Go to contents (site navigation)

 


Realised by ALMS™
developer of the AIDS-HIV Reference project
Abstract No.: ThP-LB2
Session: LATE-BREAKING/Bioinformatics
Presentation date: Thu, Aug 31, 2006
Presentation time: 14:30 – 16:00

Variation in allergen amount was assessed within and between strawberry varieties with 2D-gel DIGE, and 5 phenotypic traits were coupled to protein profiles with following identification of proteins and biological pathways.

Rikard Alm1, Andreas Ekefjard2, Jari Hakkinen3, Cecilia Emanuelsson1

1 Dep. of Biochemistry, Lund, Sweden
2 Ludesi, Lund, Sweden
3 Dep. of theoretical physics, Lund, Sweden

Correspondence address: Rikard Alm, Department of Biochemistry, Getingevagen 60, Lund, SE-22100 Sweden.

Web site: http://www.biokem.lu.se/peoplePhD/almrikard.htm

Keywords: Computer Program; MALDI; MS/MS; Protein Identification.

Novel aspect: Assesment of variation between strawberry varieties and improving protein identification rate with clustering

 

Allergy to food is a growing problem. Food allergy is mostly depending on cross reaction against pollen. One such cross reaction is strawberry against birch (ref). Strawberry is used in the food industries as an additive in many products. Since the allergy reaction is dose-dependent, a strawberry variety with low contents of allergen is desirable. To successfully grow a low allergenic strawberry variety, the variation within varieties must be much lower that the variation between varieties. Otherwise it will cause problems for the consumer if he/she will need to ask about the growing conditions in order to buy a low allergenic strawberry.
Ten varieties from one location and one growing condition were screened with 2D-gel technique (DIGE) to assess the variation between varieties. Another variety, that were grown under different conditions and collected from different places were also screened in order to assess the variation within a variety. Spot detection, matching and statistical analysis was performed using the service “2D analysis center” from the company LUDESI. Statistical tests ANOVA and MannWhitney were used to assess differential expression of protein abundance between the different groups. Normalizations and missing values were treated according to LUDESI:s normal high standard. MALDI-MS and MSMS mass spectra were acquired on a Applied Biosystems 4700. In order to improve the protein identifications the MS spectra were clustered with the in house developed software SPECLUST (http://bioinfo.thep.lu.se/speclust.html (ref)). Filtered and calibrated peaklists from MS spectra were clustered and spectra containing the same set of peptides (protein isoforms) was clustered together.

This report also investigates the possibility of finding biochemical pathways that correlate with strawberry phenotypes like flavor, early ripening, mould sensitivity and fruit firmness. Jonckheere-Terpstra:s test was used to find proteins with expression profiles correlating with different strawberry properties.

Another question addressed is the function of the allergen. In our previous article where we compared a red and a white strawberry, we found that the allergen was down regulated together with enzymes from the flavonoid pathway. To se if the allergen were somehow connected to the color, the ten varieties were chosen to represent different shades of red, from pure white to pure red. By applying Jonckheere-Terpstra:s test it was possible to check which proteins correlated with redness. The number of proteins significantly correlated with color was approximately ten times higher than expected by chance.