Beyond Eyeballing: Fitting Models to Experimental Data

Abstract

As we learn more about the biology of the Toll-like receptors (TLRs), a wide range of molecules that can activate this fascinating family of pattern recognition receptors emerges. In addition to conserved pathogenic components, endogenous danger signals created upon tissue damage are also sensed by TLRs. Detection of these types of stimuli results in TLR mediated inflammation that is vital to fight pathogenic invasion and drive tissue repair. Aberrant activation of TLRs by pathogenic and endogenous ligands has also been linked with the pathogenesis of an increasing number of infectious and autoimmune diseases, respectively. Most recently, allergen activation of TLRs has also been described, creating a third broad class of TLR stimulus that has helped to shed light on the pathogenesis of allergic disease. To date, microbial activation of TLRs remains best characterized. Each member of the TLR family senses a specific subset of pathogenic ligands, pathogen associated molecular patterns (PAMPS), and a wealth of structural and biochemical data continues to reveal the molecular mechanisms of TLR activation by PAMPs, and to demonstrate how receptor specificity is achieved. In contrast, the mechanisms by which endogenous molecules and allergens activate TLRs remain much more mysterious. Here, we provide an overview of our current knowledge of how very diverse stimuli activate the same TLRs and the structural basis of these modes of immunity.     

Seasonal incidence of airborne fungal allergens in Riyadh,Saudi Arabia

Aerobiological studies to evaluate allergenic fungal spores in the atmosphere of Riyadh were conducted. Burkard personal volumetric sampler were operated as volumetric viable spore traps at two different sites (Al-Batha, a more developed area in the south and Al-Ulia, a less developed area in the north) in Riyadh. Twice a week samplings were carried out over a period of 12 month. The seasonal fluctuations of the most frequent fungi were plotted as major components. The dominant species at the two sites were members of the genera Alternaria, Aspergillus, Cladosporium, Penicillium and Ulocladium. Drechslera, Fusarium, Rhizopus and Stachybotrytis species were minor components or sporadic. Seasonal variations of the total colonies were significantly (p < 0.05) different. They showed higher concentrations in the winter season and the lowest in summer. The Al-Batha site was always higher in spore concentrations than the Al-Ulia site. The results provide valuable information for the diagnosis and prophylaxis of allergic diseases due to airborne fungi.This revised version was published online in October 2005 with corrections to the Cover Date.     

Der p 5 Crystal Structure Provides Insight into the Group 5 Dust Mite Allergens

Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK. The crystallographic asymmetric unit contains three dimers of Der p 5 that are not exactly alike. Solution scattering techniques were used to assess the multimeric state of Der p 5 in vitro and showed that the predominant state was monomeric, similar to Blo t 5, but larger multimeric species are also present. In the crystal, the formation of the Der p 5 dimer creates a large hydrophobic cavity of ∼3000 ų that could be a ligand-binding site. Many allergens are known to bind hydrophobic ligands, which are thought to stimulate the innate immune system and have adjuvant-like effects on IgE-mediated inflammatory responses.     

Structural characterization of the N-glycans of gpMuc from Mucuna pruriens seeds

Mucuna pruriens seeds are used in some countries as a human prophylactic oral anti-snake remedy. Aqueous extracts of M. pruriens seeds possess in vivo activity against cobra and viper venoms, and protect mice against Echis carinatus venom. It was recently demonstrated that the seed immunogen generating the antibody that cross-reacts with the venom proteins is a multiform glycoprotein (gpMuc), and the immunogenic properties of gpMuc seemed to mainly reside in its glycan chains. In the present study, gpMuc was found to contain only N-glycans. Part of the N-glycans could be released with peptide-(N ⁴-(N-acetyl-β -glucosaminyl)asparagine amidase F (PNGase F-sensitive N-glycans); the PNGase F-resistant N-glycans were PNGase A-sensitive. The oligosaccharides released were analyzed by a combination of MALDI-TOF mass spectrometry, HPLC profiling of 2-aminobenzamide-labelled derivatives and ¹H NMR spectroscopy. The PNGase F-sensitive N-glycans comprised a mixture of oligomannose-type structures ranging from Man₅GlcNAc₂ to Man₉GlcNAc₂, and two xylosylated structures, Xyl₁Man₃GlcNAc₂ and Xyl₁Man₄GlcNAc₂. The PNGase A-sensitive N-glycans, containing (α 1-3)-linked fucose, were identified as Fuc₁Xyl₁Man₂GlcNAc₂ and Fuc₁Xyl₁Man₃GlcNAc₂. In view of the determined N-glycan ensemble, the immunoreactivity of gpMuc was ascribed to the presence of core (β 1-2)-linked xylose- and core α (1-3)-linked fucose-modified N-glycan chains.     

Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.     

Proteomic profiling and characterization of differential allergens in the nematodes Anisakis simplex sensu stricto and A. pegreffii

The parasite species complex Anisakis simplex sensu lato (Anisakis simplex sensu stricto; (A. simplex s.s.), A. pegreffii, A. simplex C) is the main cause of severe anisakiasis (allergy) worldwide and is now an important health matter. In this study, the relationship of this Anisakis species complex and their allergenic capacities is assessed by studying the differences between the two most frequent species (A. simplex s.s., A. pegreffii) and their hybrid haplotype by studying active L3 larvae parasiting Merluccius merluccius. They were compared by 2D gel electrophoresis and parallel Western blot (2DE gels were hybridized with pools of sera from Anisakis allergenic patients). Unambiguous spot differences were detected and protein assignation was made by MALDI‐TOF/TOF analysis or de novo sequencing. Seventy‐five gel spots were detected and the corresponding proteins were identified. Differentially expressed proteins for A. simplex s.s., A. pegreffii, and their hybrid are described and results are statistically supported. Twenty‐eight different allergenic proteins are classified according to different families belonging to different biological functions. These proteins are described for the first time as antigenic and potentially new allergens in Anisakis. Comparative proteomic analyses of allergenic capacities are useful for diagnosis, epidemiological surveys, and clinical research. All MS data have been deposited in the ProteomeXchange with identifier PXD000662 ( http://proteomecentral.proteomexchange.org/dataset/PXD000662 ).     

Inhibitory activities against heterologous α-amylases and in vitro allergenic reactivity of Einkorn wheats

Salt extracts from seeds of 36 lines of Einkorn wheats were analyzed for their inhibitory activity towards two insect (Tenebrio molitor, Coleoptera, and Ephestia kuehniella, Lepidoptera) and one mammalian (human salivary) -amylases. Whereas all ten T. monococcum accessions tested were active towards the lepidopteran enzyme, they had no effect on the coleopteran or the mammalian ones. More variability was found among the 21 lines of T. boeticum analyzed, although none of them inhibited human -amylase. The five accessions of T. urartu showed even greater diversity. Among all Einkorn accessions tested, only two urartu lines affected the three -amylases. These lines displayed inhibition patterns similar to those of T. aestivum and T. turgidum cultivars. Since several breadwheat -amylase inhibitors are major allergens associated with baker's asthma, we also studied the in vitro allergenic activity of salt extracts from the Einkorn wheats under study. No significant differences in IgE-binding were found between these accessions and theT. aestivum or T. turgidum cultivars. Furthermore, putative allergens with molecular sizes in the range of 20–60 kDa were detected in these Einkorn wheats.     

Detection of allergen specific immunoglobulins by microarrays coupled to microfluidics

Allergen microarrays are under development for a component‐resolved diagnosis of Type I (IgE‐mediated) allergies. Here we report an improved microarray coupled to microfluidics for the detection of allergen specific immunoglobulin E (IgE). The signal intensity for IgE detection in serum has been improved by using glass slides coated with a novel poly[DMA‐co‐NAS] brush copolymer which is able to immobilize allergens in their native conformation and by carrying out the incubation step in dynamic conditions. The assay, fully automated, was performed in a microcell, using a software‐controlled fluidic processor, to bring assay reagents on the surface of the array. Microfluidics turns the binding between serum immunoglobulins and immobilized allergens from a diffusion‐limited to a kinetic‐limited process by ensuring an efficient mixing of serum samples on the surface of the microarray. As a result of this, the binding of high affinity IgE antibodies is enhanced whereas that of low affinity IgG antibodies, which are present at higher concentration, is impaired paving the way to more accurate and sensitive results.     

Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant

Proteomic screening of strawberry (Fragaria ananassa) yielded a 58% success rate in protein identification in spite of the fact that no genomic sequence is available for this species. This was achieved by a combination of MALDI-MS/MS de novo sequencing of double-derivatized peptides and indel-tolerant searching against local protein databases built on both EST and full-length nucleotide sequences. The amino acid sequence of a strawberry allergen, homologous to the well-known major birch pollen allergen Bet v 1, was partially determined. This strawberry allergen, named Fra a 1 according to the nomenclature for allergen proteins, showed sequence identity of 54 and 77%, respectively, with corresponding allergens from birch and apple. Differential expression, as evaluated by 2-D DIGE, occurred in 10% of protein spots when red strawberries were compared to a colorless (white) strawberry mutant. White strawberries, known to be tolerated by individuals affected by allergy, were found to be virtually free from the strawberry allergen. Also several enzymes in the pathway for biosynthesis of flavonoids, to which the red color pelargonidin belongs, were down-regulated. This approach to assess differential protein expression without access to genomic sequence information can also be applied to other crop plants and phenotypic traits.     

A physiological and biochemical model for digestion in the ectoparasitic mite,Psoroptes ovis (Acari: Psoroptidae)

Mites are an important group of arthropod pests affecting crops, animals and humans. Despite this, detailed physiological studies on these organisms remain sparse due largely to their small size. Unifying models are required to draw together the diverse information from studies on different groups and species. This paper describes a model for digestion in the parasitic mite, Psoroptes ovis, the causative agent of psoroptic mange or sheep scab disease. The limited information about this species is supplemented with data from other acarines, especially house dust mites and ticks. We review the range of enzymes and allergens found in mites and consider their possible roles in digestion in mites, generally and in particular, P. ovis. Histological studies, enzyme biochemistry and molecular biology and experimental evidence suggest that P. ovis utilises a digestive system reliant upon acid peptidases functioning in a largely intracellular environment. The actions of the digestive enzymes are supplemented by the involvement of bacteria as potential direct and indirect sources of nutrition. It is possible that some extra-corporeal digestion also takes place. The interaction of bacteria and digestive enzymes on the skin surface of the sheep may be responsible for the excessive pathological reactions evident in clinical sheep scab.