Variation in Shrimp Allergens: Place of Origin Effects on Food Safety Assessment

Due to the widespread use of shellfish ingredients in food products, accurate food labelling is urgently needed for consumers with shellfish allergies. Most crustacean allergen detection systems target the immunorecognition of the allergenic protein tropomyosin. However, this mode of detection may be affected by an origin-dependent protein composition. This study determined if the geographic location of capture, or aquaculture, influenced the allergenic protein profiles of Black Tiger Shrimp (Penaeus monodon), one of the most farmed and consumed shrimp species worldwide. Protein composition was analysed in shrimp from nine different locations in the Asia-Pacific by SDS-PAGE, immunoblotting, and mass spectrometry. Ten of the twelve known shrimp allergens were detected, but with considerable differences between locations. Sarcoplasmic calcium-binding protein, myosin light chain, and tropomyosin were the most abundant allergens in all locations. Hemocyanin-specific antibodies could identify up to six different isoforms, depending on the location of origin. Similarly, tropomyosin abundance varied by up to 13 times between locations. These findings suggest that allergen abundance may be related to shrimp origin and, thus, shrimp origin might directly impact the readout of commercial crustacean allergen detection kits, most of which target tropomyosin, and this should be considered in food safety assessments.

Comparison of protein extraction protocols and allergen mapping from black soldier fly Hermetia illucens

Exploration of important insect proteins - including allergens - and proteomes can be limited by protein extraction buffer selection and the complexity of the proteome. Herein, LC-MS/MS-based proteomics experiments were used to assess the protein extraction efficiencies for a suite of extraction buffers and the effect of ingredient processing on proteome and allergen detection. Discovery proteomics revealed that SDS-based buffer yields the maximum number of protein groups from three types of BSF samples. Bioinformatic analysis revealed that buffer composition and ingredient processing could influence allergen detection. Upon applying multi-level filtering criteria, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. A targeted LC-MRM-MS assay was developed for the pan-allergen tropomyosin and used to assess the influence of buffer composition and ingredient processing using peptide abundance measurements. SIGNIFICANCE: We demonstrated that the selection of protein extraction buffer and the processing method could influence protein yield and cross-reactive allergen detection from processed and un-processed black soldier fly (BSF) samples. In total, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. An LC-MRM-MS assay was developed for tropomyosin, indicating the importance of buffer selection and processing conditions to reduce BSF samples' allergenicity.

Recombinant Tropomyosin from the Pacific Oyster (Crassostrea gigas) for Better Diagnosis

The Pacific oyster is a commercially important mollusc and, in contrast to most other shellfish species, frequently consumed without prior heat treatment. Oysters are rich in many nutrients but can also cause food allergy. Knowledge of their allergens and cross-reactivity remains very limited. These limitations make an optimal diagnosis of oyster allergy difficult, in particular to the Pacific oyster (Crassostrea gigas), the most cultivated and consumed oyster species worldwide. This study aimed to characterise IgE sensitisation profiles of 21 oyster-sensitised patients to raw and heated Pacific oyster extract using immunoblotting and advanced mass spectrometry, and to assess the relevance of recombinant oyster allergen for improved diagnosis. Tropomyosin was identified as the major allergen recognised by IgE from 18 of 21 oyster-sensitised patients and has been registered with the WHO/IUIS as the first oyster allergen (Cra g 1). The IgE-binding capacity of oyster-sensitised patients’ IgE to purified natural and recombinant tropomyosin from oyster, prawn, and dust mite was compared using enzyme-linked immunosorbent assay. The degree of IgE binding varied between patients, indicating partial cross-sensitisation and/or co-sensitisation. Amino acid sequence alignment of tropomyosin from these three species revealed five regions that contain predicted IgE-binding epitopes, which are most likely responsible for this cross-reactivity. This study fully biochemically characterises the first and major oyster allergen Cra g 1 and demonstrates that the corresponding recombinant tropomyosin should be implemented in improved component-resolved diagnostics and guide future immunotherapy.

Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment

Insects have been consumed by people for millennia and have recently been proposed as a complementary, sustainable source of protein to feed the world's growing population. Insects and crustaceans both belong to the arthropod family. Crustacean (shellfish) allergies are common and potentially severe; hence, the cross-reactivity of the immune system with insect proteins is a potential health concern. Herein, LC-MS/MS was used to explore the proteome of whole, roasted whole and roasted powdered cricket products. Eight protein extraction protocols were compared using the total number of protein and distinct peptide identifications. Within these data, 20 putative allergens were identified, of which three were arginine kinase (AK) proteoforms. Subsequently, a multiple reaction monitoring MS assay was developed for the AK proteoforms and applied to a subset of extracts. This targeted assay demonstrated that allergen abundance/detectability varies according to the extraction method as well as the food processing method.

Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species

Shellfish allergy affects 2% of the world’s population and persists for life in most patients. The diagnosis of shellfish allergy, in particular shrimp, is challenging due to the similarity of allergenic proteins from other invertebrates. Despite the clinical importance of immunological cross-reactivity among shellfish species and between allergenic invertebrates such as dust mites, the underlying molecular basis is not well understood. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo, using Trinity, from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). BLAST searching using the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. The analyses revealed up to 39 unreported allergens in the different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment (Clustal Omega) demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.

A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment

Food allergy is rising at an alarming rate and is a major public health concern. Globally, food allergy affects over 500 million people, often starting in early childhood and increasingly reported in adults. Commercially, only one approved oral immunotherapy-based treatment is currently available and other allergen-based immunotherapeutic are being investigated in clinical studies. As an alternative approach, a substantial amount of research has been conducted on natural compounds and probiotics, focusing on the immune modes of action, and therapeutic uses of such sources to tackle various immune-related diseases. Food allergy is primarily mediated by IgE antibodies and the suppression of allergic symptoms seems to be mostly modulated through a reduction of allergen-specific IgE antibodies, upregulation of blocking IgG, and downregulation of effector cell activation (e.g., mast cells) or expression of T-helper 2 (Th-2) cytokines. A wide variety of investigations conducted in small animal models or cell-based systems have reported on the efficacy of natural bioactive compounds and probiotics as potential anti-allergic therapeutics. However, very few lead compounds, unlike anti-cancer and anti-microbial applications, have been selected for clinical trials in the treatment of food allergies. Natural products or probiotic-based approaches appear to reduce the symptoms and/or target specific pathways independent of the implicated food allergen. This broad range therapeutic approach essentially provides a major advantage as several different types of food allergens can be targeted with one approach and potentially associated with a lower cost of development. This review provides a brief overview of the immune mechanisms underlying food allergy and allergen-specific immunotherapy, followed by a comprehensive collection of current studies conducted to investigate the therapeutic applications of natural compounds and probiotics, including discussions of their mode of action and immunological aspects of their disease-modifying capabilities.

Inhibitors of bacterial transcription initiation complex formation

Antibiotic resistance is a growing global problem, with very few new compounds in development. Bacterial transcription is an underutilized target for antibiotics, which has been attributed to the similarity of the active site of RNA polymerases (RNAPs) across all domains of life and the ease with which resistance can arise through point mutation at multiple sites within this conserved region. In this study we have taken a rational approach to design a novel set of compounds that specifically target the formation of transcription initiation complexes by preventing the unique bacterial σ initiation factor from binding to RNAP. We have identified the region of RNAP to which these compounds bind and demonstrate that one compound, GKL003, has an inhibition constant in the low nanomolar range. This compound has activity against both Gram-positive and -negative organisms, including a community acquired methicillin-resistant strain of the major pathogen Staphylococcus aureus.

The interaction of Bacillus subtilis sigmaA with RNA polymerase

RNA polymerase (RNAP) is an essential and highly conserved enzyme in all organisms. The process of transcription initiation is fundamentally different between prokaryotes and eukaryotes. In prokaryotes, initiation is regulated by sigma factors, making the essential interaction between sigma factors and RNAP an attractive target for antimicrobial agents. Our objective was to achieve the first step in the process of developing novel antimicrobial agents, namely to prove experimentally that the interaction between a bacterial RNAP and an essential sigma factor can be disrupted by introducing carefully designed mutations into sigma(A) of Bacillus subtilis. This disruption was demonstrated qualitatively by Far-Western blotting. Design of mutant sigmas was achieved by computer-aided visualization of the RNAP-sigma interface of the B. subtilis holoenzyme (RNAP + sigma) constructed using a homology modeling approach with published crystal structures of bacterial RNAPs. Models of the holoenzyme and the core RNAP were rigorously built, evaluated, and validated. To allow a high-quality RNAP-sigma interface model to be constructed for the design of mutations, a crucial error in the B. subtilis sigma(A) sequence in published databases at amino acid 165 had to be corrected first. The new model was validated through determination of RNAP-sigma interactions using targeted mutations.

The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA

There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well-understood biochemically. However, despite the plethora of structural information made available on RNA polymerase in the last decade, little is available for RNA polymerase in complex with transcription elongation factors. To understand the mechanisms of transcriptional regulation, we describe the first structure, to our knowledge, for a bacterial RNA polymerase in complex with an essential transcription elongation factor. The resulting structure formed between the RNA polymerase and NusA from Bacillus subtilis provides important insights into the transition from an initiation complex to an elongation complex, and how NusA is able to modulate transcription elongation and termination.

The repeated reproduction of Bartlett's Remembering

There is a striking parallel between the treatment of F. C. Bartlett's theories of memory in the psychological literature and Bartlett's own characterization of reproductive memory as interest driven and constructive. Three periods of intensified interest in Bartlett's classic book Remembering (1932/1995) can be identified. The 1st occurred in the wake of the publication of Remembering and focused on replication and extension of the empirical work. The 2nd was during the period of the "cognitive revolution" and treated Bartlett's key theoretical concept of "schema" within an information-processing framework. The 3rd is an ongoing revitalization of interest in the cultural and social aspects of Bartlett's multifaceted theory. Each wave of increased interest in Bartlett's work has brought different aspects of his thinking to the fore, producing different versions of his theory of remembering that reflect the theoretical climate of the time.

Measurement and modeling of depth cue combination: in defense of weak fusion

Various visual cues provide information about depth and shape in a scene. When several of these cues are simultaneously available in a single location in the scene, the visual system attempts to combine them. In this paper, we discuss three key issues relevant to the experimental analysis of depth cue combination in human vision: cue promotion, dynamic weighting of cues, and robustness of cue combination. We review recent psychophysical studies of human depth cue combination in light of these issues. We organize the discussion and review as the development of a model of the depth cue combination process termed modified weak fusion (MWF). We relate the MWF framework to Bayesian theories of cue combination. We argue that the MWF model is consistent with previous experimental results and is a parsimonious summary of these results. While the MWF model is motivated by normative considerations, it is primarily intended to guide experimental analysis of depth cue combination in human vision. We describe experimental methods, analogous to perturbation analysis, that permit us to analyze depth cue combination in novel ways. In particular these methods allow us to investigate the key issues we have raised. We summarize recent experimental tests of the MWF framework that use these methods.

Integration of stereopsis and motion shape cues

A global shape judgement task was used to investigate the combination of stereopsis and kinetic depth. With both cues present, there were no distortions of shape perception, even under conditions where either cue alone did show such distortions. We suggest that the addition of motion information overcomes the stereo distance scaling problem. However, when incongruent combinations of disparity and motion were used, the results did not match predictions of a number of combination theories. These data could be described by a model which used weighted linear combination after correctly scaling disparities for viewing distance. When the motion cue was weakened by presenting only two frames of each motion sequence, stereo was weighted more heavily.

Effects of different texture cues on curved surfaces viewed stereoscopically

Stereoscopic shape judgements can be modified by the addition of texture cues. This paper examines the properties of texture that are responsible for this effect. When a three-dimensional curved surface is projected onto a two-dimensional image, changes in surface orientation result in gradients of texture element size (or area), shape (compression) and density in the image. Manipulating each of these gradients independently we found that 97% of the variance in the results could be accounted for by the compression gradient. When the texture pattern corresponds to a highly anisotropic texture on the object's surface, shape-from-texture becomes ineffective. These results suggest that human shape-from-texture proceeds under the assumption that textures are statistically isotropic, and not that they are homogeneous.

Integration of depth modules: stereopsis and texture

Global shape judgements were employed to examine the combination of stereopsis and shape-from-texture in the determination of three-dimensional shape. Adding textural variations to stereograms increased perceived depth. Thus, texture was not simply vetoed by the strong stereo cue. In experiments where the depth specified by texture was incongruent with that specified by stereo, the data were well described by a weighted linear combination rule. Although only a small weight was assigned to texture, this weight was somewhat greater at a farther viewing distance. This could be a consequence of the decreased reliability of stereopsis at far viewing distances.

Vertical disparities and perception of three-dimensional shape

The information about depth and three-dimensional shape available from the horizontal component of the stereo disparity field requires interpretation in conjunction with information about egocentric viewing distance (D). A novel computational approach for estimating D was proposed by Mayhew and Longuet-Higgins, who demonstrated that the horizontal gradient of vertical disparities uniquely specifies the viewing distance. We have now used random dot stereograms in a shape judgement task to show that changes in vertical disparities have no effect on perceived three-dimensional shape. Changes in ocular convergence do alter perceived shape, suggesting substantial changes in the subjects' scaling of horizontal disparities. We conclude that vertical disparities are not used to scale disparities for viewing distance, and that extraretinal signals must be considered when analysing human three-dimensional shape perception.

Systematic distortions of shape from stereopsis

The effectiveness of disparity information in defining 3-D shape was investigated by means of judgements of the shape of cylindrical continuous curved surfaces presented as random dot stereograms. At a close viewing distance, truly circular cylinders appeared elongated; at an intermediate distance, perception was close to veridical; and, at a far distance, cylinders appeared flattened. Indirect measures of scaling distance were calculated from these data. The results strongly suggest that the observed shape distortions are a consequence of scaling horizontal disparities with an incorrect measure of egocentric distance.

Postgraduate study award report

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