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

2020 ◽  
Vol 22 (1) ◽  
pp. 32
Author(s):  
Shaymaviswanathan Karnaneedi ◽  
Roger Huerlimann ◽  
Elecia B. Johnston ◽  
Roni Nugraha ◽  
Thimo Ruethers ◽  
...  
Keyword(s):  
De Novo ◽  
Penaeus Monodon ◽  
Clinical Importance ◽  
Major Allergen ◽  
Cross Reactivity ◽  
Multiple Sequence ◽  
Alpha Tubulin ◽  
Shrimp Species ◽  
Allergen Sources ◽  
Shellfish Allergy

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.

scholarly journals Novel allergen discovery through comprehensive de novo transcriptomic analyses of 5 shrimp species

2020 ◽  
Author(s):  
Shaymaviswanathan Karnaneedi ◽  
Roger Huerlimann ◽  
Elecia B. Johnston ◽  
Roni Nugraha ◽  
Thimo Ruethers ◽  
...  
Keyword(s):  
Calcium Binding ◽  
De Novo ◽  
Arginine Kinase ◽  
Penaeus Monodon ◽  
Clinical Importance ◽  
Major Allergen ◽  
Multiple Sequence ◽  
Alpha Tubulin ◽  
Shrimp Species ◽  
Shellfish Allergy

AbstractShellfish allergy affects up to 2% of the world’s population and persists for life in most patients. The diagnosis of a shellfish allergy, in particular shrimp, is however often challenging due to the similarity of allergenic proteins in other invertebrates. Despite the clinical importance, the complete allergen repertoire of allergy-causing shrimps remains unclear. 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 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). Trinity was used to assemble the transcriptome, and Transrate and BUSCO applied to verify the assembly. Blast search with the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. Salmon was utilised to measure their relative abundance, demonstrating sarcoplasmic calcium-binding protein, arginine kinase and myosin light chain as highly abundant allergens. In addition, the analyses revealed up to 40 unreported allergens in 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, conducted in Jalview 2.1 with 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 genomic resource for investigating shellfish allergens, comparing invertebrate allergens and developing improved diagnostics and novel immunotherapeutics for food allergy.

scholarly journals Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses

2020 ◽  
Author(s):  
Kathrin Balz ◽  
Meng Chen ◽  
Abhinav Kaushik ◽  
Franz Cemic ◽  
Vanessa Heger ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
De Novo ◽  
Class Ii ◽  
Cross Reactivity ◽  
Phleum Pratense ◽  
Class I ◽  
T Cell Epitopes ◽  
Allergen Sources

Abstract The outbreak of the new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus, Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.

scholarly journals Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathrin Balz ◽  
Abhinav Kaushik ◽  
Meng Chen ◽  
Franz Cemic ◽  
Vanessa Heger ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
De Novo ◽  
Class Ii ◽  
Cross Reactivity ◽  
Phleum Pratense ◽  
Class I ◽  
T Cell Epitopes ◽  
Allergen Sources

AbstractThe outbreak of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus, Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.

scholarly journals Multifractal Analysis of Hemodynamic Behavior

2012 ◽  
Vol 117 (4) ◽  
pp. 810-821 ◽  
Author(s):  
Steven M. Bishop ◽  
Sarah I. Yarham ◽  
Vilas U. Navapurkar ◽  
David K. Menon ◽  
Ari Ercole
Keyword(s):  
Heart Rate ◽  
Mean Arterial Pressure ◽  
Arterial Pressure ◽  
De Novo ◽  
Clinical Importance ◽  
Multifractal Spectrum ◽  
Clinical Problem ◽  
Abdominal Aortic Aneurysm Repair ◽  
Feedback Systems ◽  
Modulus Maxima

Background Physiologic instability is a common clinical problem in the critically ill. Many natural feedback systems are nonlinear, and seemingly random fluctuations may result from the amplification of external perturbations or even arise de novo as a consequence of their underlying dynamics. Characterization of the underlying nonlinear state may be of clinical importance, providing a technique to monitor complex physiology in real-time, guiding patient care and improving outcomes. Methods We employ the wavelet modulus maxima technique to characterize the multifractal properties of heart rate and mean arterial pressure physiology retrospectively for four patients during open abdominal aortic aneurysm repair. We calculated point-estimates for the dominant Hölder exponent (hm, hm) and multifractal spectrum width-at-half-height for both heart rate and mean arterial pressure signals. We investigated how these parameters changed with the administration of an intravenous vasoconstrictor and examined how this varied with atropine pretreatment. Results Hypotensive patients showed lower values of hm, consistent with a more highly fluctuating and complex behavior. Treatment with a vasoconstrictor led to a transient increase in hm, revealing the appearance of longer-range correlations, but did not impact hm. On the other hand, prior treatment with atropine had no effect on hm behavior but did tend to increase hm. Conclusions Hypotension leads to a reduction in dominant Hölder exponents for mean arterial pressure, demonstrating an increasing signal complexity consistent with the activation of important homeokinetic processes. Conversely, pharmacological interventions may also alter the underlying dynamics. Pharmacological restoration of homeostasis leads to system decomplexification, suggesting that homeokinetic mechanisms are derecruited as homeostasis is restored.

Identification of sole parvalbumin as a major allergen: study of cross-reactivity between parvalbumins in a Spanish fish-allergic population

2011 ◽  
Vol 41 (5) ◽  
pp. 750-758 ◽  
Author(s):  
M. Perez-Gordo ◽  
J. Cuesta-Herranz ◽  
A. S. Maroto ◽  
B. Cases ◽  
M. D. Ibáñez ◽  
...  
Keyword(s):  
Major Allergen ◽  
Cross Reactivity

Major Allergen and Its IgE Cross-Reactivity among Salmonid Fish Roe Allergy

2009 ◽  
Vol 57 (6) ◽  
pp. 2314-2319 ◽  
Author(s):  
Yutaka Shimizu ◽  
Atsushi Nakamura ◽  
Hideki Kishimura ◽  
Akihiko Hara ◽  
Kazuhiko Watanabe ◽  
...  
Keyword(s):  
Major Allergen ◽  
Cross Reactivity ◽  
Salmonid Fish ◽  
Fish Roe

scholarly journals T-cell Receptors Engineered De Novo for Peptide Specificity Can Mediate Optimal T-cell Activity without Self Cross-Reactivity

2019 ◽  
Vol 7 (12) ◽  
pp. 2025-2035 ◽  
Author(s):  
Preeti Sharma ◽  
Daniel T. Harris ◽  
Jennifer D. Stone ◽  
David M. Kranz
Keyword(s):  
T Cell ◽  
T Cell Receptors ◽  
De Novo ◽  
Cell Activity ◽  
Cross Reactivity ◽  
Cell Receptors ◽  
Peptide Specificity
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