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Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs.

ABSTRACT: Quantitative guidelines to distinguish allergenic proteins from related, but non-allergenic ones are urgently needed for regulatory agencies, biotech companies and physicians. In a previous study, we found that allergenic proteins populate a relatively small number of protein families, as characterized by the Pfam database. However, these families also contain non-allergenic proteins, meaning that allergenic determinants must lie within more discrete regions of the sequence. Thus, new methods are needed to discriminate allergenic proteins within those families. Physical-Chemical Properties (PCP)-motifs specific for allergens within a Pfam class were determined for 17 highly populated protein domains. A novel scoring method based on PCP-motifs that characterize known allergenic proteins within these families was developed, and validated for those domains. The motif scores distinguished sequences of allergens from a large selection of 80,000 randomly selected non-allergenic sequences. The motif scores for the birch pollen allergen (Bet v 1) family, which also contains related fruit and nut allergens, correlated better than global sequence similarities with clinically observed cross-reactivities among those allergens. Further, we demonstrated that the average scores of allergen specific motifs for allergenic profilins are significantly different from the scores of non-allergenic profilins. Several of the selective motifs coincide with experimentally determined IgE epitopes of allergenic profilins. The motifs also discriminated allergenic pectate lyases, including Jun a 1 from mountain cedar pollen, from similar proteins in the human microbiome, which can be assumed to be non-allergens. The latter lacked key motifs characteristic of the known allergens, some of which correlate with known IgE binding sites.

SUBMITTER: Lu W

PROVIDER: S-EPMC5994374 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs.

Lu Wenzhe W Negi Surendra S SS Schein Catherine H CH Maleki Soheila J SJ Hurlburt Barry K BK Braun Werner W

Molecular immunology 20180406

Quantitative guidelines to distinguish allergenic proteins from related, but non-allergenic ones are urgently needed for regulatory agencies, biotech companies and physicians. In a previous study, we found that allergenic proteins populate a relatively small number of protein families, as characterized by the Pfam database. However, these families also contain non-allergenic proteins, meaning that allergenic determinants must lie within more discrete regions of the sequence. Thus, new methods ar ...[more]

PMID: 29627609

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Project description:BACKGROUND:To obtain information on feasibility and acceptability, as well as preliminary data on efficacy, of an Osteoarthritis Physical activity Care Pathway (OA-PCP). METHODS:This was a single group pilot study involving 60 participants with symptomatic, physician diagnosed knee or hip OA, recruited from primary care clinics. Participants self-reported completing less than 150?min per week of moderate-to-vigorous physical activity (MVPA) at baseline. The 3-month OA-PCP intervention involved 3 physical activity (PA) coaching calls (focused on goal setting), three check-in emails and linkage with community-based or online resources to support PA. Efficacy outcomes were collected at baseline and 4-month follow-up. The primary efficacy outcome was minutes of MVPA, assessed via accelerometer. Secondary outcomes included minutes of light intensity activity, sedentary minutes, step counts, and Western Ontario and McMaster Universities (WOMAC) pain and function subscales. Participants were also asked to rate the helpfulness of the OA-PCP intervention on a scale of 0-10. Differences in efficacy outcomes between baseline and 4-month follow-up were assessed using paired t-tests. RESULTS:Among participants beginning the study, 88% completed follow-up assessments and???90% completed each of the intervention calls. Average daily minutes of MVPA was 8.0 at baseline (standard deviation (SD)?=?9.9) and 8.9 at follow-up (SD?=?12.1, p?=?0.515). There were no statistically significant changes in light intensity activity, sedentary time or step counts. The mean WOMAC pain score improved from 8.1 (SD?=?3.6) at baseline to 6.2 (SD?=?3.8) at follow-up (p?<?0.001); the mean WOMAC function score improved from 26.2 (SD?=?13.2) to 20.2 (SD?=?12.5; p?<?0.001). The mean rating of helpfulness was 7.6 (SD?=?2.5). CONCLUSIONS:Results supported the feasibility and acceptability of the study, and participants reported clinically relevant improvements in pain and function. PA metrics did not improve substantially. Based on these results and participant feedback, modifications including enhanced self-monitoring are being made to increase the impact of the OA-PCP intervention on PA behavior. TRIAL REGISTRATION:NCT03780400, December 19, 2018.

Project description:BACKGROUND:Pneumocystis pneumonia (PCP) is a disease affecting immunocompromised patients. PCP among these patients is associated with significant morbidity and mortality. OBJECTIVES:To assess the effectiveness of PCP prophylaxis among non-HIV immunocompromised patients; and to define the type of immunocompromised patient for whom evidence suggests a benefit for PCP prophylaxis. SEARCH METHODS:Electronic searches of the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2014, Issue 1), MEDLINE and EMBASE (to March 2014), LILACS (to March 2014), relevant conference proceedings; and references of identified trials. SELECTION CRITERIA:Randomised controlled trials (RCTs) or quasi-RCTs comparing prophylaxis with an antibiotic effective against PCP versus placebo, no intervention, or antibiotic(s) with no activity against PCP; and trials comparing different antibiotics effective against PCP among immunocompromised non-HIV patients. We only included trials in which Pneumocystis infections were available as an outcome. DATA COLLECTION AND ANALYSIS:Two review authors independently assessed risk of bias in each trial and extracted data from the included trials. We contacted authors of the included trials to obtain missing data. The primary outcome was documented PCP infections. Risk ratios (RR) with 95% confidence intervals (CI) were estimated and pooled using the random-effects model. MAIN RESULTS:Thirteen trials performed between the years 1974 and 2008 were included, involving 1412 patients. Four trials included 520 children with acute lymphoblastic leukemia and the remaining trials included adults with acute leukemia, solid organ transplantation or autologous bone marrow transplantation. Compared to no treatment or treatment with fluoroquinolones (inactive against Pneumocystis), there was an 85% reduction in the occurrence of PCP in patients receiving prophylaxis with trimethoprim/sulfamethoxazole, RR of 0.15 (95% CI 0.04 to 0.62; 10 trials, 1000 patients). The evidence was graded as moderate due to possible risk of bias. PCP-related mortality was also significantly reduced, RR of 0.17 (95% CI 0.03 to 0.94; nine trials, 886 patients) (low quality of evidence due to possible risk of bias and imprecision), but in trials comparing PCP prophylaxis against placebo or no treatment there was no significant effect on all-cause mortality (low quality of evidence due to imprecision). Occurrence of leukopenia or neutropenia and their duration were not reported consistently. No significant differences in overall adverse events or events requiring discontinuation were seen comparing trimethoprim/sulfamethoxazole to no treatment or placebo (four trials, 470 patients, moderate quality evidence). No differences between once daily versus thrice weekly trimethoprim/sulfamethoxazole were seen (two trials, 207 patients). AUTHORS' CONCLUSIONS:Given an event rate of 6.2% in the control groups of the included trials, prophylaxis for PCP using trimethoprim/sulfamethoxazole is highly effective among non-HIV immunocompromised patients, with a number needed to treat to prevent PCP of 19 patients (95% CI 17 to 42). Prophylaxis should be considered for patients with a similar baseline risk of PCP.

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Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs.

Publications

Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs.

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