptides to construct a vaccine model using I-TASSER and GalaxyRefine server. The vaccine construct showed favorable physicochemical properties, high antigenicity, no allergenicity, no toxicity, and high stability. Structural validation using the Ramachandran plot showed that 98% of the residues were in favorable or mostly allowed regions. Molecular docking and simulation showed a strong binding affinity and stability of the subunit vaccine with toll-like receptor 4 (TLR4). Furthermore, the subunit vaccine showed a strong IgG/IgM response, with the disappearance of the antigen. We propose that our vaccine construct should be further evaluated using cellular and animal models to develop a vaccine that is safe and effective against LF.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Pratik Singh
- Centre of Research for Development, Parul University, Vadodara, India
| | - Samir Shaikh
- Centre of Research for Development, Parul University, Vadodara, India
| | - Sakshi Gupta
- Centre of Research for Development, Parul University, Vadodara, India
| | - Reeshu Gupta
- Centre of Research for Development, Parul University, Vadodara, India
| |
Collapse
|
19
|
Ballegaard ASR, Sancho AI, Zhou C, Knudsen NPH, Rigby NM, Bang-Berthelsen CH, Gupta S, Mackie AR, Lübeck M, Pilegaard K, Bøgh KL. Allergenicity evaluation of quinoa proteins - A study in Brown Norway rats. Food Chem Toxicol 2023; 182:114118. [PMID: 37863384 DOI: 10.1016/j.fct.2023.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The popularity of quinoa seeds has increased in the last decade due to their high nutritional value and natural gluten-free composition. Consumption of new proteins may pose a risk of introducing new allergies. In the present study the immunogenicity and sensitising capacity of quinoa proteins were assessed in a dose-response experiment in Brown Norway rats in comparison to proteins from spinach and peanut. Cross-reactivity between quinoa proteins and known allergens was evaluated by in silico analyses followed by analyses with 11 selected protein extracts and their anti-sera by means of ELISAs and immunoblotting. Further, an in vitro simulated gastro-duodenal digestion was performed. Quinoa proteins were found to have an inherent medium to high immunogenicity and sensitising capacity, being able to induce specific IgG1 and IgE levels higher than spinach but lower than peanut and elicit reactions of clinical relevance similar to peanut. Quinoa proteins were generally shown to resist digestion and retain capacity to bind quinoa-specific antibodies. Quinoa proteins were shown to be cross-reactive with peanut and tree nut allergens as high sequence homology and antibody cross-binding were demonstrated. Present study suggests that quinoa pose a medium to high level of allergenicity that should be further investigated in human studies.
Collapse
Affiliation(s)
- Anne-Sofie Ravn Ballegaard
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark
| | - Ana Isabel Sancho
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark
| | - Cui Zhou
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark
| | | | - Neil Marcus Rigby
- School of Food Science & Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Claus Heiner Bang-Berthelsen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark
| | - Shashank Gupta
- Immunology, ALK, Bøge Allé 1, DK-2970, Hørsholm, Denmark
| | - Alan Robert Mackie
- School of Food Science & Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Mette Lübeck
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9100, Aalborg, Denmark
| | - Kirsten Pilegaard
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark
| | - Katrine Lindholm Bøgh
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, DK-2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
20
|
Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. Food allergen detection by mass spectrometry: From common to novel protein ingredients. Proteomics 2023; 23:e2200427. [PMID: 37691088 DOI: 10.1002/pmic.202200427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
Food allergens are molecules, mainly proteins, that trigger immune responses in susceptible individuals upon consumption even when they would otherwise be harmless. Symptoms of a food allergy can range from mild to acute; this last effect is a severe and potentially life-threatening reaction. The European Union (EU) has identified 14 common food allergens, but new allergens are likely to emerge with constantly changing food habits. Mass spectrometry (MS) is a promising alternative to traditional antibody-based assays for quantifying multiple allergenic proteins in complex matrices with high sensitivity and selectivity. Here, the main allergenic proteins and the advantages and drawbacks of some MS acquisition protocols, such as multiple reaction monitoring (MRM) and data-dependent analysis (DDA) for identifying and quantifying common allergenic proteins in processed foodstuffs are summarized. Sections dedicated to novel foods like microalgae and insects as new sources of allergenic proteins are included, emphasizing the significance of establishing stable marker peptides and validated methods using database searches. The discussion involves the in-silico digestion of allergenic proteins, providing insights into their potential impact on immunogenicity. Finally, case studies focussing on microalgae highlight the value of MS as an effective analytical tool for ensuring regulatory compliance throughout the food control chain.
Collapse
Affiliation(s)
- Mariachiara Bianco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Giovanni Ventura
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Cosima D Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Ilario Losito
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| |
Collapse
|
21
|
Abd El-Aal AAA, Jayakumar FA, Reginald K. Dual-action potential of cationic cryptides against infections and cancers. Drug Discov Today 2023; 28:103764. [PMID: 37689179 DOI: 10.1016/j.drudis.2023.103764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 09/11/2023]
Abstract
Cryptides are a subfamily of bioactive peptides embedded latently in their parent proteins and have multiple biological functions. Cationic cryptides could be used as modern drugs in both infectious diseases and cancers because their mechanism of action is less likely to be affected by genetic mutations in the treated cells, therefore addressing a current unmet need in these two areas of medicine. In this review, we present the current understanding of cryptides, methods to mine them sustainably using available online databases and prediction tools, with a particular focus on their antimicrobial and anticancer potential, and their potential applicability in a clinical setting.
Collapse
Affiliation(s)
- Amr A A Abd El-Aal
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500 Selangor, Malaysia
| | - Fairen A Jayakumar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500 Selangor, Malaysia
| | - Kavita Reginald
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500 Selangor, Malaysia.
| |
Collapse
|
22
|
Li Y, Sackett PW, Nielsen M, Barra C. NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction. BIOINFORMATICS ADVANCES 2023; 3:vbad151. [PMID: 37901344 PMCID: PMC10603389 DOI: 10.1093/bioadv/vbad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/28/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Motivation Allergy is a pathological immune reaction towards innocuous protein antigens. Although only a narrow fraction of plant or animal proteins induce allergy, atopic disorders affect millions of children and adults and cost billions in healthcare systems worldwide. In silico predictors can aid in the development of more innocuous food sources. Previous allergenicity predictors used sequence similarity, common structural domains, and amino acid physicochemical features. However, these predictors strongly rely on sequence similarity to known allergens and fail to predict protein allergenicity accurately when similarity diminishes. Results To overcome these limitations, we collected allergens from AllergenOnline, a curated database of IgE-inducing allergens, carefully removed allergen redundancy with a novel protein partitioning pipeline, and developed a new allergen prediction method, introducing MHC presentation propensity as a novel feature. NetAllergen outperformed a sequence similarity-based BLAST baseline approach, and previous allergenicity predictor AlgPred 2 when similarity to known allergens is limited. Availability and implementation The web service NetAllergen and the datasets are available at https://services.healthtech.dtu.dk/services/NetAllergen-1.0/.
Collapse
Affiliation(s)
- Yuchen Li
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
| | - Peter Wad Sackett
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martin 1650, Argentina
| | - Carolina Barra
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
| |
Collapse
|
23
|
Kumar A, Rana PS. A deep learning based ensemble approach for protein allergen classification. PeerJ Comput Sci 2023; 9:e1622. [PMID: 37869456 PMCID: PMC10588724 DOI: 10.7717/peerj-cs.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/07/2023] [Indexed: 10/24/2023]
Abstract
In recent years, the increased population has led to an increase in the demand for various industrially processed edibles and other consumable products. These industries regularly alter the proteins found in raw materials to generate more commercially viable end-products in order to keep up with consumer demand. These modifications result in a substance that may cause allergic reactions in consumers, thereby creating a protein allergen. The detection of such proteins in various substances is essential for the prevention, diagnosis and treatment of allergic conditions. Bioinformatics and computational methods can be used to analyze the information contained in amino-acid sequences to detect possible allergens. The article presents a deep learning based ensemble approach to identify protein allergens using Extra Tree, Deep Belief Network (DBN), and CatBoost models. The proposed ensemble model achieves higher detection accuracy by combining the prediction results of the three models using majority voting. The evaluation of the proposed model was carried out on the benchmark protein allergen dataset, and the performance analysis revealed that the proposed model outperforms the other state-of-the-art literature techniques with a protein allergen detection accuracy of 89.16%.
Collapse
Affiliation(s)
- Arun Kumar
- Computer Science and Engineering, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Prashant Singh Rana
- Computer Science and Engineering, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| |
Collapse
|
24
|
Liu M, Huang J, Ma S, Yu G, Liao A, Pan L, Hou Y. Allergenicity of wheat protein in diet: Mechanisms, modifications and challenges. Food Res Int 2023; 169:112913. [PMID: 37254349 DOI: 10.1016/j.foodres.2023.112913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023]
Abstract
Wheat is widely available in people's daily diets. However, some people are currently experiencing IgE-mediated allergic reactions to wheat-based foods, which seriously impact their quality of life. Thus, it is imperative to provide comprehensive knowledge and effective methods to reduce the risk of wheat allergy (WA) in food. In the present review, recent advances in WA symptoms, the major allergens, detection methods, opportunities and challenges in establishing animal models of WA are summarized and discussed. Furthermore, an updated overview of the different modification methods that are currently being applied to wheat-based foods is provided. This study concludes that future approaches to food allergen detection will focus on combining multiple tools to rapidly and accurately quantify individual allergens in complex food matrices. Besides, biological modification has many advantages over physical or chemical modification methods in the development of hypoallergenic wheat products, such as enzymatic hydrolysis and fermentation. It is worth noting that using biotechnology to edit wheat allergen genes to produce allergen-free food may be a promising method in the future which could improve the safety of wheat foods and the health of allergy sufferers.
Collapse
Affiliation(s)
- Ming Liu
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China; College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, PR China
| | - Jihong Huang
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China; College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, PR China; State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475004, PR China; School of Food and Pharmacy, Xuchang University, Xuchang 461000, PR China.
| | - Sen Ma
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, PR China.
| | - Guanghai Yu
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Aimei Liao
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Long Pan
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Yinchen Hou
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450044, PR China
| |
Collapse
|
25
|
Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
Collapse
Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| |
Collapse
|
26
|
López-Pedrouso M, Lorenzo JM, Alché JDD, Moreira R, Franco D. Advanced Proteomic and Bioinformatic Tools for Predictive Analysis of Allergens in Novel Foods. BIOLOGY 2023; 12:biology12050714. [PMID: 37237526 DOI: 10.3390/biology12050714] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
In recent years, novel food is becoming an emerging trend increasingly more demanding in developed countries. Food proteins from vegetables (pulses, legumes, cereals), fungi, bacteria and insects are being researched to introduce them in meat alternatives, beverages, baked products and others. One of the most complex challenges for introducing novel foods on the market is to ensure food safety. New alimentary scenarios drive the detection of novel allergens that need to be identified and quantified with the aim of appropriate labelling. Allergenic reactions are mostly caused by proteins of great abundance in foods, most frequently of small molecular mass, glycosylated, water-soluble and with high stability to proteolysis. The most relevant plant and animal food allergens, such as lipid transfer proteins, profilins, seed storage proteins, lactoglobulins, caseins, tropomyosins and parvalbumins from fruits, vegetables, nuts, milk, eggs, shellfish and fish, have been investigated. New methods for massive screening in search of potential allergens must be developed, particularly concerning protein databases and other online tools. Moreover, several bioinformatic tools based on sequence alignment, motif identification or 3-D structure predictions should be implemented as well. Finally, targeted proteomics will become a powerful technology for the quantification of these hazardous proteins. The ultimate objective is to build an effective and resilient surveillance network with this cutting-edge technology.
Collapse
Affiliation(s)
- María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, 15872 A Coruña, Spain
| | - José M Lorenzo
- Centro Tecnolóxico da Carne de Galicia, Rúa Galicia Nº 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain
| | - Juan de Dios Alché
- Plant Reproductive Biology and Advanced Microscopy Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Ramón Moreira
- Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Daniel Franco
- Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
27
|
Choo KW, Mao L, Mustapha A. CAM-21, a novel lytic phage with high specificity towards Escherichia coli O157:H7 in food products. Int J Food Microbiol 2023; 386:110026. [PMID: 36444789 DOI: 10.1016/j.ijfoodmicro.2022.110026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Escherichia coli O157:H7 is a foodborne pathogen that has become a serious global concern for food safety. Despite the application of different traditional biocontrol methods in the food industry, food borne disease outbreaks linked to this organism remain. Due to their high specificity, lytic bacteriophages are promising antimicrobial agents that could be utilized to control pathogens in foods. In this study, a novel Escherichia phage, CAM-21, was isolated from a dairy farm environment. CAM-21 showed targeted host specificity towards various serotypes of Shiga toxin-producing E. coli, including O157:H7, O26, O103, and O145. Morphological analyses revealed that CAM-21 has a polyhedron capsid and a contractile tail with a diameter of about 92.83 nm, and length of about 129.75 nm, respectively. CAM-21 showed a strong inhibitory effect on the growth of E. coli O157:H7, even at a multiplicity of infection (MOI) of as low as 0.001. Phage adsorption and one-step growth analysis indicated that the target pathogen was rapidly lysed by CAM-21 that exhibited a short latent time (20 min). Electron microscopic and genomic DNA analyses suggested that CAM-21 is a lytic phage, classified as a new species in the Tequatrovirus genus of the Myoviridae Family. Based on whole genome sequencing, CAM-21 has a double-stranded DNA with 166,962 bp, 265 open reading frames and 11 tRNA. The genome of CAM-21 did not encode toxins, virulence factors, antibiotic resistance, lysogeny or allergens. Phylogenetic and genomic comparative analyses suggested that CAM-21 is a T4-like phage species. The growth of E. coli O157:H7 was effectively controlled in milk, ground beef and baby spinach at MOIs of 1000 and 10,000. CAM-21 significantly (P ≤ 0.05) reduced the bacterial counts of the treated foods, ranging from 1.4-2.0 log CFU/mL in milk to 1.3-1.4 log CFU/g in ground beef and baby spinach. These findings suggest that the lytic phage, CAM-21, is a potential candidate for controlling E. coli O157:H7 contamination in foods.
Collapse
Affiliation(s)
- Kai Wen Choo
- Food Science Program, University of Missouri, Columbia, United States of America
| | - Liang Mao
- Food Science Program, University of Missouri, Columbia, United States of America
| | - Azlin Mustapha
- Food Science Program, University of Missouri, Columbia, United States of America.
| |
Collapse
|
28
|
Vashisht S, Singh N, Sharma A, Saini N, Gaur SN, Arora N. In silico tools to assess the potential allergenicity of shiitake mushrooms (Lentinula edodes). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:877-890. [PMID: 36057923 DOI: 10.1002/jsfa.12199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Computational tools may have an edge over conventional methods for the preliminary evaluation of food allergenicity. In this study, the allergenic potential of Lentinula edodes was evaluated and validated using in silico tools. RESULTS The potential cross-reactivity of mushroom proteins with fungal allergens was determined using sequence alignment - the Fast Alignment (FASTA) and Basic Local Alignment Search Tool (BLAST) algorithm. Eight L. edodes proteins were cross-reactive with allergens from fungal origin, showing 52%-89% sequence identity using FASTA algorithm-based alignment. The BLAST data were corroborated by percentage identity and query coverage. Physico-chemical property-based allergenicity was deciphered by AlgPred, Allermatch, and AllergenFP software, which predicted six out of eight proteins as potential allergens. Sequence alignment showed 66%-86% conservancy between mushroom protein and known fungal allergens. Secondary structure and amino acid composition supported structural affinity between query and fungal proteins. Three-dimensional structures of five mushroom proteins were generated, quality assessed, and superimposed with fungal allergens, suggesting possible allergenicity of mushroom proteins. An enzyme-linked immunosorbent assay (ELISA) demonstrated immunoglobulin E (IgE) binding in 13 out of 21 food-hypersensitive patients' sera. CONCLUSION In silico tools provide preliminary indications about the potential allergenicity and cross-reactivity of mushroom proteins. This approach may be used for the prelusive allergenicity assessment of allergen sources. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Srishti Vashisht
- Allergy and Immunology Section, CSIR-Institute of Genomicsand Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Naresh Singh
- Allergy and Immunology Section, CSIR-Institute of Genomicsand Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akansha Sharma
- Allergy and Immunology Section, CSIR-Institute of Genomicsand Integrative Biology, Delhi, India
| | - Neeru Saini
- Allergy and Immunology Section, CSIR-Institute of Genomicsand Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shailendra Nath Gaur
- Department of Respiratory Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Naveen Arora
- Allergy and Immunology Section, CSIR-Institute of Genomicsand Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
29
|
Tomer R, Patiyal S, Dhall A, Raghava GPS. Prediction of celiac disease associated epitopes and motifs in a protein. Front Immunol 2023; 14:1056101. [PMID: 36742312 PMCID: PMC9893285 DOI: 10.3389/fimmu.2023.1056101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
Introduction Celiac disease (CD) is an autoimmune gastrointestinal disorder causes immune-mediated enteropathy against gluten. Gluten immunogenic peptides have the potential to trigger immune responses which leads to damage the small intestine. HLA-DQ2/DQ8 are major alleles that bind to epitope/antigenic region of gluten and induce celiac disease. There is a need to identify CD associated epitopes in protein-based foods and therapeutics. Methods In this study, computational tools have been developed to predict CD associated epitopes and motifs. Dataset used for training, testing and evaluation contain experimentally validated CD associated and non-CD associate peptides. We perform positional analysis to identify the most significant position of an amino acid residue in the peptide and checked the frequency of HLA alleles. We also compute amino acid composition to develop machine learning based models. We also developed ensemble method that combines motif-based approach and machine learning based models. Results and Discussion Our analysis support existing hypothesis that proline (P) and glutamine (Q) are highly abundant in CD associated peptides. A model based on density of P&Q in peptides has been developed for predicting CD associated peptides which achieve maximum AUROC 0.98 on independent data. We discovered motifs (e.g., QPF, QPQ, PYP) which occurs specifically in CD associated peptides. We also developed machine learning based models using peptide composition and achieved maximum AUROC 0.99. Finally, we developed ensemble method that combines motif-based approach and machine learning based models. The ensemble model-predict CD associated motifs with 100% accuracy on an independent dataset, not used for training. Finally, the best models and motifs has been integrated in a web server and standalone software package "CDpred". We hope this server anticipate the scientific community for the prediction, designing and scanning of CD associated peptides as well as CD associated motifs in a protein/peptide sequence (https://webs.iiitd.edu.in/raghava/cdpred/).
Collapse
|
30
|
Sarkar RK, Ghosh N, Sircar G, Saha S. Updates on Databases of Allergens and Allergen-Epitopes. Methods Mol Biol 2023; 2673:151-165. [PMID: 37258912 DOI: 10.1007/978-1-0716-3239-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The increasing prevalence of allergic diseases is of great public health concern. Environmental and food allergens are the major triggers of allergic diseases via respiratory or gastrointestinal routes, respectively. A major setback in the clinical management of allergies is the unavailability of purified allergens required for diagnostic purposes. Furthermore, manipulation of allergen sequences and structures by employing protein-engineering approaches is needed to design immunotherapeutic vaccines. All these approaches rely upon the sequence, structure, and epitope location of allergens. A number of databases have therefore been developed that serve as repositories of molecular information of allergens. In this chapter, we discuss the five most important widely used allergen databases that might be helpful for the research community working on molecular allergology.
Collapse
Affiliation(s)
- Rajat Kanti Sarkar
- Department of Genetics and Plant Breeding, Visva-Bharati University, Bolpur, West Bengal, India
- Institute of Health Sciences, Presidency University (Newtown Campus), Kolkata, West Bengal, India
| | - Nandini Ghosh
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, India
| | - Gaurab Sircar
- Institute of Health Sciences, Presidency University (Newtown Campus), Kolkata, West Bengal, India.
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, Kolkata, West Bengal, India.
| |
Collapse
|
31
|
Lynch B, Wang T, Vo T, Tafazoli S, Ryder J. Safety evaluation of oubli fruit sweet protein (brazzein) derived from Komagataella phaffii, intended for use as a sweetener in food and beverages. TOXICOLOGY RESEARCH AND APPLICATION 2023. [DOI: 10.1177/23978473231151258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Naturally sweet proteins have no glycemic effect and offer a fundamentally new approach to sweetness and health for individuals seeking to reduce their added sugar intake. However, unlike many commercial sweeteners, little research has been performed on the potential safety implications of adding these uniquely sweet proteins to food and beverages. In this study, a naturally sweet protein found in the West African Oubli plant ( Pentadiplandra brazzeana), referred to as Oubli fruit sweet protein or brazzein, was expressed in Komagataella phaffii (formerly Pichia pastoris) and produced via precision fermentation, and a safety and risk assessment was undertaken for its use as a sweetener in food and beverages. Potential consumption levels of brazzein were estimated to be 3 mg/kg body weight/day based on the National Health and Nutrition Examination Survey. The safety of brazzein derived from K. phaffii was evaluated through in silico allergenicity, in vitro genotoxicity (reverse mutation and mammalian micronucleus assays), and a 90-day dietary oral toxicity study in rats. There was no indication of allergenicity in the in silico analyses. Brazzein was non-genotoxic in the in vitro assays and showed no adverse effects in the 90-day oral toxicity study up to the highest dose tested, where the no-observed-adverse-effect level (NOAEL) was 978 and 985 mg/kg body weight/day in males and females, respectively. The totality of evidence in the in silico allergenicity, in vitro genotoxicity, and 90-day dietary toxicity studies demonstrates that brazzein derived from K. phaffii is considered safe for use as a sweetener in food and beverages.
Collapse
Affiliation(s)
| | | | - Trung Vo
- Intertek, Mississauga, ON, Canada
| | | | - Jason Ryder
- Oobli Inc, Davis, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
32
|
Randall TA, Kurtz DM. Assembly of a Draft Genome for the Mouse Ectoparasite Myocoptes musculinus. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2023; 62:55-63. [PMID: 36755207 PMCID: PMC9936850 DOI: 10.30802/aalas-jaalas-22-000066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Myocoptes musculinus is a common ectoparasite of wild mice and is occasionally found on research mice. Infestations of research mice are often subclinical but can cause severe dermatitis. Perhaps more importantly, infestations can cause immunologic reactions that may alter research outcomes, and most animal research facilities strive to prevent or eliminate mites from their mouse colonies. M. musculinus infestations are currently detected by using microscopic evaluation of the fur and skin and PCR assays of pelt swabs targeting the rRNA genes of this mite. In our facility, we encountered multiple, false-positive 18S rRNA PCR results from a closed mouse colony. We could not identify the source of the false positives even after performing PCR analysis of other Myocoptes gene targets using assays developed from the few other target genomic sequences available for M. musculinus or Myocoptes japonensis in public databases. This situation highlighted the limited genetic resources available for development of diagnostic tests specific for this ectoparasite. To expand the available genetic resources, we generated a metagenome of M. musculinus derived by sequencing from fur plucks of an infected mouse. We also determined the completeness of this metagenome and compared it with those of related mites.
Collapse
Affiliation(s)
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina,Corresponding author.
| |
Collapse
|
33
|
Herman RA, Song P. Comprehensive COMPARE database reduces allergenic risk of novel food proteins. GM CROPS & FOOD 2022; 13:112-118. [PMID: 35674136 PMCID: PMC9196780 DOI: 10.1080/21645698.2022.2079180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The comprehensiveness of the allergen database used to bioinformatically compare a novel food protein with known allergens is critical to the ability to assess the allergenic risk of newly expressed proteins in genetically engineered crops. The strength of the relationship between a candidate GE protein's amino acid sequence and that of known allergens is used to predict cross-reactive risk. The number of truly novel allergen sequences added annually to the COMPARE database reflects on the comprehensiveness of our knowledge of allergen amino acid sequence diversity. Here, we investigated the most recent five years of updates to the COMPARE allergen database for truly novel entries. Results indicate that few truly novel sequences are added each year, suggesting that the database and our knowledge of allergen sequence diversity is currently quite comprehensive, and that current in silico prediction of allergenic risk for novel food proteins is robust.
Collapse
Affiliation(s)
- Rod A. Herman
- Regulatory and Stewardship, Corteva Agriscience, Indianapolis, Indiana, USA,CONTACT Rod A. Herman Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana46268
| | - Ping Song
- Regulatory and Stewardship, Corteva Agriscience, Indianapolis, Indiana, USA
| |
Collapse
|
34
|
Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
Collapse
|
35
|
Liguori B, Sancho AI, Poulsen M, Lindholm Bøgh K. Novel foods: allergenicity assessment of insect proteins. EFSA J 2022; 20:e200910. [DOI: 10.2903/j.efsa.2022.e200910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
36
|
Mia MM, Hasan M, Ahmed S, Rahman MN. Insight into the first multi-epitope-based peptide subunit vaccine against avian influenza A virus (H5N6): An immunoinformatics approach. INFECTION, GENETICS AND EVOLUTION 2022; 104:105355. [PMID: 36007760 PMCID: PMC9394107 DOI: 10.1016/j.meegid.2022.105355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/22/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
The rampant spread of highly pathogenic avian influenza A (H5N6) virus has drawn additional concerns along with ongoing Covid-19 pandemic. Due to its migration-related diffusion, the situation is deteriorating. Without an existing effective therapy and vaccines, it will be baffling to take control measures. In this regard, we propose a revers vaccinology approach for prediction and design of a multi-epitope peptide based vaccine. The induction of humoral and cell-mediated immunity seems to be the paramount concern for a peptide vaccine candidate; thus, antigenic B and T cell epitopes were screened from the surface, membrane and envelope proteins of the avian influenza A (H5N6) virus, and passed through several immunological filters to determine the best possible one. Following that, the selected antigenic with immunogenic epitopes and adjuvant were linked to finalize the multi-epitope-based peptide vaccine by appropriate linkers. For the prediction of an effective binding, molecular docking was carried out between the vaccine and immunological receptors (TLR8). Strong binding affinity and good docking scores clarified the stringency of the vaccines. Furthermore, molecular dynamics simulation was performed within the highest binding affinity complex to observe the stability, and minimize the designed vaccine's high mobility region to order to increase its stability. Then, Codon optimization and other physicochemical properties were performed to reveal that the vaccine would be suitable for a higher expression at cloning level and satisfactory thermostability condition. In conclusion, predicting the overall in silico assessment, we anticipated that our designed vaccine would be a plausible prevention against avian influenza A (H5N6) virus.
Collapse
Affiliation(s)
- Md Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Shakil Ahmed
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Nahian Rahman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| |
Collapse
|
37
|
Paull RE, Zerpa‐Catanho D, Chen NJ, Uruu G, Wai CMJ, Kantar M. Taro raphide-associated proteins: Allergens and crystal growth. PLANT DIRECT 2022; 6:e443. [PMID: 36091877 PMCID: PMC9440338 DOI: 10.1002/pld3.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Calcium oxalate raphide crystals are found in bundles in intravacuolar membrane chambers of specialized idioblasts cells of most plant families. Aroid raphides are proposed to cause acridity in crops such as taro (Colocasia esculenta (L.) Schott). Acridity is irritation that causes itchiness and pain when raw/insufficiently cooked tissues are eaten. Since raphides do not always cause acridity and since acridity can be inactivated by cooking and/or protease treatment, it is possible that a toxin or allergen-like compound is associated with the crystals. Using two-dimensional (2D) gel electrophoresis and mass spectrometry (MS) peptide sequencing of selected peptides from purified raphides and taro apex transcriptome sequencing, we showed the presence on the raphides of peptides normally associated with mitochrondria (ATP synthase), chloroplasts (chaperonin ~60 kDa), cytoplasm (actin, profilin), and vacuole (V-type ATPase) that indicates a multistage biocrystallation process ending with possible invagination of the tonoplast and addition of mucilage that may be derived from the Golgi. Actin might play a crucial role in the generation of the needle-like raphides. One of the five raphide profilins genes was highly expressed in the apex and had a 17-amino acid insert that significantly increased that profilin's antigenic epitope peak. A second profilin had a 2-amino acid insert and also had a greater B-cell epitope prediction. Taro profilins showed 83% to 92% similarity to known characterized profilins. Further, commercial allergen test strips for hazelnuts, where profilin is a secondary allergen, have potential for screening in a taro germplasm to reduce acridity and during food processing to avoid overcooking.
Collapse
Affiliation(s)
- Robert E. Paull
- Tropical Plant and Soil SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
| | | | - Nancy J. Chen
- Tropical Plant and Soil SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
| | - Gail Uruu
- Tropical Plant and Soil SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
| | | | - Michael Kantar
- Tropical Plant and Soil SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
| |
Collapse
|
38
|
Bartholomai BM, Ruwe KM, Thurston J, Jha P, Scaife K, Simon R, Abdelmoteleb M, Goodman RE, Farhi M. Safety evaluation of Neurospora crassa mycoprotein for use as a novel meat alternative and enhancer. Food Chem Toxicol 2022; 168:113342. [PMID: 35963473 DOI: 10.1016/j.fct.2022.113342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Cultivation of filamentous fungi to produce sustainable, nutrient rich meat replacements has recently attracted significant commercial and research interest. Here, we report evidence for the safety and nutritional value of Neurospora crassa mycoprotein, a whole mycelium food ingredient produced by fermentation and minimal downstream processing. N. crassa has a long history of human use in fermented foods and in molecular biology research. A survey of studies that used N. crassa in animal feed revealed no adverse effects to the health of the animals. Furthermore, a review of the literature found no reports of confirmed allergenicity or toxicity in humans involving N. crassa. Genomic toxigenicity analysis and in vitro testing did not identify any toxins in N. crassa mycoprotein. Two independent genomic allergenicity studies did not identify proteins that would be considered a particular risk for allergenic potential. Furthermore, nutritional analysis demonstrated that N. crassa mycoprotein is a good source of complete protein and is rich in fiber, potassium, and iron. Taken together, the presented data and the history of human use without evidence of human or animal harm indicate that foods containing N. crassa can generally be regarded as safe.
Collapse
Affiliation(s)
| | | | | | - Prachi Jha
- The Better Meat Co., West Sacramento, CA, USA
| | - Kevin Scaife
- Intertek Health Sciences Inc., Mississauga, ON, Canada
| | - Ryan Simon
- Intertek Health Sciences Inc., Mississauga, ON, Canada
| | | | - Richard E Goodman
- Food Allergy Research and Resource Program, University of Nebraska, Lincoln, NE, USA
| | - Moran Farhi
- The Better Meat Co., West Sacramento, CA, USA
| |
Collapse
|
39
|
Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J. In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile. Front Genet 2022; 13:878012. [PMID: 36035185 PMCID: PMC9403866 DOI: 10.3389/fgene.2022.878012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridium difficile (C. difficile) is a multi-strain, spore-forming, Gram-positive, opportunistic enteropathogen bacteria, majorly associated with nosocomial infections, resulting in severe diarrhoea and colon inflammation. Several antibiotics including penicillin, tetracycline, and clindamycin have been employed to control C. difficile infection, but studies have suggested that injudicious use of antibiotics has led to the development of resistance in C. difficile strains. However, many proteins from its genome are still considered uncharacterized proteins that might serve crucial functions and assist in the biological understanding of the organism. In this study, we aimed to annotate and characterise the 6 C. difficile strains using in silico approaches. We first analysed the complete genome of 6 C. difficile strains using standardised approaches and analysed hypothetical proteins (HPs) employing various bioinformatics approaches coalescing, including identifying contigs, coding sequences, phage sequences, CRISPR-Cas9 systems, antimicrobial resistance determination, membrane helices, instability index, secretory nature, conserved domain, and vaccine target properties like comparative homology analysis, allergenicity, antigenicity determination along with structure prediction and binding-site analysis. This study provides crucial supporting information about the functional characterization of the HPs involved in the pathophysiology of the disease. Moreover, this information also aims to assist in mechanisms associated with bacterial pathogenesis and further design candidate inhibitors and bona fide pharmaceutical targets.
Collapse
Affiliation(s)
| | | | | | | | | | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- School of Computational and Data Sciences, Vidyashilp University, Bengaluru, India
- Department of Computer Science, FLAME University, Pune, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
| |
Collapse
|
40
|
The Fate of IgE Epitopes and Coeliac Toxic Motifs during Simulated Gastrointestinal Digestion of Pizza Base. Foods 2022; 11:foods11142000. [PMID: 35885243 PMCID: PMC9318710 DOI: 10.3390/foods11142000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/27/2022] [Accepted: 07/03/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding how food processing may modify allergen bioaccessibility and the evolution of immunologically active peptides in the gastrointestinal tract is essential if knowledge-based approaches to reducing the allergenicity of food are to be realised. A soy-enriched wheat-based pizza base was subjected to in vitro oral–gastro–duodenal digestion and resulting digests analysed using a combination of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometry (MS). The digestion profile of pizza base resembled that of bread crust where higher temperatures during baking reduced protein solubility but still resulted in the generation of a complex mixture of peptides. MS profiling showed numerous peptides carrying IgE epitopes, and coeliac toxic motifs were in excess of 20–30 residues long and were only released after either 120 min of gastric digestion or a combination of gastric and duodenal digestion. In silico prediction tools showed an overestimated number of cleavage sites identified experimentally, with low levels of atypical peptic and chymotryptic cleavage sites identified particularly at glutamine residues. These data suggest that such alternative pepsin cleavage sites may play a role in digestion of glutamine-rich cereal foods. They also contribute to efforts to provide benchmarks for mapping in vitro digestion products of novel proteins which form part of the allergenicity risk assessment.
Collapse
|
41
|
Singh P, G. K. S, Thakur S, Rathore M, Verma OP, Singh NP, Das A. Evaluation of transgenic chickpea harboring codon-modified Vip3Aa against gram pod borer (Helicoverpa armigera H.). PLoS One 2022; 17:e0270011. [PMID: 35749522 PMCID: PMC9231776 DOI: 10.1371/journal.pone.0270011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022] Open
Abstract
The gram pod borer is a major pest of chickpea, accounting for average annual yield losses to the tune of 40-50%. VIP3Aa, a class of insecticidal protein with different receptor binding site in the insect's midgut compared to Bt-crystal protein, offers an alternative protection strategy against Lepidopteran insects. Here, we report evaluation of genetically engineered chickpea lines harboring codon modified Vip3Aa (cmVip3Aa) against the Lepidopteran insect pest, gram pod borer. The synthetic codon modified, cmVip3Aa gene of 2,370 bp was sub-cloned in modified plant expression vector and used for direct transformation of embryonic axis explants of chickpea (cv. DCP 92-3), with transformation efficiency of 4.30%. Presence and transmission of transgene across two generations were confirmed by PCR and Southern blot analyses in the five selected transgenic chickpea lines. Real Time PCR analyses indicated variable levels of cmVip3Aa expression in the transgenic chickpea lines (average Cq values 15.01±0.86 to 19.32±0.10), which were absent in the non-transgenic counterpart. Detached leaf insect bioassay indicate larval mortality (up to 39.75%), reduced larval feeding (up to 82.91%) and reduced larval weight gain (up to 68.23%), compared to control lines. Evaluation of gene offers a platform to identify efficacious insecticidal gene that can be used for insect resistance management in chickpea.
Collapse
Affiliation(s)
- Prateek Singh
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, SHUATS, Prayagraj, Uttar Pradesh, India
| | - Sujayanand G. K.
- Division of Crop Protection, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Shallu Thakur
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Meenal Rathore
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Om Prakash Verma
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, SHUATS, Prayagraj, Uttar Pradesh, India
| | - Narendra Pratap Singh
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Alok Das
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| |
Collapse
|
42
|
Chen S, Downs ML. Proteomic Analysis of Oil-Roasted Cashews Using a Customized Allergen-Focused Protein Database. J Proteome Res 2022; 21:1694-1706. [PMID: 35658452 DOI: 10.1021/acs.jproteome.2c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cashews are one of the most prevalent causes of tree nut allergies. However, the cashew proteome is far from complete, which limits the quality of peptide identification in mass spectrometric analyses. In this study, bioinformatics tools were utilized to construct a customized cashew protein database and improve sequence quality for proteins of interest, based on a publicly available cashew genome database. As a result, two additional isoforms for cashew 2S albumins and five other isoforms for cashew 11S proteins were identified, along with several other potential allergens. Using the optimized protein database, the protein profiles of cashew nuts subjected to different oil-roasting conditions (139 and 166 °C for 2-10 min) were analyzed using discovery LC-MS/MS analysis. The results showed that the cashew 2S protein is most heat-stable, followed by 11S and 7S proteins, though protein isoforms might be affected differently. Preliminary target peptide selection indicated that out of the 29 potential targets, 18 peptides were derived from the newly developed database. In the evaluation of thermal processing effects on cashew proteins, several Maillard reaction adducts were also identified. The cashew protein database developed in this study allows for comprehensive analyses of cashew proteins and development of high-quality allergen detection methods.
Collapse
Affiliation(s)
- Shimin Chen
- Food Allergy Research and Resource Program, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Melanie L Downs
- Food Allergy Research and Resource Program, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| |
Collapse
|
43
|
Abbasi BA, Saraf D, Sharma T, Sinha R, Singh S, Sood S, Gupta P, Gupta A, Mishra K, Kumari P, Rawal K. Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches. PeerJ 2022; 10:e13380. [PMID: 35611169 PMCID: PMC9124463 DOI: 10.7717/peerj.13380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
An unusual pneumonia infection, named COVID-19, was reported on December 2019 in China. It was reported to be caused by a novel coronavirus which has infected approximately 220 million people worldwide with a death toll of 4.5 million as of September 2021. This study is focused on finding potential vaccine candidates and designing an in-silico subunit multi-epitope vaccine candidates using a unique computational pipeline, integrating reverse vaccinology, molecular docking and simulation methods. A protein named spike protein of SARS-CoV-2 with the GenBank ID QHD43416.1 was shortlisted as a potential vaccine candidate and was examined for presence of B-cell and T-cell epitopes. We also investigated antigenicity and interaction with distinct polymorphic alleles of the epitopes. High ranking epitopes such as DLCFTNVY (B cell epitope), KIADYNKL (MHC Class-I) and VKNKCVNFN (MHC class-II) were shortlisted for subsequent analysis. Digestion analysis verified the safety and stability of the shortlisted peptides. Docking study reported a strong binding of proposed peptides with HLA-A*02 and HLA-B7 alleles. We used standard methods to construct vaccine model and this construct was evaluated further for its antigenicity, physicochemical properties, 2D and 3D structure prediction and validation. Further, molecular docking followed by molecular dynamics simulation was performed to evaluate the binding affinity and stability of TLR-4 and vaccine complex. Finally, the vaccine construct was reverse transcribed and adapted for E. coli strain K 12 prior to the insertion within the pET-28-a (+) vector for determining translational and microbial expression followed by conservancy analysis. Also, six multi-epitope subunit vaccines were constructed using different strategies containing immunogenic epitopes, appropriate adjuvants and linker sequences. We propose that our vaccine constructs can be used for downstream investigations using in-vitro and in-vivo studies to design effective and safe vaccine against different strains of COVID-19.
Collapse
|
44
|
Complete Genome Sequence of Enterobacter Phage vB_EcRAM-01, a New Pseudotevenvirus against the Enterobacter cloacae Complex. Microbiol Resour Announc 2022; 11:e0004522. [PMID: 35536031 PMCID: PMC9202438 DOI: 10.1128/mra.00045-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the complete genome sequence of Enterobacter phage vB_EcRAM-01, isolated from waters of the Río Abajo river, in Panama City, Panama. This phage has deployed lytic activity against the Enterobacter cloacae complex, a pathogen of clinical importance in intensive care units. It belongs to the Myoviridae family and has a double-stranded DNA genome that is 178,477 bp long and contains 293 open reading frames (ORFs).
Collapse
|
45
|
Díaz-Perales A, Escribese MM, Garrido-Arandia M, Obeso D, Izquierdo-Alvarez E, Tome-Amat J, Barber D. The Role of Sphingolipids in Allergic Disorders. FRONTIERS IN ALLERGY 2022; 2:675557. [PMID: 35386967 PMCID: PMC8974723 DOI: 10.3389/falgy.2021.675557] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Allergy is defined as a complex chronic inflammatory condition in which genetic and environmental factors are implicated. Sphingolipids are involved in multiple biological functions, from cell membrane components to critical signaling molecules. To date, sphingolipids have been studied in different human pathologies such as neurological disorders, cancer, autoimmunity, and infections. Sphingolipid metabolites, in particular, ceramide and sphingosine-1-phosphate (S1P), regulate a diverse range of cellular processes that are important in immunity and inflammation. Moreover, variations in the sphingolipid concentrations have been strongly associated with allergic diseases. This review will focus on the role of sphingolipids in the development of allergic sensitization and allergic inflammation through the activation of immune cells resident in tissues, as well as their role in barrier remodeling and anaphylaxis. The knowledge gained in this emerging field will help to develop new therapeutic options for allergic disorders.
Collapse
Affiliation(s)
- Araceli Díaz-Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Maria M Escribese
- Basic Medical Sciences Department, Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - David Obeso
- Centro de Excelencia en Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Elena Izquierdo-Alvarez
- Basic Medical Sciences Department, Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Jaime Tome-Amat
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Domingo Barber
- Basic Medical Sciences Department, Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| |
Collapse
|
46
|
Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. A new paradigm to search for allergenic proteins in novel foods by integrating proteomics analysis and in silico sequence homology prediction: Focus on spirulina and chlorella microalgae. Talanta 2022; 240:123188. [PMID: 34990986 DOI: 10.1016/j.talanta.2021.123188] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
Since novel nutrient sources with high protein content, such as yeast, fungi, bacteria, algae, and insects, are increasingly introduced in the consumer market, safety evaluation studies on their potentially allergenic proteins are required. A pipeline for in silico establishing the sequence-based homology between proteins of spirulina (Arthrospira platensis) and chlorella (Chlorella vulgaris) micro-algae and those included in the AllergenOnline (AO) database (AllergenOnline.org) is described. The extracted proteins were first identified through tryptic peptides analysis by reversed-phase liquid chromatography and high resolution/accuracy Fourier-transform tandem mass spectrometry (RPLC-ESI-FTMS/MS), followed by a quest on the UniProt database. The AO database was subsequently interrogated to assess sequence similarity between identified microalgal proteins and known allergens, based on criteria established by the World Health Organization (WHO) and Food and Agriculture Organization (FAO). A direct search for microalgal proteins already included in allergen databases was also performed using the Allergome database. Six proteins exhibiting a significant homology with food allergens were identified in spirulina extracts. Five of them, i.e., two thioredoxins (D4ZSU6, K1VP15), a superoxide dismutase (C3V3P3), a glyceraldehyde-3-phosphate dehydrogenase (K1W168), and a triosephosphate isomerase (D5A635), resulted from the search on AO. The sixth protein, C-phycocyanin beta subunit (P72508), was directly obtained after examining the Allergome database. Two proteins exhibiting significant sequence homology with food allergens were retrieved in chlorella extracts, viz. calmodulin (A0A2P6TFR8), which is related to troponin c (D7F1Q2), and fructose-bisphosphate aldolase (A0A2P6TDD0). Specific serum screenings based on immunochemical tests should be undertaken to confirm or rule out the allergenicity of the identified proteins.
Collapse
Affiliation(s)
- Mariachiara Bianco
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| |
Collapse
|
47
|
Identification and characterization of phosphoproteins in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Food Chem 2022; 372:131242. [PMID: 34818726 DOI: 10.1016/j.foodchem.2021.131242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022]
Abstract
Many proteins are known to be phosphorylated, affecting important regulatory factors of muscle quality in the aquatic animals. The striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis were used to investigate muscle texture and identify phosphoproteins by histological methods and phosphoproteomic analysis. Our present study reveals that muscle fiber density is in relation to meat texture of the striated and smooth adductor muscles. The phosphoproteomic analysis has identified 764 down-regulated and 569 up-regulated phosphosites on 743 phosphoproteins in the smooth muscle compared to the striated part. The identification of unique phosphorylation sites in glycolytic enzymes may increase the activity of glycolytic enzymes and the rate of glycolysis in the striated adductor muscle. The present findings will provide new evidences on the role of muscle structure and protein phosphorylation in scallop muscle quality and thus help to develop strategies for improving meat quality of scallop products.
Collapse
|
48
|
Patil PJ, Usman M, Zhang C, Mehmood A, Zhou M, Teng C, Li X. An updated review on food-derived bioactive peptides: Focus on the regulatory requirements, safety, and bioavailability. Compr Rev Food Sci Food Saf 2022; 21:1732-1776. [PMID: 35142435 DOI: 10.1111/1541-4337.12911] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/07/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023]
Abstract
Food-derived bioactive peptides (BAPs) are recently utilized as functional food raw materials owing to their potential health benefits. Although there is a huge amount of scientific research about BAPs' identification, purification, characterization, and physiological functions, and subsequently, many BAPs have been marketed, there is a paucity of review on the regulatory requirements, bioavailability, and safety of BAPs. Thus, this review focuses on the toxic peptides that could arise from their primary proteins throughout protein extraction, protein pretreatment, and BAPs' formulation. Also, the influences of BAPs' length and administration dosage on safety are summarized. Lastly, the challenges and possibilities in BAPs' bioavailability and regulatory requirements in different countries were also presented. Results revealed that the human studies of BAPs are essential for approvals as healthy food and to prevent the consumers from misinformation and false promises. The BAPs that escape the gastrointestinal tract epithelium and move to the stomach are considered good peptides and get circulated into the blood using different pathways. In addition, the hydrophobicity, net charge, molecular size, length, amino acids composition/sequences, and structural characteristics of BAPs are critical for bioavailability, and appropriate food-grade carriers can enhance it. The abovementioned features are also vital to optimize the solubility, water holding capacity, emulsifying ability, and foaming property of BAPs in food products. In the case of safety, the possible allergenic and toxic peptides often exhibit physiological functions and could be produced during the hydrolysis of food proteins. It was also noted that the production of iso-peptides bonds and undesirable Maillard reaction might occur during protein extraction, sample pretreatments, and peptide synthesis.
Collapse
Affiliation(s)
- Prasanna J Patil
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Muhammad Usman
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chengnan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Arshad Mehmood
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Mingchun Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chao Teng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing, China
| |
Collapse
|
49
|
Chaudhary N, Mohan B, Mavuduru RS, Kumar Y, Taneja N. Characterization, genome analysis and in vitro activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant and extensively drug-resistant biofilm-forming uropathogenic Escherichia coli isolates, India. J Appl Microbiol 2022; 132:3387-3404. [PMID: 34989075 DOI: 10.1111/jam.15439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/23/2022]
Abstract
AIM We aimed to study host range, stability, genome and antibiofilm activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant (MDR) and extensively drug-resistant (XDR) biofilm-forming uropathogenic Escherichia coli isolates. METHODS AND RESULTS A novel lytic phage vB_EcoA_RDN8.1 active against UPEC strains resistant to third-generation cephalosporins, fluoroquinolones, aminoglycosides, imipenem, beta-lactamase inhibitor combination and polymyxins was isolated from community raw sewage water of Chandigarh. It exhibited a clear plaque morphology and a burst size of 250. In the time-kill assay, the maximum amount of killing was achieved at MOI 1.0. vB_EcoA_RDN8.1 belongs to the family Autographiviridae, has a genome size of 39.5 kb with a GC content of 51.6%. It was stable over a wide range of temperatures and pH. It was able to inhibit biofilm formation which may be related to an endolysin encoded by ORF 19. CONCLUSIONS The vB_EcoA_RDN8.1 is a novel lytic phage that has the potential for inclusion into phage cocktails being developed for the treatment of urinary tract infections (UTIs) caused by highly drug-resistant UPEC. SIGNIFICANCE AND IMPACT OF THE STUDY We provide a detailed characterization of a novel lytic Escherichia phage with antibiofilm activity having a potential application against MDR and XDR UPEC causing UTIs.
Collapse
Affiliation(s)
- Naveen Chaudhary
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ravimohan S Mavuduru
- Department of Urology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yashwant Kumar
- Central Research Institute, National Salmonella and Escherichia Centre, Kasauli, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
50
|
Allergic Diseases: A Comprehensive Review on Risk Factors, Immunological Mechanisms, Link with COVID-19, Potential Treatments, and Role of Allergen Bioinformatics. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182212105. [PMID: 34831860 PMCID: PMC8622387 DOI: 10.3390/ijerph182212105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022]
Abstract
The prevalence of allergic diseases is regarded as one of the key challenges in health worldwide. Although the precise mechanisms underlying this rapid increase in prevalence are unknown, emerging evidence suggests that genetic and environmental factors play a significant role. The immune system, microbiota, viruses, and bacteria have all been linked to the onset of allergy disorders in recent years. Avoiding allergen exposure is the best treatment option; however, steroids, antihistamines, and other symptom-relieving drugs are also used. Allergen bioinformatics encompasses both computational tools/methods and allergen-related data resources for managing, archiving, and analyzing allergological data. This study highlights allergy-promoting mechanisms, algorithms, and concepts in allergen bioinformatics, as well as major areas for future research in the field of allergology.
Collapse
|