Similar localization of conformational IgE epitopes on the house dust mite allergens Der p 5 and Der p 21 despite limited IgE cross-reactivity.

BACKGROUND: Due to high IgE recognition frequency and high allergenic activity, Der p 5 and Der p 21 are clinically important house dust mite (HDM) allergens. The objective of this study was to characterize the immunodominant IgE epitopes of Der p 5 and Der p 21 responsible for their high allergenic activity. METHODS: A panel of 12 overlapping peptides spanning the Der p 5 and Der p 21 sequence were synthesized to search for sequential IgE epitopes by direct testing for allergic patients' IgE reactivity. Peptide-specific antibodies raised in rabbits were used in inhibition studies for localizing conformational IgE epitopes which were visualized on the surfaces of the allergen structures by molecular modelling. IgE cross-reactivity between the allergens was investigated by IgE inhibition studies. RESULTS: Immunodominant IgE epitopes defined by allergic patients' IgE on Der p 5 and Der p 21 were primarily of the conformational, discontinuous type including N- and C-terminal portions of the protein. They could be located on each allergen on one area with similar localization, but despite similar structure of the allergens, no relevant IgE cross-reactivity could be detected. CONCLUSION: Our study shows that Der p 5 and Der p 21 contain a major conformational IgE epitope-containing area located on similar portions of their structure, but they lack relevant IgE cross-reactivity. These data are important for the development of modern allergy vaccines based on defined molecules for allergen-specific immunotherapy of HDM allergy.

Isolation of a high-affinity Bet v 1-specific IgG-derived ScFv from a subject vaccinated with hypoallergenic Bet v 1 fragments.

BACKGROUND: Recombinant hypoallergenic allergen derivatives have been used in clinical immunotherapy studies, and clinical efficacy seems to be related to the induction of blocking IgG antibodies recognizing the wild-type allergens. However, so far no treatment-induced IgG antibodies have been characterized. OBJECTIVE: To clone, express, and characterize IgG antibodies induced by vaccination with two hypoallergenic recombinant fragments of the major birch pollen allergen, Bet v 1 in a nonallergic subject. METHODS: A phage-displayed combinatorial single-chain fragment (ScFv) library was constructed from blood of the immunized subject and screened for Bet v 1-reactive antibody fragments. ScFvs were tested for specificity and cross-reactivity to native Bet v 1 and related pollen and food allergens, and epitope mapping was performed. Germline ancestor genes of the antibody were analyzed with the ImMunoGeneTics (IMGT) database. The affinity to Bet v 1 and cross-reactive allergens was determined by surface plasmon resonance measurements. The ability to inhibit patients' IgE binding to ELISA plate-bound allergens and allergen-induced basophil activation was assessed. RESULTS: A combinatorial ScFv library was obtained from the vaccinated donor after three injections with the Bet v 1 fragments. Despite being almost in germline configuration, ScFv (clone H3-1) reacted with high affinity to native Bet v 1 and homologous allergens, inhibited allergic patients' polyclonal IgE binding to Bet v 1, and partially suppressed allergen-induced basophil activation. CONCLUSION: Immunization with unfolded hypoallergenic allergen derivatives induces high-affinity antibodies even in nonallergic subjects which recognize the folded wild-type allergens and inhibit polyclonal IgE binding of allergic patients.

Epitope specificity determines cross-protection of a SIT-induced IgG4 antibody.

BACKGROUND: The calcium-binding 2EF-hand protein Phl p 7 from timothy grass pollen is a highly cross-reactive pollen pan-allergen that can induce severe clinical symptoms in allergic patients. Recently, a human monoclonal Phl p 7-specific IgG4 antibody (mAb102.1F10) was isolated from a patient who had received grass pollen-specific immunotherapy (SIT). METHODS: We studied epitope specificity, cross-reactivity, affinity and cross-protection of mAb102.1F10 towards homologous calcium-binding pollen allergens. Sequence comparisons and molecular modelling studies were performed with ClustalW and SPADE, respectively. Surface plasmon resonance measurements were made with purified recombinant allergens. Binding and cross-reactivity of patients' IgE and mAb102.1F10 to calcium-binding allergens and peptides thereof were studied with quantitative RAST-based methods, in ELISA, basophil activation and IgE-facilitated allergen presentation experiments. RESULTS: Allergens from timothy grass (Phl p 7), alder (Aln g 4), birch (Bet v 4), turnip rape (Bra r 1), lamb's quarter (Che a 3) and olive (Ole e 3, Ole e 8) showed high sequence similarity and cross-reacted with allergic patients' IgE. mAb102.1F10 bound the C-terminal portion of Phl p 7 in a calcium-dependent manner. It cross-reacted with high affinity with Ole e 3, whereas binding and affinity to the other allergens were low. mAb102.1F10 showed limited cross-inhibition of patients' IgE binding and basophil activation. Sequence comparison and surface exposure calculations identified three amino acids likely to be responsible for limited cross-reactivity. CONCLUSIONS: Our results demonstrate that a small number of amino acid differences among cross-reactive allergens can reduce the affinity of binding by a SIT-induced IgG and thus limit cross-protection.

High-resolution crystal structure and IgE recognition of the major grass pollen allergen Phl p 3.

BACKGROUND: Group 2 and 3 grass pollen allergens are major allergens with high allergenic activity and exhibit structural similarity with the C-terminal portion of major group 1 allergens. In this study, we aimed to determine the crystal structure of timothy grass pollen allergen, Phl p 3, and to study its IgE recognition and cross-reactivity with group 2 and group 1 allergens. METHODS: The three-dimensional structure of Phl p 3 was solved by X-ray crystallography and compared with the structures of group 1 and 2 grass pollen allergens. Cross-reactivity was studied using a human monoclonal antibody which inhibits allergic patients' IgE binding and by IgE inhibition experiments with patients' sera. Conformational Phl p 3 IgE epitopes were predicted with the algorithm SPADE, and Phl p 3 variants containing single point mutations in the predicted IgE binding sites were produced to analyze allergic patients' IgE binding. RESULTS: Phl p 3 is a globular ß-sandwich protein showing structural similarity to Phl p 2 and the Phl p 1-C-terminal domain. Phl p 3 showed IgE cross-reactivity with group 2 allergens but not with group 1 allergens. SPADE identified two conformational IgE epitope-containing areas, of which one overlaps with the epitope defined by the monoclonal antibody. The mutation of arginine 68 to alanine completely abolished binding of the blocking antibody. This mutation and a mutation of D13 in the predicted second IgE epitope area also reduced allergic patients' IgE binding. CONCLUSION: Group 3 and group 2 grass pollen allergens are cross-reactive allergens containing conformational IgE epitopes. They lack relevant IgE cross-reactivity with group 1 allergens and therefore need to be included in diagnostic tests and allergen-specific treatments in addition to group 1 allergens.

Global warming triggers the loss of a key Arctic refugium.

We document the rapid transformation of one of the Earth's last remaining Arctic refugia, a change that is being driven by global warming. In stark contrast to the amplified warming observed throughout much of the Arctic, the Hudson Bay Lowlands (HBL) of subarctic Canada has maintained cool temperatures, largely due to the counteracting effects of persistent sea ice. However, since the mid-1990s, climate of the HBL has passed a tipping point, the pace and magnitude of which is exceptional even by Arctic standards, exceeding the range of regional long-term variability. Using high-resolution, palaeolimnological records of algal remains in dated lake sediment cores, we report that, within this short period of intense warming, striking biological changes have occurred in the region's freshwater ecosystems. The delayed and intense warming in this remote region provides a natural observatory for testing ecosystem resilience under a rapidly changing climate, in the absence of direct anthropogenic influences. The environmental repercussions of this climate change are of global significance, influencing the huge store of carbon in the region's extensive peatlands, the world's southern-most polar bear population that depends upon Hudson Bay sea ice and permafrost for survival, and native communities who rely on this landscape for sustenance.

Carrier-bound nonallergenic Der p 2 peptides induce IgG antibodies blocking allergen-induced basophil activation in allergic patients.

BACKGROUND: More than 90% of house dust mite-allergic patients are sensitized to the major Dermatophagoides pteronyssinus allergen, Der p 2. The aim of this study was to develop and characterize an allergy vaccine based on carrier-bound Der p 2 peptides, which should allow reducing IgE- and T-cell-mediated side-effects during specific immunotherapy (SIT). METHODS: Five Der p 2 peptides (P1-P5) were synthesized and analyzed regarding IgE reactivity and allergenic activity. Lymphoproliferative and cytokine responses induced with Der p 2 and Der p 2 peptides were determined in peripheral blood mononuclear cells from mite-allergic patients. Der p 2-specific IgG antibodies induced with carrier-bound Der p 2 peptides in mice and rabbits were tested for their capacity to inhibit IgE binding and basophil activation in allergic patients. RESULTS: Of five overlapping peptides (P1-P5) covering the Der p 2 sequence, two peptides (P2 and P4) were identified, which showed no relevant IgE reactivity, allergenic activity, and induced lower Der p 2-specific T-cell activation than Der p 2. However, when coupled to a carrier, P2 and P4 induced Der p 2-specific IgG antibodies in animals, which inhibited allergic patients' IgE binding to the allergen and allergen-induced basophil activation similar as antibodies induced with Der p 2. CONCLUSIONS: Carrier-bound Der p 2 peptides should allow avoiding IgE-mediated side-effects, and because of their low potential to activate allergen-specific T cells, they may reduce late-phase side-effects during SIT. Further, these peptides may be also useful for prophylactic vaccination.

Application of Biotic Ligand and Toxic Unit modeling approaches to predict improvements in zooplankton species richness in smelter-damaged lakes near Sudbury, Ontario.

Using a 30-year record of biological and water chemistry data collected from seven lakes near smelters in Sudbury (Ontario, Canada) we examined the link between reductions of Cu, Ni, and Zn concentrations and zooplankton species richness. The toxicity of the metal mixtures was assessed using an additive Toxic Unit (TU) approach. Four TU models were developed based on total metal concentrations (TM-TU); free ion concentrations (FI-TU); acute LC50s calculated from the Biotic Ligand Model (BLM-TU); and chronic LC50s (acute LC50s adjusted by metal-specific acute-to-chronic ratios, cBLM-TU). All models significantly correlated reductions in metal concentrations to increased zooplankton species richness over time (p < 0.01) with a rank based on r(2) values of cBLM-TU > BLM-TU = FI-TU > TM-TU. Lake-wise comparisons within each model showed that the BLM-TU and cBLM-TU models provided the best description of recovery across all seven lakes. These two models were used to calculate thresholds for chemical and biological recovery using data from reference lakes in the same region. A threshold value of TU = 1 derived from the cBLM-TU provided the most accurate description of recovery. Overall, BLM-based TU models that integrate site-specific water chemistry-derived estimates of toxicity offer a useful predictor of biological recovery.

Recombinant monoclonal human immunoglobulin E to investigate the allergenic activity of major grass pollen allergen Phl p 5.

BACKGROUND: Allergen recognition by IgE antibodies is a key event in allergic inflammation. OBJECTIVE: To construct a plasmid for the expression of human monoclonal IgE antibodies of any desired specificity and to express IgE specific for the major timothy grass pollen allergen Phl p 5. METHODS: In a first step, the DNA sequence coding for the IgG(1) heavy chain was excised and replaced by the sequence coding for the human ɛ constant region gene in plasmid pLNOH2 expressing a human Phl p 5-specific IgG(1) heavy chain. Then, this construct together with a second plasmid expressing the corresponding Phl p 5-specific light chain was co-expressed in COS-7 cells. The Phl p 5-specific IgE (rhuMabEP5) was analysed for allergen-specificity and isotype by ELISA. Cross-reactivity of rhuMabEP5 was investigated by immunoblotting using pollen extracts from various grass species. The allergenic activity of Phl p 5 was studied by exposing rat basophil leukaemia (RBL) cells expressing human-FcɛRI to rhuMabEP5 and Phl p 5. RESULTS: We report the construction of vector pLNOH2-P5IgE, for the expression of human IgE and exemplify its usefulness by the production of a complete and functional human monoclonal IgE (rhuMabEP5). rhuMabEP5 is specific for the grass pollen allergen Phl p 5 and cross-reacts with group 5 allergens in natural grass pollen extracts. RBL-release assays with rhuMabEP5 demonstrated that oligomerization does not contribute to the high allergenic activity of Phl p 5. CONCLUSION AND CLINICAL RELEVANCE: Plasmid pLNOH2-P5IgE allowed the production of a fully functional human monoclonal IgE antibody specific for Phl p 5. Recombinant human IgE antibodies of defined specificity represent useful tools to investigate mechanisms underlying IgE-mediated allergies.

A comparison of mammalian and yeast pre-mRNA 3'-end processing.

Many components of the mammalian and yeast pre-mRNA 3'-end-processing machinery have recently been purified and cDNAs or genes coding for these factors have been cloned. Most of the factors consist of multiple subunits, some of which serve to bind the RNA substrate, others of which are involved in forming a complex network of protein-protein interactions. Most of the mammalian 3'-end-processing factors are similar in their amino acid sequence to the yeast factors, indicating that they have a common evolutionary history.

mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription.

Eukaryotic mRNA precursors are processed at their 3' ends by a coupled cleavage/polyadenylation reaction. In recent years, most of the factors involved in 3'-end processing have been identified and evidence has been presented for the coupling of mRNA 3'-end formation to capping, splicing and transcription. These links are important for the quality control of the mRNA during synthesis.

The use of WHAM-FTOX, parameterized with laboratory data, to simulate zooplankton species richness in acid- and metal- contaminated lakes.

The WHAM-FTOX model quantifies cation toxicity towards freshwater organisms, assuming an additive toxic response to the amounts of protons and metals accumulated by an organism. We combined a parameterization of the model, using data from multi-species laboratory toxicity tests, with a fitted field species sensitivity distribution, to simulate the species richness (nsp) of crustacean zooplankton in acid- and metal-contaminated lakes near Sudbury, Ontario over several decades, and also in reference (uncontaminated) lakes. A good description of variation in toxic response among the zooplankton species was achieved with a log-normal distribution of a new parameter, ß, which characterizes an organism's intrinsic sensitivity towards toxic cations; the greater is ß, the more sensitive is the species. The use of ß assumes that while species vary in their sensitivity, the relative toxicities of different metals are the same for each species (common relative sensitivity). Unbiased agreements between simulated and observed nsp were obtained with a high correlation (r2 = 0.81, p < 0.0001, n = 217). Variations in zooplankton species richness in the Sudbury lakes are calculated to be dominated by toxic responses to H, Al, Cu and Ni, with a small contribution from Zn, and negligible effects of Cd, Hg and Pb. According to the model, some of the Sudbury lakes were affected predominantly by acidification (H and Al), while others were most influenced by toxic heavy metals (Ni, Cu, Zn); for lakes in the latter category, the relative importance of heavy metals, compared to H and Al, has increased over time. The results suggest that, if common relative sensitivity operates, nsp can be modelled on the basis of a single set of parameters characterizing the average toxic effects of different cations, together with a species sensitivity distribution.

Arsenic, chromium, and other elements of concern in fish from remote boreal lakes and rivers: Drivers of variation and implications for subsistence consumption.

Eating fish provides numerous health benefits, but it is also a dominant pathway for human exposure to contaminants. Many studies have examined mercury (Hg) accumulation in fish, but fewer have considered other elements, such as arsenic (As) and chromium (Cr). Recently, freshwater fish from several pristine boreal systems across northern Ontario, Canada, have been reported with elevated concentrations of As and Cr for reasons that are not well understood. Our goal was to investigate the ecological and environmental influences over concentrations of As, Cr, and other elements in these fish to better understand what affects metal uptake and the risk to consumers. We measured 10 elements (including As, Cr, Hg) as well as carbon (δ13C), nitrogen (δ15N), and sulfur (δ34S) stable isotopes in 388 fish from 25 lake and river sites across this remote region. These data were used to determine the effect of: 1) trophic ecology; and 2) watershed geology on piscine elemental content. Overall, most element concentrations were low, often below provincial advisory benchmarks (ABs). However, traces of Hg, As, Cr, and selenium (Se) were detected in most fish. Based on their exceedance of their respective ABs, the most restrictive elements on fish consumption in these boreal systems were Hg > As > Cr. Arsenic and Se, but not Cr concentrations were related to fish size and trophic ecology (inferred from δ13C and δ15N), suggesting bioaccumulation of the former elements. Fish with enriched δ34S values, suggestive of anadromous behaviour, had marginally lower Hg but higher Se concentrations. Modeling results suggested a strong effect of site-specific factors, though we found weak trends between piscine elemental content and geological features (e.g., mafic intrusions), potentially due to the broad spatial scale of this study. Results from this study address gaps in our understanding of As and Cr bioaccumulation and will help to inform fish consumption guidelines.

An adenosine deaminase that generates inosine at the wobble position of tRNAs.

Several transfer RNAs (tRNAs) contain inosine (I) at the first position of their anticodon (position 34); this modification is thought to enlarge the codon recognition capacity during protein synthesis. The tRNA-specific adenosine deaminase of Saccharomyces cerevisiae that forms I(34) in tRNAs is described. The heterodimeric enzyme consists of two sequence-related subunits (Tad2p/ADAT2 and Tad3p/ADAT3), both of which contain cytidine deaminase (CDA) motifs. Each subunit is encoded by an essential gene (TAD2 and TAD3), indicating that I(34) is an indispensable base modification in elongating tRNAs. These results provide an evolutionary link between the CDA superfamily and RNA-dependent adenosine deaminases (ADARs/ADATs).

Higher order structure of simian virus 40 chromatin.

Simian virus 40 nucleoprotein complexes undergo an ionic strength-dependent structural transition. At moderate ionic strength they contain histone H1 as well as the nucleosomal histones and have a compact conformation with globular subunits 190 angstroms in diameter. At high ionic strength histone H1 is released, and the structure unfolds into chains with an average of 24 nucleosomes. The extended viral chromatin converts to the compact form by the addition of histone H1. Transcriptionally active simian virus 40 chromatin undergoes the same structural transitions. The higher order structure of viral chromatin may be analogous to the compact state of cellular chromatin fibers observed at physiological ionic strength.

RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3'-end processing factor.

Most eukaryotic pre-messenger RNAs are processed at their 3' ends by endonucleolytic cleavage and polyadenylation. In yeast, this processing requires polyadenylate [poly(A)] polymerase (PAP) and other proteins that have not yet been characterized. Here, mutations in the PAP1 gene were shown to be synergistically lethal with previously identified mutations in the RNA14 and RNA15 genes, which suggests that their encoded proteins participate in 3'-end processing. Indeed, extracts from ma14 and rna15 mutants were shown to be deficient in both steps of processing. Biochemical complementation experiments and reconstitution of both activities with partially purified cleavage factor I (CF I) validated the genetic prediction.

Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I.

The 3' ends of most eukaryotic messenger RNAs are generated by endonucleolytic cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) plays a central role in both steps of the processing reaction. Here, the cloning of the 73-kilodalton subunit of CPSF is reported. Sequence analyses revealed that a yeast protein (Ysh1) was highly similar to the 73-kD polypeptide. Ysh1 constitutes a new subunit of polyadenylation factor I (PFI), which has a role in yeast pre-mRNA 3'-end formation. This finding was unexpected because in contrast to CPSF, PFI is only required for the polyadenylation reaction. These results contribute to the understanding of how 3'-end processing factors may have evolved.

Coupling termination of transcription to messenger RNA maturation in yeast.

The direct association between messenger RNA (mRNA) 3'-end processing and the termination of transcription was established for the CYC1 gene of Saccharomyces cerevisiae. The mutation of factors involved in the initial cleavage of the primary transcript at the poly(A) site (RNA14, RNA15, and PCF11) disrupted transcription termination at the 3' end of the CYC1 gene. In contrast, the mutation of factors involved in the subsequent polyadenylation step (PAP1, FIP1, and YTH1) had little effect. Thus, cleavage factors link transcription termination of RNA polymerase II with pre-mRNA 3'-end processing.

The three-dimensional structure of canine parvovirus and its functional implications.

The three-dimensional atomic structure of a single-stranded DNA virus has been determined. Infectious virions of canine parvovirus contain 60 protein subunits that are predominantly VP-2. The central structural motif of VP-2 has the same topology (an eight-stranded antiparallel beta barrel) as has been found in many other icosahedral viruses but represents only about one-third of the capsid protein. There is a 22 angstrom (A) long protrusion on the threefold axes, a 15 A deep canyon circulating about each of the five cylindrical structures at the fivefold axes, and a 15 A deep depression at the twofold axes. By analogy with rhinoviruses, the canyon may be the site of receptor attachment. Residues related to the antigenic properties of the virus are found on the threefold protrusions. Some of the amino termini of VP-2 run to the exterior in full but not empty virions, which is consistent with the observation that some VP-2 polypeptides in full particles can be cleaved by trypsin. Eleven nucleotides are seen in each of 60 symmetry-related pockets on the interior surface of the capsid and together account for 13 percent of the genome.

The biochemistry of polyadenylation.

During the synthesis of mRNA in the nucleus, 3'-ends are generated by endonucleolytic cleavage followed by polyadenylation. The machinery responsible for this simple reaction is surprisingly complex. In vitro reconstitution of 3'-end processing has demonstrated the importance of cooperative interactions in RNA recognition and catalysis. However, the inventory of processing factors is still incomplete and important mechanistic questions have not yet been answered.

RNA editing by base deamination: more enzymes, more targets, new mysteries.

The posttranscriptional modification of messenger RNA precursors (pre-mRNAs) by base deamination can profoundly alter the physiological function of the encoded proteins. The recent identification of tRNA-specific adenosine deaminases (ADATs) has led to the suggestion that these enzymes, as well as the cytidine and adenosine deaminases acting on pre-mRNAs (CDARs and ADARs), belong to a superfamily of RNA-dependent deaminases. This superfamily might have evolved from an ancient cytidine deaminase. This article reviews the reactions catalysed by these enzymes and discusses their evolutionary relationships.