In search for hypoallergenic trees: Screening for genetic diversity in birch pollen allergens, a multigene family of Bet v 1 (PR 10) proteins MJM
|
|
|
- Bernard Casey
- 5 years ago
- Views:
Transcription
1 In search for hypoallergenic trees: Screening for genetic diversity in birch pollen allergens, a multigene family of Bet v 1 (PR 10) proteins MJM Smulders, MF Schenk, LJWJ Gilissen
2 Hay fever Hay fever affects 10 19% of the population in Western Europe Birch pollen is a major allergen source, especially in Central and North European countries Allergy to birch is associated with a type of food allergy called Oral Allergy Syndrome (OAS)
3
4 Birch allergens Eight birch allergens are known: Bet v 1 8 These allergens differ according to the number of birch sensitized patients that are allergic to them Bet v 1 is the only major birch allergen (>50% of the birch allergic patients react to this protein)
5 Bet v 1 Bet v 1 is a pathogenesis related (PR) 10 protein PR 10 proteins are present as a multigene family in many species Several Bet v 1 isoforms are found in birch pollen mixtures Bet v 1 isoforms differ in their IgE binding activity and T cell proliferation score > Are multiple genes involved? Do several isoforms also exist within pollen of one tree?
6 This study Genetics: How many Bet v 1 genes are there? What differences exist among birch species? Which are (similar to) hyperallergic isoforms? Proteomics: Which isoforms are being expressed in pollen? Can we predict (hypo)allergenicity? Schenk et al. BMC Genomics 7:168 (2006) Schenk et al. BMC Plant Biology (submitted)
7 Plant material B. pendula B. pendula cultivar Tristis B. pendula cultivar Youngii B. pendula cultivar Schneverdinger Goldbirke Close relatives of B. pendula: B. plathyphylla B. populifolia Other Betula species: B. lenta B. costata B. schmidtii B. chichibuensis B. nigra
8 Alleles cloned and sequenced 134 unique alleles B. pendula Sch. Goldbirke B. pendula Tristis B. pendula Youngii B. populifolia B. plathyphylla B. lenta B. costata B. schmidtii B. chichibuensis B. nigra 14 alleles 15 alleles 16 alleles 17 alleles 20 alleles 14 alleles 20 alleles 12 alleles 22 alleles 25 alleles
9 PR Tr PR Sv PR Sv PR Tr PR Lt PR Sv Lt PR Tr PR-10.03B01.01 Lt PR-10.03B.p01 Sv PR-10.03A01.01 Sv Lt Tr PR-10.03A02.01 Sv PR-10.03C01.01 Sv Lt PR-10.03C02.01 Sv Lt Tr PR-10.03C02.02 Tr PR-10.03D01.01 Tr PR-10.03D02.01 Lt PR-10.03B02.01 Tr PR-10.02A01.01 Sv Lt PR-10.02A02.01 Sv PR-10.02B01.01 Sv PR-10.02B02.01 Tr Lt PR-10.02C01.01 Tr PR-10.02C02.01 Lt PR-10.02C02.02 Lt PR-10.01A01.01 Sv Lt Tr PR-10.01A02.01 Tr PR-10.01A03.01 Lt PR-10.01B01.01 Sv Lt Tr PR-10.01C01.01 Sv PR-10.01C02.01 Lt PR-10.01D01.01 Tr PR-10.01D02.01 Lt PR intron 146, 147, 152bp PR intron 93, 96bp PR-10.03B intron 84bp (c) PR-10.03A intron 84bp (a,b) PR-10.03C intron 85bp (a,b) PR-10.03D intron 85bp (c) PR-10.03B* intron 85bp (b) PR-10.02A intron 104bp PR-10.02B intron 99 (a,b), 101 bp (a) PR-10.02C intron 101 (b), 105, 151bp PR-10.01A intron 93bp (a,b) PR-10.01B intron 92bp (a) PR-10.01C intron 96, 98bp PR-10.01D intron 92bp (b,c) Results: B. pendula 13 distinct genes, based on: Clustering of the alleles Cut off value of 98% similarity in exons > Maximum of 2 alleles per locus in a diploid tree) Outgroup 0.05
10 PR Tr PR Sv PR Sv PR Tr PR Lt PR Sv Lt PR Tr PR-10.03B01.01 Lt PR-10.03B.p01 Sv PR-10.03A01.01 Sv Lt Tr PR-10.03A02.01 Sv PR-10.03C01.01 Sv Lt PR-10.03C02.01 Sv Lt Tr PR-10.03C02.02 Tr PR-10.03D01.01 Tr PR-10.03D02.01 Lt PR-10.03B02.01 Tr PR-10.02A01.01 Sv Lt PR-10.02A02.01 Sv PR-10.02B01.01 Sv PR-10.02B02.01 Tr Lt PR-10.02C01.01 Tr PR-10.02C02.01 Lt PR-10.02C02.02 Lt PR-10.01A01.01 Sv Lt Tr PR-10.01A02.01 Tr PR-10.01A03.01 Lt PR-10.01B01.01 Sv Lt Tr PR-10.01C01.01 Sv PR-10.01C02.01 Lt PR-10.01D01.01 Tr PR-10.01D02.01 Lt PR intron 146, 147, 152bp PR intron 93, 96bp PR-10.03B intron 84bp (c) PR-10.03A intron 84bp (a,b) PR-10.03C intron 85bp (a,b) PR-10.03D intron 85bp (c) PR-10.03B* intron 85bp (b) PR-10.02A intron 104bp PR-10.02B intron 99 (a,b), 101 bp (a) PR-10.02C intron 101 (b), 105, 151bp PR-10.01A intron 93bp (a,b) PR-10.01B intron 92bp (a) PR-10.01C intron 96, 98bp PR-10.01D intron 92bp (b,c) Outgroup Results: B. pendula Division into 5 subfamilies Within a subfamily genes have >95 % sequence similarity Between subfamilies sequence similarity is 80 90% Transcription Information of 30 mrna derived (tissue specific) GenBank sequences Pollen Root/Leaves 0.05
11 Results for other Betula species Genetic composition of PR 10 genes in B. populifolia and B. plathyphylla is similar to B. pendula Not possible to distinguish homologues from paralogues in the other Betula sp. Gene duplication, extinction, unequal crossing over, and possibly gene conversion play a role Subfamily division is consistent across species Two new subfamilies were identified, but composed of few (pseudo) genes
12 IgE reactivity at the genomic level The isoforms with varying IgE reactivity are encoded by different genes In each of the cultivars and/or species protein variants are found that differ by 1 or 2 amino acids PR-10.02A01.01 Sv Lt PR-10.02A02.01 Sv PR-10.02B01.01 Sv PR-10.02B02.01 Tr Lt PR-10.02C01.01 Tr PR-10.02C02.01 Lt PR-10.02C02.02 Lt PR-10.01A01.01 Sv Lt Tr PR-10.01A02.01 Tr PR-10.01A03.01 Lt?? PR-10.02A intron 104bp PR-10.02B intron 99 (a,b), 101 bp (a) PR-10.02C intron 101 (b), 105, 151bp PR-10.01A intron 93bp (a,b) However, we do not know whether these isoforms are actually expressed and in which quantities? PR-10.01B01.01 Sv Lt Tr PR-10.01C01.01 Sv PR-10.01C02.01 Lt PR-10.01D01.01 Tr PR-10.01D02.01 Lt? PR-10.01B intron 92bp (a) PR-10.01C intron 96, 98bp PR-10.01D intron 92bp (b,c) Outgroup 0.05
13 Methods: protein extraction and sequencing Pollen collection ( ) B. nigra B. lenta B. chichibuensis B. costata B. nigra Protein extraction in aqueous buffer Analyzed with SDS PAGE kda band cut out In gel protein digestion with trypsin Analyzed with Q TOF LC MS/MS and LC MS E
14 SDS PAGE 1. B. chichibuensis 2. B. costata 3. B. nigra 4. B. lenta 5. B. pendula
15 Comparative LC MS approach Protein extracts Trypsin digest 1 Digest 1 2 Digest 2 3 Digest 3 replicate nanolc-ms MS E MS Protein Identification and Quantification Peak detection, Alignment, Quantitative Comparison, Peak selection & identification DDA nanolc-ms/ms Selective Peptide MS/MS Include list for LC-MS/MS Quantification And pre-id table Database Search of MS/MS data m/z Ret É É É É Mw Ret. Peptide SLLDFAR EDTSISLYK FGIAATGÉ GLTATMGÉ NQHGCVTÉ QDFANFÉ É É É É É É
16 Putative peptide fragments Example: Bet v 1 01A01 = PR-10 01A01 MGVFNYETETTSVIPAARLFKAFILDGDNLFPKV APQAISSVENIEGNGGPGTIKKISFPEGFPFKYV KDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNE IKIVATPDGGSILKISNKYHTKGDHEVKAEQVKA SKEMGETLLRAVESYLLAHSDAYN Bet v 1 01A01 = PR-10 01A01 MGVFNYETETTSVIPAAR AFILDGDNLFPKV APQAISSVENIEGNGGPGTIK(K)ISFPEGFPFK (DR)VDEVDHTNFKYNYSVIEGGPIGDTLEK IVATPDGGSILK EMGETLLRAVESYLLAHSDAYN MGVFNYETETTSVIPAAR AFILDGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK (DR)VDEVDHTNFK YNYSVIEGGPIGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN
17 Putative peptide fragments 01A01 - MGVFNYETETTSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK 01B01 - MGVFNYEIETTSVIPAAR AFILDGDNLFVK VAPQAISSVENIEGNGGPGTIK(K) (K)INFPEGFPFK 01C01 - MGVFNYEIEATSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK 01D01 - MGVFNYEIEATSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGIPFK 02A01 - MGVFNYESETTSVIPAAR AFILDGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 02B01 - MGVFNYESETTSVIPAAR AFILDGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 02C01 - MGVFNYESETTSVIPAAR AFILEGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 03A01 - MGVFDYEGETTSVIPAAR AFILDGDNLFPK VAPQAVSCVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 03B01 - MGVFNYEGETTSVIPAAR AFILDGDNLFPK VAPQAVSCVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 03C01 - MGVFDYEGETTSVIPAAR AFILDGDNLFPK VAPQAVSCVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 03D01 - MGVFDYEGETTSVIPAAR AFILDGDNLFPK VAPQAVSCVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 04A01 - MGVFNDEAETTSVIPPAR SFILDADNILSK SAENIEGNGGPGTIK(K) (K)ITFVEGSPFK 05A01 - MGVFNYEDEATSVIAPAR SFVLDADNLFPK VAPENVSSAENIEGNGGPGTIK(K) (K)ITFPEGSPFK 01A01 (DR)VDEVDHTNFK YNYSVIEGGPIGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN 01B01 (DR)VDEVDHTNFK YNYSVIEGGPVGDTLEK IVATPDGGCVLK EMGETLLR AVESYLLAHSDAYN 01C01 (DR)VDEVDHTNFK YNYSVIEGGPVGDTLEK IVATPNGGSILK EMGETLLR AVESYLLAHSDAYN 01D01 (DR)VDEVDHANFK YSYSLIEGGPVGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN 02A01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 02B01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 02C01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 03A01 (ER)IDEVDHVNFK YSYSVIEGGAVGDTLEK IVAAPGGGSILK AVESYLLAHSDAYN 03B01 (ER)VDEVDHVNFK YSYSVIEGGVVGDTLEK IVAAPGGGSILK AVESYLLAHSDAYN 03C01 YSYSVIEGGAVGDTLEK IVPAPGGGSILK AVESYLLAHSDAYN 03D01 (ER)VDEVDHENFK YSYSVIEGGAVGDTLEK IVPAPGGGSILK AVESYLLAHSDAYN 04A01 (QR)IDEIDHTNFK YSYSLIEGGPLGDTLEK IAAAPDGGSILK GNISINQEQIK AIEGYLLAHSDAYN 05A01 (HR)VDEIDHTNFK YCYSIIEGGPLGDTLEK IVAAPGGGSILK GNISLNEEEIK AVENYLLAHSDAYN
18 Results: recovered fragments 01A01 - GVFNYETETTSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK 01A06 - GVFNYETETTSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)INFPEGFPFK 01B01 - GVFNYEIETTSVIPAAR AFILDGDNLFVK VAPQAISSVENIEGNGGPGTIK(K) (K)INFPEGFPFK 01C04 - GVFNYEIEATSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK 01C05 - GVFNYEIEATSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGFPFK 01D01 - GVFNYEIEATSVIPAAR AFILDGDNLFFK VAPQAISSVENIEGNGGPGTIK(K) (K)ISFPEGIPFK 02A01 - GVFNYESETTSVIPAAR AFILDGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 02B01 - GVFNYESETTSVIPAAR AFILDGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 02C01 - GVFNYESETTSVIPAAR AFILEGDNLFPK VAPQAISSVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 03A01 - GVFDYEGETTSVIPAAR AFILDGDNLFPK VAPQAVSCVENIEGNGGPGTIK(K) (K)ITFPEGSPFK 04A01 - GVFNDEAETTSVIPPAR SFILDADNILSK SAENIEGNGGPGTIK(K) (K)ITFVEGSPFK 05A01 - GVFNYEDEATSVIAPAR SFVLDADNLFPK VAPENVSSAENIEGNGGPGTIK(K) (K)ITFPEGSPFK 01A01 (DR)VDEVDHTNFK YNYSVIEGGPIGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN 01A06 - (DR)VDEVDHTNFK YNYSVIEGGPIGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN 01B01 (DR)VDEVDHTNFK YNYSVIEGGPVGDTLEK IVATPDGGCVLK EMGETLLR AVESYLLAHSDAYN 01C04 (DR)VDEVDHTNFK YSYSVIEGGPVGDTLEK IVATPNGGSILK EMGETLLR AVESYLLAHSDAYN 01C05 - (DR)VDEVDHTNFK YSYSVIEGGPVGDTLEK IVATPNGGSILK EMGETLLR AVESYLLAHSDAYN 01D01 (DR)VDEVDHANFK YSYSLIEGGPVGDTLEK IVATPDGGSILK EMGETLLR AVESYLLAHSDAYN 02A01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 02B01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 02C01 (ER)VDEVDHANFK YSYSMIEGGALGDTLEK LVATPDGGSILK AVESYLLAHSDAYN 03A01 (ER)IDEVDHVNFK YSYSVIEGGAVGDTLEK IVAAPGGGSILK AVESYLLAHSDAYN 04A01 (QR)IDEIDHTNFK YSYSLIEGGPLGDTLEK IAAAPDGGSILK GNISINQEQIK AIEGYLLAHSDAYN 05A01 (HR)VDEIDHTNFK YCYSIIEGGPLGDTLEK IVAAPGGGSILK GNISLNEEEIK AVENYLLAHSDAYN
19 Conclusions: Bet v 1 expression in B. pendula Only the genes in subfamily 01 and 02 are expressed in pollen The expression of at least 5 PR 10 genes was confirmed in B. pendula pollen Both isoforms with a high and low IgE reactivity can be detected in pollen from one birch tree
20 Isoform expression Unique peptides elucidate expression of isoforms/genes Examined 3 B. pendula cultivars: 01A ~30% 01B ~20% 01C ~10% 02A/B ~20% 02C ~20%
21 Isoform expression For other Betula species, determining expression of individual isoforms is not useful because in most cases we do not know the allergenicity of all isoforms In stead we determined the relative quantity of those peptides that constitute isoforms with high, intermediate and low allergenicity in B. pendula
22
23 Conclusion Q TOF LC MS E data provide: Presence/absence of peptides/isoforms Quantitative data All (examined) Betula pendula cultivars are likely to be highly allergenic Allergens that are similar to the most allergenic isoforms are probably present in all species, except possibly B. lenta
24 Hypoallergenic birch trees? Perhaps in B. lenta or Use male sterile hybrid cultivars Decrease length of the pollen season by limiting the number of different species planted in a city
25
26 Acknowledgements Genomics D. Esselink W. Van t Westende Proteomics A.H.P. America J.H.G. Cordewener
Seven different genes encode a diverse mixture of isoforms of Bet v 1, the major birch pollen allergen
BMC Genomics This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed
Introduction to Proteomics 1.0
Introduction to Proteomics 1.0 CMSP Workshop Pratik Jagtap Managing Director, CMSP Objectives Why are we here? For participants: Learn basics of MS-based proteomics Learn what s necessary for success using
Food Allergy. Soheila J. Maleki. Food Allergy Research USDA-ARS-Southern Regional Research Center
Food Allergy Soheila J. Maleki Food Allergy Research USDA-ARS-Southern Regional Research Center The prevalence of food allergy has increased and in some cases doubled since 1997: Better diagnosis New cases/increased
Nature Biotechnology: doi: /nbt Supplementary Figure 1
Supplementary Figure 1 The timeline of the NGAG method for extraction of N-linked glycans and glycosite-containing peptides. The timeline can be changed based on the number of samples. Supplementary Figure
Supplemental Data. Integrating omics and alternative splicing i reveals insights i into grape response to high temperature
Supplemental Data Integrating omics and alternative splicing i reveals insights i into grape response to high temperature Jianfu Jiang 1, Xinna Liu 1, Guotian Liu, Chonghuih Liu*, Shaohuah Li*, and Lijun
Emerging Allergens. Karin Hoffmann-Sommergruber Dept. of Pathophysiology & Allergy Research, Medical University of Vienna, Austria
Emerging Allergens Karin Hoffmann-Sommergruber Dept. of Pathophysiology & Allergy Research, Medical University of Vienna, Austria Allergens Proteins Small mol mass Resistant against enzymatic digestion
Mass Spectrometry and Proteomics - Lecture 4 - Matthias Trost Newcastle University
Mass Spectrometry and Proteomics - Lecture 4 - Matthias Trost Newcastle University matthias.trost@ncl.ac.uk previously Peptide fragmentation Hybrid instruments 117 The Building Blocks of Life DNA RNA Proteins
Double charge of 33kD peak A1 A2 B1 B2 M2+ M/z. ABRF Proteomics Research Group - Qualitative Proteomics Study Identifier Number 14146
Abstract The 2008 ABRF Proteomics Research Group Study offers participants the chance to participate in an anonymous study to identify qualitative differences between two protein preparations. We used
Precise results for safe decisions. How to better define and manage peanut allergy
Precise results for safe decisions How to better define and manage peanut allergy Better risk assessment with allergen components How can you differentiate between true peanut allergy or symptoms caused
Improving allergy outcomes. Allergen Component Testing. Jay Weiss Ph.D and Gary Kitos, Ph.D. H.C.L.D.
Improving allergy outcomes Allergen Component Testing Jay Weiss Ph.D and Gary Kitos, Ph.D. H.C.L.D. Allergen Component Testing Allergic disease is an immunologic response to an allergen or allergens that
http://www.diva-portal.org This is the published version of a paper presented at Indoor Air 2016, 14th International Conference of Indoor Air Quality and Climate, Ghent, Belgium, 3-8 July 2016. Citation
Protein Safety Assessments Toxicity and Allergenicity
Protein Safety Assessments Toxicity and Allergenicity Laura Privalle, Ph.D. BAYER CropScience HESI PATC ILSI IFBiC September 20, 2013 Biotechnology is an Extension of Traditional Plant Breeding TRADITIONAL
Mass Spectrometry. Mass spectrometer MALDI-TOF ESI/MS/MS. Basic components. Ionization source Mass analyzer Detector
Mass Spectrometry MALDI-TOF ESI/MS/MS Mass spectrometer Basic components Ionization source Mass analyzer Detector 1 Principles of Mass Spectrometry Proteins are separated by mass to charge ratio (limit
Dr. Janice M. Joneja, Ph.D. FOOD ALLERGIES - THE DILEMMA
Dr. Janice M. Joneja, Ph.D. FOOD ALLERGIES - THE DILEMMA 2002 The Dilemma Accurate identification of the allergenic food is crucial for correct management of food allergy Inaccurate identification of the
appropriate olive pollen SIT
OLIVE POLLEN Molecular Allergology Use components to identify patients for appropriate olive pollen SIT Resolve multiple positivity to pollen tests Use components to resolve multiple positivity to pollen
Multiplex Protein Quantitation using itraq Reagents in a Gel-Based Workflow
Multiplex Protein Quantitation using itraq Reagents in a Gel-Based Workflow Purpose Described herein is a workflow that combines the isobaric tagging reagents, itraq Reagents, with the separation power
Mustard Allergy Review and Discussion of Mustard Data. Dr. Sébastien La Vieille Bureau of Chemical Safety Food Directorate
Mustard Allergy Review and Discussion of Mustard Data Dr. Sébastien La Vieille Bureau of Chemical Safety Food Directorate Mustard /canola labelling considerations The mustard plant belongs to the Brassicaceae
PTM Discovery Method for Automated Identification and Sequencing of Phosphopeptides Using the Q TRAP LC/MS/MS System
Application Note LC/MS PTM Discovery Method for Automated Identification and Sequencing of Phosphopeptides Using the Q TRAP LC/MS/MS System Purpose This application note describes an automated workflow
Comparison of mass spectrometers performances
Comparison of mass spectrometers performances Instrument Mass Mass Sensitivity resolution accuracy Quadrupole 1 x 10 3 0.1 Da* 0.5-1.0 pmol DE-MALDI 2 x 10 4 20 ppm 1-10 fmol peptide 1-5 pmol protein Ion
MSSimulator. Simulation of Mass Spectrometry Data. Chris Bielow, Stephan Aiche, Sandro Andreotti, Knut Reinert FU Berlin, Germany
Chris Bielow Algorithmic Bioinformatics, Institute for Computer Science MSSimulator Chris Bielow, Stephan Aiche, Sandro Andreotti, Knut Reinert FU Berlin, Germany Simulation of Mass Spectrometry Data Motivation
Pollen immunotherapy reduces the development of asthma in children with allergic rhinoconjunctivitis (The PAT-Study)
Pollen immunotherapy reduces the development of asthma in children with allergic rhinoconjunctivitis (The PAT-Study) Christian Möller 1, Sten Dreborg 2, Hosne A. Ferdousi 3, Susanne Halken 4, Arne Høst
Transgenic Crops and Soybean Protein Analysis
Transgenic Crops and Soybean Protein Analysis Savithiry S. Natarajan, Ph.D. United States Department of Agriculture Agricultural Research Service Soybean Genomics & Improvement Laboratory Savi.natarajan@ars.usda.gov
Evaluating Variability of Allergens in Commodity Crops (Peanuts)
Evaluating Variability of Allergens in Commodity Crops (Peanuts) Peggy Ozias-Akins Laura Ramos Paola Faustinelli Ye Chu University of Georgia Manel Jordana Katherine Arias McMaster University Soheila Maleki
Hypersensitivity Reactions and Peanut Component Testing 4/17/ Mayo Foundation for Medical Education and Research. All rights reserved.
1 Hello everyone. My name is Melissa Snyder, and I am the director of the Antibody Immunology Lab at the Mayo Clinic in Rochester, MN. I m so glad you are able to join me for a brief discussion about the
09 Liechtenstein, /03/2014
Chronic inflammatory disease Chronic inflammatory disease Chronic inflammatory disease Rheumatic fever Hepatitis A Multiple sclerosis Crohn s disease TH1 (or TH17) Multiple sclerosis Rheumatic Type 1 diabetes
Joint FAO/WHO Expert Consultation on Foods Derived from Biotechnology
Food and Agriculture Organization of the United Nations World Health Organization Biotech 01/03 Joint FAO/WHO Expert Consultation on Foods Derived from Biotechnology Headquarters of the Food and Agriculture
The use of components in allergy diagnostics. Dr. Sc. E. Van Hoeyveld Laboratory Medicine
The use of components in allergy diagnostics Dr. Sc. Laboratory Medicine Use of components in the clinic Basics of allergen components and their clinical implications I. Allergen component names II. Properties
Mechanismen der allergenspezifischen Immuntherapie
Mechanismen der allergenspezifischen Immuntherapie Medizinische Universität Wien Zentrum für Pathophysiologie, Infektiologie und Immunologie Institut für Pathophysiologie und Allergieforschung Abteilung
Principles of Adaptive Immunity
Principles of Adaptive Immunity Chapter 3 Parham Hans de Haard 17 th of May 2010 Agenda Recognition molecules of adaptive immune system Features adaptive immune system Immunoglobulins and T-cell receptors
Improve Protein Analysis with the New, Mass Spectrometry- Compatible ProteasMAX Surfactant
Improve Protein Analysis with the New, Mass Spectrometry- Compatible Surfactant ABSTRACT Incomplete solubilization and digestion and poor peptide recovery are frequent limitations in protein sample preparation
LECTURE-15. itraq Clinical Applications HANDOUT. Isobaric Tagging for Relative and Absolute quantitation (itraq) is a quantitative MS
LECTURE-15 itraq Clinical Applications HANDOUT PREAMBLE Isobaric Tagging for Relative and Absolute quantitation (itraq) is a quantitative MS based method for quantifying proteins subject to various different
Identification and characterization of multiple splice variants of Cdc2-like kinase 4 (Clk4)
Identification and characterization of multiple splice variants of Cdc2-like kinase 4 (Clk4) Vahagn Stepanyan Department of Biological Sciences, Fordham University Abstract: Alternative splicing is an
New Developments in LC-IMS-MS Proteomic Measurements and Informatic Analyses
New Developments in LC-IMS-MS Proteomic Measurements and Informatic Analyses Erin Shammel Baker Kristin E. Burnum-Johnson, Xing Zhang, Cameron P. Casey, Yehia M. Ibrahim, Matthew E. Monroe, Tao Liu, Brendan
Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated
Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C genes. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated from 7 day-old seedlings treated with or without
Protein Identification and Phosphorylation Site Determination by de novo sequencing using PepFrag TM MALDI-Sequencing kit
Application Note Tel: +82-54-223-2463 Fax : +82-54-223-2460 http://www.genomine.com venture ldg 306 Pohang techno park Pohang, kyungbuk, Korea(ROK) Protein Identification and Phosphorylation Site Determination
The Future of Allergy Treatment Ultra-Fast Allergy Immunotherapy
The Future of Allergy Treatment Ultra-Fast Allergy Immunotherapy 1 Anergis Focus on Allergy Immunotherapy (AIT) High Medical Need and Patient Demand 500 M allergic patients - fastest growing chronic condition
genomics for systems biology / ISB2020 RNA sequencing (RNA-seq)
RNA sequencing (RNA-seq) Module Outline MO 13-Mar-2017 RNA sequencing: Introduction 1 WE 15-Mar-2017 RNA sequencing: Introduction 2 MO 20-Mar-2017 Paper: PMID 25954002: Human genomics. The human transcriptome
Biological Mass spectrometry in Protein Chemistry
Biological Mass spectrometry in Protein Chemistry Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi MASS SPECTROMETRY is an analytical technique that identifies the chemical composition of
A Method to Determine an E-score Threshold to Identify Potential Cross Reactive Allergens
A Method to Determine an E-score Threshold to Identify Potential Cross Reactive Allergens Andre Silvanovich Ph. D. Gary Bannon Ph. D. Scott McClain Ph. D. Monsanto Company Regulatory Product Characterization
2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry
Dr. Sanjeeva Srivastava 1. Fundamental of Mass Spectrometry Role of MS and basic concepts 2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry 2 1 MS basic concepts Mass spectrometry - technique
A computational framework for discovery of glycoproteomic biomarkers
A computational framework for discovery of glycoproteomic biomarkers Haixu Tang, Anoop Mayampurath, Chuan-Yih Yu Indiana University, Bloomington Yehia Mechref, Erwang Song Texas Tech University 1 Goal:
The Detection of Allergens in Food Products with LC-MS
The Detection of Allergens in Food Products with LC-MS Something for the future? Jacqueline van der Wielen Scope of Organisation Dutch Food and Consumer Product Safety Authority: Law enforcement Control
Drug Metabolism Disposition
Drug Metabolism Disposition The CYP2C19 intron 2 branch point SNP is the ancestral polymorphism contributing to the poor metabolizer phenotype in livers with CYP2C19*35 and CYP2C19*2 alleles Amarjit S.
Proteins: Proteomics & Protein-Protein Interactions Part I
Proteins: Proteomics & Protein-Protein Interactions Part I Jesse Rinehart, PhD Department of Cellular & Molecular Physiology Systems Biology Institute DNA RNA PROTEIN DNA RNA PROTEIN Proteins: Proteomics
The N-terminal loop of IRAK-4 death domain regulates ordered assembly of the Myddosome signalling scaffold
The N-terminal loop of IRAK-4 death domain regulates ordered assembly of the Myddosome signalling scaffold Anthony C.G. Dossang * 1, Precious G. Motshwene * 1, Yang Yang* 1, Martyn F. Symmons*, Clare E.
Supplementary Material
Supplementary Material 2 4 6 Single-locus gene screening methods We screened for single nucleotide polymorphisms (SNPs) at 16 candidate immune genes (Table S1) by initially sequencing three captive-bred
Discover the connection
Emma is worried about having a systemic reaction, so she avoids all nuts Walnuts FOOD ALLERGY Hazelnuts Peanuts Systemic reactions and underlying proteins Discover the connection ImmunoCAP Complete Allergens
Antibodies and T Cell Receptor Genetics Generation of Antigen Receptor Diversity
Antibodies and T Cell Receptor Genetics 2008 Peter Burrows 4-6529 peterb@uab.edu Generation of Antigen Receptor Diversity Survival requires B and T cell receptor diversity to respond to the diversity of
Hazelnut allergens by the numbers. a14
Hazelnut allergen component testing Hazelnut allergens by the numbers a1 a8 a9 a14 Testing for whole allergen proteins can help you better diagnose allergies and prepare personalized management plans.
Novel biomarkers of chemical-induced asthma: a murine model. Jeroen Vanoirbeek
Novel biomarkers of chemical-induced asthma: a murine model Jeroen Vanoirbeek Asthma 1. Chronic airway disease: prevalence: 5-10%, 300.000 people affected world-wide 2. Reversible airflow limitation, airway
The Human Major Histocompatibility Complex
The Human Major Histocompatibility Complex 1 Location and Organization of the HLA Complex on Chromosome 6 NEJM 343(10):702-9 2 Inheritance of the HLA Complex Haplotype Inheritance (Family Study) 3 Structure
Allergies & Hypersensitivies
Allergies & Hypersensitivies Type I Hypersensitivity: Immediate Hypersensitivity Mediated by IgE and mast cells Reactions: Allergic rhinitis (hay fever) Pollens (ragweed, trees, grasses), dust mite feces
THE SMART WAY TO EXPLORE ALLERGY
ALEX Allergy Explorer THE SMART WAY TO EXPLORE ALLERGY FRUITS ANIMAL DANDER LEGUMES MILK LATEX POLLEN HYMENOPTERA VENOMS CCDs SEA FOOD SPICES SEEDS EGG TREE NUTS CEREALS TOTAL IgE MEAT VEGETABLES SPORES
Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells.
SUPPLEMENTAL FIGURE AND TABLE LEGENDS Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. A) Cirbp mrna expression levels in various mouse tissues collected around the clock
Production of hypoallergenic plant foods by selection, breeding and genetic modification
11 Production of hypoallergenic plant foods by selection, breeding and genetic modification Luud J.W.J. Gilissen 1,2, Suzanne T.H.P. Bolhaar 3, André C. Knulst 3, Laurian Zuidmeer 3,4, Ronald van Ree 3,4,
TECHNICAL BULLETIN. R 2 GlcNAcβ1 4GlcNAcβ1 Asn
GlycoProfile II Enzymatic In-Solution N-Deglycosylation Kit Product Code PP0201 Storage Temperature 2 8 C TECHNICAL BULLETIN Product Description Glycosylation is one of the most common posttranslational
Molecular Allergy Diagnostics Recombinant or native Allergens in Type I Allergy Diagnostics
Molecular Allergy Diagnostics Recombinant or native Allergens in Type I Allergy Diagnostics Dr. Fooke Achterrath Laboratorien GmbH Habichtweg 16 41468 Neuss Germany Tel.: +49 2131 29840 Fax: +49 2131 2984184
Application Note # LCMS-89 High quantification efficiency in plasma targeted proteomics with a full-capability discovery Q-TOF platform
Application Note # LCMS-89 High quantification efficiency in plasma targeted proteomics with a full-capability discovery Q-TOF platform Abstract Targeted proteomics for biomarker verification/validation
Proteomic Biomarker Discovery in Breast Cancer
Proteomic Biomarker Discovery in Breast Cancer Rob Baxter Laboratory for Cellular and Diagnostic Proteomics Kolling Institute, University of Sydney, Royal North Shore Hospital robert.baxter@sydney.edu.au
Introduction. Methods RESEARCH FUND FOR THE CONTROL OF INFECTIOUS DISEASES. TCW Poon *, HLY Chan, HWC Leung, A Lo, RHY Lau, AY Hui, JJY Sung
RESEARCH FUND FOR THE CONTROL OF INFECTIOUS DISEASES Liver specific glycoforms of serum proteins in chronic hepatitis B infection: identification by lectin affinity chromatography and quantitative proteomic
5 Identification of Binding Partners of the Annexin A2 / P11 Complex by Chemical Cross-Linking
5 Identification of Binding Partners of the Annexin A2 / P11 Complex by Chemical Cross-Linking In the quest of the omics sciences for holistic schemes, the identification of binding partners of proteins
Breast cancer. Risk factors you cannot change include: Treatment Plan Selection. Inferring Transcriptional Module from Breast Cancer Profile Data
Breast cancer Inferring Transcriptional Module from Breast Cancer Profile Data Breast Cancer and Targeted Therapy Microarray Profile Data Inferring Transcriptional Module Methods CSC 177 Data Warehousing
SALSA MLPA probemix P169-C2 HIRSCHSPRUNG-1 Lot C As compared to version C1 (lot C1-0612), the length of one probe has been adjusted.
mix P169-C2 HIRSCHSPRUNG-1 Lot C2-0915. As compared to version C1 (lot C1-0612), the length of one has been adjusted. Hirschsprung disease (HSCR), or aganglionic megacolon, is a congenital disorder characterised
SALSA MLPA probemix P241-D2 MODY mix 1 Lot D As compared to version D1 (lot D1-0911), one reference probe has been replaced.
mix P241-D2 MODY mix 1 Lot D2-0413. As compared to version D1 (lot D1-0911), one reference has been replaced. Maturity-Onset Diabetes of the Young (MODY) is a distinct form of non insulin-dependent diabetes
PRADER WILLI/ANGELMAN
SALSA MS-MLPA probemix ME028-B2 PRADER WILLI/ANGELMAN Lot B2-0811: As compared to version B1 (lot B1-0609, B1-1108), the 88 and 96 nt control fragments have been replaced (QDX2). PRADER-WILLI SYNDROME
Quantitative chromatin proteomics reveals a dynamic histone. post-translational modification landscape that defines asexual
Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites Nanika Coetzee 1, Simone Sidoli 2,
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers Gordon Blackshields Senior Bioinformatician Source BioScience 1 To Cancer Genetics Studies
SALSA MLPA KIT P050-B2 CAH
SALSA MLPA KIT P050-B2 CAH Lot 0510, 0909, 0408: Compared to lot 0107, extra control fragments have been added at 88, 96, 100 and 105 nt. The 274 nt probe gives a higher signal in lot 0510 compared to
N α -Acetylation of yeast ribosomal proteins and its effect on protein synthesis
JOURNAL OF PROTEOMICS 74 (2011) 431 441 available at www.sciencedirect.com www.elsevier.com/locate/jprot N α -Acetylation of yeast ribosomal proteins and its effect on protein synthesis Masahiro Kamita
Reduced in vivo allergenicity of Bet v 1d isoform, a natural component of birch pollen
Reduced in vivo allergenicity of Bet v 1d isoform, a natural component of birch pollen Oliver Arquint, MD, a Arthur Helbling, MD, a Reto Crameri, PhD, b Fátima Ferreira, PhD, c Michael Breitenbach, PhD,
Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein
Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein content relative to GAPDH in two independent experiments.
Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev
Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev Institute for Biochemical Physics, Rus. Acad. Sci., Moscow, Russia. Institute for Energy Problems
Genomic structural variation
Genomic structural variation Mario Cáceres The new genomic variation DNA sequence differs across individuals much more than researchers had suspected through structural changes A huge amount of structural
Proteomics to identify novel biomarkers and therapeutic targets in cardiovascular disease
Proteomics to identify novel biomarkers and therapeutic targets in cardiovascular disease Markus Kubicek Laboratorios de Biologia Vascular y Proteínómica Estructural, Instituto de Biomedicina de Valencia
Nature Methods: doi: /nmeth Supplementary Figure 1
Supplementary Figure 1 Subtiligase-catalyzed ligations with ubiquitin thioesters and 10-mer biotinylated peptides. (a) General scheme for ligations between ubiquitin thioesters and 10-mer, biotinylated
Nature Methods: doi: /nmeth.3177
Supplementary Figure 1 Characterization of LysargiNase, trypsin and LysN missed cleavages. (a) Proportion of peptides identified in LysargiNase and trypsin digests of MDA-MB-231 cell lysates carrying 0,
Ambient temperature regulated flowering time
Ambient temperature regulated flowering time Applications of RNAseq RNA- seq course: The power of RNA-seq June 7 th, 2013; Richard Immink Overview Introduction: Biological research question/hypothesis
Network-assisted data analysis
Network-assisted data analysis Bing Zhang Department of Biomedical Informatics Vanderbilt University bing.zhang@vanderbilt.edu Protein identification in shotgun proteomics Protein digestion LC-MS/MS Protein
Lecture 3. Tandem MS & Protein Sequencing
Lecture 3 Tandem MS & Protein Sequencing Nancy Allbritton, M.D., Ph.D. Department of Physiology & Biophysics 824-9137 (office) nlallbri@uci.edu Office- Rm D349 Medical Science D Bldg. Tandem MS Steps:
ALLERGIES ARE A LOW PROFILE HIGH IMPACT DISEASE. MASOOD AHMAD,M.D.
ALLERGIES ARE A LOW PROFILE HIGH IMPACT DISEASE. MASOOD AHMAD,M.D. What Is a Food Allergy? A food allergy is a medical condition in which exposure to a food triggers an IgE mediated immune response. The
Application of an immunoproteomic approach to detect anti-profilin antibodies in sera of
Application of an immunoproteomic approach to detect anti-profilin antibodies in sera of Parietaria judaica allergic patients Marilisa Barranca, Simona Fontana, Simona Taverna, Giacomo De Leo and Riccardo
Biological Mass Spectrometry. April 30, 2014
Biological Mass Spectrometry April 30, 2014 Mass Spectrometry Has become the method of choice for precise protein and nucleic acid mass determination in a very wide mass range peptide and nucleotide sequencing
Practical Course Allergen Immunotherapy (AIT) How to be effective. Michel Dracoulakis HSPE- FMO São Paulo-SP Brazil
Practical Course Allergen Immunotherapy (AIT) How to be effective Michel Dracoulakis HSPE- FMO São Paulo-SP Brazil Allergen immunotherapy - beginning Dunbar almost died with first inoculation 1911 Noon
Studying Alternative Splicing
Studying Alternative Splicing Meelis Kull PhD student in the University of Tartu supervisor: Jaak Vilo CS Theory Days Rõuge 27 Overview Alternative splicing Its biological function Studying splicing Technology
Taxus cuspidata (Japanese yew) pollen nasal allergy
Taxus cuspidata (Japanese yew) pollen nasal allergy Shiroh Maguchi a *, Satoshi Fukuda b a Department of Otolaryngology, Teine Keijinkai Hospital, 1-12 Maeda, Teine-ku, Sapporo 060-8638, Japan b Department
Generating Spontaneous Copy Number Variants (CNVs) Jennifer Freeman Assistant Professor of Toxicology School of Health Sciences Purdue University
Role of Chemical lexposure in Generating Spontaneous Copy Number Variants (CNVs) Jennifer Freeman Assistant Professor of Toxicology School of Health Sciences Purdue University CNV Discovery Reference Genetic
SALSA MS-MLPA KIT ME011-A1 Mismatch Repair genes (MMR) Lot 0609, 0408, 0807, 0407
SALSA MS-MLPA KIT ME011-A1 Mismatch Repair genes (MMR) Lot 0609, 0408, 0807, 0407 The Mismatch Repair (MMR) system is critical for the maintenance of genomic stability. MMR increases the fidelity of DNA
your triggers? Information about a simple lab test that lets you Know Your IgE.
What your are CAT DANDER DUST MITE triggers? Knowing if you have allergic triggers can help you manage your symptoms. Know yours and take control. OAK Information about a simple lab test that lets you
(A) PCR primers (arrows) designed to distinguish wild type (P1+P2), targeted (P1+P2) and excised (P1+P3)14-
1 Supplemental Figure Legends Figure S1. Mammary tumors of ErbB2 KI mice with 14-3-3σ ablation have elevated ErbB2 transcript levels and cell proliferation (A) PCR primers (arrows) designed to distinguish
Supporting Information. Lysine Propionylation to Boost Proteome Sequence. Coverage and Enable a Silent SILAC Strategy for
Supporting Information Lysine Propionylation to Boost Proteome Sequence Coverage and Enable a Silent SILAC Strategy for Relative Protein Quantification Christoph U. Schräder 1, Shaun Moore 1,2, Aaron A.
MODULE NO.14: Y-Chromosome Testing
SUBJECT Paper No. and Title Module No. and Title Module Tag FORENSIC SIENCE PAPER No.13: DNA Forensics MODULE No.21: Y-Chromosome Testing FSC_P13_M21 TABLE OF CONTENTS 1. Learning Outcome 2. Introduction:
One Gene, Many Proteins. Applications of Mass Spectrometry to Proteomics. Why Proteomics? Raghothama Chaerkady, Ph.D.
Applications of Mass Spectrometry to Proteomics Raghothama Chaerkady, Ph.D. McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry Why Proteomics? One Gene, Many Proteins
MRC-Holland MLPA. Related SALSA MLPA probemixes P190 CHEK2: Breast cancer susceptibility, genes included: CHEK2, ATM, PTEN, TP53.
SALSA MLPA probemix P056-C1 TP53 Lot C1-0215 & lot C1-0214. As compared to version B1 (lot B1-1011) most of the reference and flanking probes have been replaced and several have been added. Furthermore,
Food Allergens. Food Allergy. A Patient s Guide
Food Allergens Food Allergy A Patient s Guide Food allergy is an abnormal response to a food triggered by your body s immune system. About 3 percent of children and 1 percent of adults have food allergy.
Allergènes «outdoor» Pollen, spores et changements climatiques
Département fédéral de l intérieur DFI Office fédéral de météorologie et de climatologie MétéoSuisse Allergènes «outdoor» Pollen, spores et changements climatiques Bernard Clot Aérobiologie et allergies
T Cell Receptor & T Cell Development
T Cell Receptor & T Cell Development Questions for the next 2 lectures: How do you generate a diverse T cell population with functional TCR rearrangements? How do you generate a T cell population that
The Future of Allergy Treatment Ultra-Fast Allergy Immunotherapy
The Future of Allergy Treatment Ultra-Fast Allergy Immunotherapy 1 Anergis Focus on Allergy Immunotherapy (AIT) High Medical Need and Patient Demand 500 M allergic patients - fastest growing chronic condition
Mass Spectrometry at the Laboratory of Food Chemistry. Edwin Bakx Laboratory of Food Chemistry Wageningen University
Mass Spectrometry at the Wageningen University Mass Spectrometry at the 3 UPLC/CE - ESI - Ion trap MS systems UPLC Thermo Acella with a Velos or VelosPro CE Beckman PA800 with a Thermo VelosPro 1 UPLC-
Automating Mass Spectrometry-Based Quantitative Glycomics using Tandem Mass Tag (TMT) Reagents with SimGlycan
PREMIER Biosoft Automating Mass Spectrometry-Based Quantitative Glycomics using Tandem Mass Tag (TMT) Reagents with SimGlycan Ne uaca2-3galb1-4glc NAcb1 6 Gal NAca -Thr 3 Ne uaca2-3galb1 Ningombam Sanjib
Quantification by Mass Spectrometry
Quantification by Mass Spectrometry PC219 Lecture 5 30 April, 2010 sguan@cgl.ucsf.edu 1 Applications of Quantitative Proteomics Qualitative protein identification is NOT sufficient to describe a biological