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Amphibians and reptiles, like all animals, are prone to periodic infections. However, crocodilians stand out for their remarkable ability to remain generally healthy and infection-free despite frequent exposure to a wide variety of microorganisms in their habitats and often sustaining significant injuries. These animals have evolved highly active immune mechanisms that provide rapid and effective defense. This is evidenced by the superior hemolytic capacity of their plasma compared to that of other organisms. To date, several host defense peptides (HDPs) have been identified in crocodilians, including cathelicidins, beta-defensins, hepcidins, leucrocins, hemocidins, and omwaprins. These peptides exhibit potent and broad-spectrum antimicrobial, antibiofilm, antifungal, and anticancer activities. Due to the relatively low but diverse evolutionary rate of crocodilians, the HDPs found in this species offer valuable insights into proteins and mechanisms of action that are highly conserved across many animals related to immune defense. The potential applications of HDPs in modern medicine represent a promising strategy for developing new therapeutic agents. Their novelty and the vast variability with which peptide sequences can be designed and modified expand the field of application for HDPs almost infinitely. This review addresses the urgent need for innovative and more effective drugs to combat the rise of antimicrobialresistant infections and evaluates the potential of crocodilian HDPs. It presents recent advances in the identification of crocodilian HDPs, particularly antimicrobial peptides (AMPs), including previously underexplored topics such as the sequential and structural conformation of different peptide types in crocodilians and the use of bioinformatics tools to enhance native peptides., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

In order to evaluate the effects of the interaction between different proteins and feeding frequency on largemouth bass (Micropterus salmoides) and to provide scientific guidance for the application of novel proteins and the corresponding optimal feeding strategy, a two-factorial design (5 × 3) with five protein feeds (fishmeal (FM), Clostridium autoethanogenum protein (CAP), Tenebrio molitor (TM), Chlorella meal (ChM), cottonseed protein concentrate (CPC)), and three feeding frequency (1, 2, and 3 times/d; FF1, FF2, FF3) was designed in culturing largemouth bass (initial weight, 2.98 ± 0.22 g/fish) for 8 weeks. Z-score combined with cluster analysis was used to analyze and compare the effects of different treatments on different indicators, such as growth performance, feed utilization, antioxidant capacity, and immune response to draw a general picture of the relationship among all these massive biomarkers. The results showed that different protein sources and feeding frequencies had significant interactive effects on growth performance, feed utilization efficiency, body lipid, and health status of largemouth bass. Fish fed with ChM feed showed similar performance to that in FM group, implying its potential for complete replacement of fishmeal in largemouth bass. Fish fed with CAP, TM, and CPC feeds showed worse performance compared to FM and ChM groups, characterized by poor growth and feed utilization, enhanced stress, chronic inflammation, and varying symptoms of histological changes in the liver and intestine, which demonstrated the adverse effects of the complete replacement of fishmeal by these three proteins. In terms of feeding frequency, fish fed with FM feed in FF3 group led to liver hypertrophy, fat accumulation, and the risk of fatty liver, while inducing liver inflammation. In addition, the TM and CAP group had the higher expression levels of inflammatory factors at FF3 group, which displayed that the interactions between FM, CAP, TM feeds and feeding frequency at FF3 might aggravate the occurrence of liver inflammation and oxidative damage of hepatocytes. Overall, FF2 had higher feed efficiency, protein efficiency, antioxidant enzyme and lysozyme activities, lower MDA content, and lower gene expression of inflammatory cytokines and could be considered as the optimum feeding frequency for largemouth bass fed with different protein feeds., Competing Interests: Declarations Ethics approval All experiments and animal-handling procedures were approved by the Ethics Committee of the Institute of Laboratory Animal Centre, Huazhong Agricultural University. Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Plant-based dairy alternatives have many benefits in terms of sustainability, animal welfare, and health, but they can only be successful in the market if consumers perceive them as suitable substitutes for conventional dairy. Consumers' expectations for new products are strongly influenced by the food categories into which they place these products. The present study aims to reveal consumers' categorizations of plant-based dairy products to gain insights into their potential as dairy substitutes. In a free sorting task, 100 participants from the German-speaking part of Switzerland sorted a variety of plant-based and conventional animal-based dairy products into groups, indicating their spontaneous similarity perceptions. Additionally, we assessed the participants' characteristics and attitudes toward plant-based dairy products to test potential differences in categorization strategies among consumer groups. Multidimensional scaling and cluster analysis showed that consumers' mental representations of plant-based dairy and conventional animal-based dairy were clearly separated across a wide range of product types. This pattern was even observed among consumers who ate less meat, had higher exposure to vegan dietary styles, and had less negative attitudes toward dairy alternatives. The results suggest that taxonomic distinctions based on plant or animal origin dominate consumers' perceptions and are likely to hinder the substitution of dairy with plant-based dairy. Nevertheless, they also imply that plant-based products that manage to emphasize shared goals and functional properties akin to conventional dairy products are more likely to form a common goal-derived category in consumers' minds and thus have better prospects as substitutes., Competing Interests: Declaration of competing interest None., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

In recent years, proteogenomics and ribosome profiling studies have identified a large number of proteins encoded by noncoding regions in the human genome. They are encoded by small open reading frames (sORFs) in the untranslated regions (UTRs) of mRNAs and long non-coding RNAs (lncRNAs). These sORF encoded proteins (SEPs) are often <150AA and show poor evolutionary conservation. A subset of them have been functionally characterized and shown to play an important role in fundamental biological processes including cardiac and muscle function, DNA repair, embryonic development and various human diseases. How many novel protein-coding regions exist in the human genome and what fraction of them are functionally important remains a mystery. In this review, we discuss current progress in unraveling SEPs, approaches used for their identification, their limitations and reliability of these identifications. We also discuss functionally characterized SEPs and their involvement in various biological processes and diseases. Lastly, we provide insights into their distinctive features compared to canonical proteins and challenges associated with annotating these in protein reference databases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

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.

New types of protein sources will enter our diet in a near future, reinforcing the need for a straightforward in vitro (cell-based) screening model to test and predict the safety of these novel proteins, in particular their potential risk for de novo allergic sensitization. The Adverse Outcome Pathway (AOP) for allergen sensitization describes the current knowledge of key events underlying the complex cellular interactions that proceed allergic food sensitization. Currently, there is no consensus on the in vitro model to study the intestinal translocation of proteins as well as the epithelial activation, which comprise the first molecular initiation events (ME1-3) and the first key event of the AOP, respectively. As members of INFOGEST, we have highlighted several critical features that should be considered for any proposed in vitro model to study epithelial protein transport in the context of allergic sensitization. In addition, we defined which intestinal cell types are indispensable in a consensus model of the first steps of the AOP, and which cell types are optional or desired when there is the possibility to create a more complex cell model. A model of these first key aspects of the AOP can be used to study the gut epithelial translocation behavior of known hypo- and hyperallergens, juxtaposed to the transport behavior of novel proteins as a first screen for risk management of dietary proteins. Indeed, this disquisition forms a basis for the development of a future consensus model of the allergic sensitization cascade, comprising also the other key events (KE2-5)., (© 2022 The Authors. Comprehensive Reviews in Food Science and Food Safety published by Wiley Periodicals LLC on behalf of Institute of Food Technologists.)

Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens showed that hundreds of ORFs derived from noncoding transcripts produce (micro)proteins, whereas other studies failed to find evidence for such types of noncanonical translation products. Here, we attempted to discover translation products from noncoding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from noncoding regions but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap-based interactome analysis of two N-terminal proteoforms originating from noncoding regions showed the functional potential of these novel proteins., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The expected global population growth to 9.7 billion people in 2050 and the significant change in global dietary patterns require an increase in global food production by about 60%. The protein supply for feed and food is most critical and requires an extension in protein sources. Edible insects can upgrade low-grade side streams of food production into high-quality protein, amino acids and vitamins in a very efficient way. Insects are considered to be the "missing link" in the food chain of a circular and sustainable economy. Insects and insect-derived products have entered the European market since first being acknowledged as a valuable protein source for feed and food production in around 2010. However, today, scaling up the insect value chain in Europe is progressing at a relatively slow pace. The mission of SUSINCHAIN (SUStainable INsect CHAIN)-a four-year project which has received funding from the European Commission-is to contribute to novel protein provision for feed and food in Europe by overcoming the remaining barriers for increasing the economic viability of the insect value chain and opening markets by combining forces in a comprehensive multi-actor consortium. The overall project objective is to test, pilot and demonstrate recently developed technologies, products and processes, to realize a shift up to Technology Readiness Level 6 or higher. In addition to these crucial activities, the project engages with stakeholders in the insect protein supply chain for feed and food by living labs and workshops. These actions provide the necessary knowledge and data for actors in the insect value chain to decrease the cost price of insect products, process insects more efficiently and market insect protein applications in animal feed and regular human diets that are safe and sustainable. This paves the way for further upscaling and commercialization of the European insect sector.

An exponential growth in the global demand for high quality proteins over the next 20 years is expected, mainly due to global population growth and the increasing awareness toward protein rich foods for more nutritive diets. Coupled with this, is the pressing need for more sustainable approaches within a bio-economy mindset. Although meat production is expected to increase to address this rising demand, a better use of the currently available resources provided by the food, and specially, the meat industry is required. In this regard, despite the high-quality proteins and other nutrients found in meat co-products; they are currently underused and their valorisation needs to be revisited. Also, emerging protein sources need to be investigated to alleviate the environmental pressure coming from the meat industry. In this review, the main focus was attributed to (i) the current and forthcoming challenges for the use of meat co-products as meat replacers to produce a new range of meat derived products (with high nutritional value, improved technological properties and better consumer acceptance); (ii) their performance regarding to the non-animal origin proteins currently used as meat protein replacers; and (iii) the allergenicity of the proteins that might fall into the category of novel protein sources., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV&#95;RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV., Competing Interests: Declaration of Competing Interest The authors declare no competing interest., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Protein hydrolysates from lesser mealworm ( Alphitobius diaperinus , LM) were obtained by enzymatic hydrolysis with protease from Bacillus licheniformis . A preliminary test performed for five hours of hydrolysis generated an insect protein hydrolysate with 15% of degree of hydrolysis (DH), optimum solubility property and oil holding capacity, but emulsifying and foaming ability were completely impaired. In order to investigate the potential implication of DH on techno-functional properties, a set of protein hydrolysates with a different DH was obtained by sub-sampling at different time points during three hours of enzymatic hydrolysis process. An increase in DH% had positive effects on the solubility property and oil holding ability, while a reduced emulsifying ability was observed up to five hours of hydrolysis. These results demonstrated that the enzymatic hydrolysis, if performed under controlled conditions and not for a long period, represents a valid method to extract high quality protein from insects with tailored techno-functionality, in order to produce tailored ingredients for feed and food purpose.

There is an increasing demand for alternative and sustainable protein sources, such as vegetables, insects and microorganisms, that can meet the nutritional and sensory pleasantness needs of consumers. This emergent interest for novel protein sources, allied with "green" and cost-effective processing technologies, such as high hydrostatic pressure, ohmic heating and pulsed electric fields, can be used as strategies to improve the consumption of proteins from sustainable sources without compromising food security. In addition to their nutritional value, these novel proteins present several technological-functional properties that can be used to create various protein systems in different scales (i.e., macro, micro and nano scale), which can be tailored for a specific application in innovative food products. However, in order for these novel protein sources to be broadly used in future food products, their fate in the human gastrointestinal tract (e.g., digestion and bioavailability) must be assessed, as well as their safety for consumers must be clearly demonstrated. In particular, these proteins may become novel allergens triggering adverse reactions and, therefore, a comprehensive allergenicity risk assessment is needed. This review presents an overview of the most promising alternative protein sources, their application in the production of innovative food systems, as well as their potential effects on human health. In addition, new insights on sustainable processing strategies are given., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Current international guidelines for the risk assessment of biotechnology-derived foods date back to 2003. We present new strategies and directions for assessing immune adverse reactions to novel food proteins. Understanding genetic factors involved in food allergy and the role of the gastrointestinal tract will streamline risk assessment strategies., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Proteins are among the most important constituents of biological systems. Because all protein-coding genes have a noncoding ancestral form, the properties of noncoding sequences and how they shape the birth of novel proteins may influence the structure and function of all proteins. Differences between the properties of young proteins and random expectations from noncoding sequences have previously been interpreted as the result of natural selection. However, interpreting such deviations requires a yet-unattained understanding of the raw material of de novo gene birth and its relation to novel functional proteins. We mathematically show that the average properties and selective filtering of the "junk" polypeptides of which this raw material is composed are not the only factors influencing the properties of novel functional proteins. We find that in some biological scenarios, they also depend on the variance of the properties of junk polypeptides and their correlation with the rate of allelic turnover, which may itself depend on mutational biases. This suggests for instance that any property of polypeptides that accelerates their exploration of the sequence space could be overrepresented in novel functional proteins, even if it has a limited effect on adaptive value. To exemplify the use of our general theoretical results, we build a simple model that predicts the mean length and mean intrinsic disorder of novel functional proteins from the genomic GC content and a single evolutionary parameter. This work provides a theoretical framework that can guide the prediction and interpretation of results when studying the de novo emergence of protein-coding genes., (Copyright © 2019 by the Genetics Society of America.)

The current allergenicity assessment of novel proteins is based on the EFSA GMO guidance. Recently, EFSA launched a new guidance document on allergenicity assessment of GM plants (2017). This document describes, amongst other topics, the new scientific and regulatory developments on in vitro protein digestibility tests. The EFSA GMO Panel stated that for in vitro protein digestibility tests, additional investigations are needed before any additional recommendation in the form of guidance can be provided. To this end, an interim phase is considered necessary to evaluate the revisions to the in vitro gastrointestinal digestion test, proposed by EFSA. This prompted the establishment of a joint workshop through two COST Action networks: COST Action ImpARAS and COST Acton INFOGEST. In 2017, a workshop was organised to discuss the relevance of digestion in allergenicity risk assessment and how to potentially improve the current methods and readouts. The outcome of the workshop is that there is no rationale for a clear readout that is predictive for allergenicity and we suggest to omit the digestion test from the allergenicity assessment strategy for now, and put an effort into filling the knowledge gaps as summarized in this paper first., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The development and introduction of new dietary protein sources has the potential to improve food supply sustainability. Understanding the potential allergenicity of these new or modified proteins is crucial to ensure protection of public health. Exposure to new proteins may result in de novo sensitization, with or without clinical allergy, or clinical reactions through cross-reactivity. In this paper we review the potential of current methodologies (in silico, in vitro degradation, in vitro IgE binding, animal models and clinical studies) to address these outcomes for risk assessment purposes for new proteins, and especially to identify and characterise the risk of sensitization for IgE mediated allergy from oral exposure. Existing tools and tests are capable of assessing potential crossreactivity. However, there are few possibilities to assess the hazard due to de novo sensitization. The only methods available are in vivo models, but many limitations exist to use them for assessing risk. We conclude that there is a need to understand which criteria adequately define allergenicity for risk assessment purposes, and from these criteria develop a more suitable battery of tests to distinguish between proteins of high and low allergenicity, which can then be applied to assess new proteins with unknown risks., (Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Currently, risk assessment of the allergenic potential of novel proteins relies heavily on evaluating protein digestibility under normal conditions based on the theory that allergens are more resistant to gastrointestinal digestion than non-allergens. There is also proposed guidance for expanded in vitro digestibility assay conditions to include vulnerable sub-populations. One of the underlying rationales for the expanded guidance is that current in vitro assays do not accurately replicate the range of physiological conditions. Animal scientists have long sought to predict protein and amino acid digestibility for precision nutrition. Monogastric production animals, especially swine, have gastrointestinal systems similar to humans, and evaluating potential allergen digestibility in this context may be beneficial. Currently, there is no compelling evidence that the mechanisms sometimes postulated to be associated with allergenic sensitization, e.g. antacid modification of stomach pH, are valid among production animals. Furthermore, examples are provided where non-biologically representative assays are better at predicting protein and amino acid digestibility compared with those designed to mimic in vivo conditions. Greater emphasis should be made to align in vitro assessments with in vivo data., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)

Annotation of protein coding genes in sequenced genomes has been routinely carried out using gene prediction programs guided by available transcript data. The advent of mass spectrometry has enabled the identification of proteins in a high-throughput manner. In addition to searching proteins annotated in public databases, mass spectrometry data can also be searched against conceptually translated genome as well as transcriptome to identify novel protein coding regions. This proteogenomics approach has resulted in the identification of novel protein coding regions in both prokaryotic and eukaryotic genomes. These studies have also revealed that some of the annotated noncoding RNAs and pseudogenes code for proteins. This approach is likely to become a part of most genome annotation workflows in the future. Here we describe a general methodology and approach that can be used for proteogenomics.

Remarkable progress continues on the annotation of the proteins identified in the Human Proteome and on finding credible proteomic evidence for the expression of "missing proteins". Missing proteins are those with no previous protein-level evidence or insufficient evidence to make a confident identification upon reanalysis in PeptideAtlas and curation in neXtProt. Enhanced with several major new data sets published in 2014, the human proteome presented as neXtProt, version 2014-09-19, has 16,491 unique confident proteins (PE level 1), up from 13,664 at 2012-12 and 15,646 at 2013-09. That leaves 2948 missing proteins from genes classified having protein existence level PE 2, 3, or 4, as well as 616 dubious proteins at PE 5. Here, we document the progress of the HPP and discuss the importance of assessing the quality of evidence, confirming automated findings and considering alternative protein matches for spectra and peptides. We provide guidelines for proteomics investigators to apply in reporting newly identified proteins.