University dissertation from pia berntsson department of cell and organism biology lund university zoofysiologiska huset helgonavšgen 3 b se 223 62 abstract. The polyamines putrescine, spermidine and spermine are polycations found within cells. They have been shown to be essential for optimal cell proliferation and cell survival. Cells maintain their polyamine levels in a well regulated system involving biosynthesis, catabolism and uptake/excretion. Read more university dissertation from chalmers university of technology abstract. Well known as genetic information carrier, dna however, in the past three decade experienced a revolution to become a fashionable fabrication material in nanotechnology as a consequence of the high predictability and accuracy of base paring recognition. Although dna can be constructed in many fancy 2d and 3d structures, this thesis work focused on constructing one dimension linear dna concatemers in order to study sequence specific dna ligand binding at the single molecule level.

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by li, dan. 2008, 90 pages 36290

the objective of differential expression analysis of proteomics data generated by 2d gel electrophoresis is to identify the differentially expressed proteins over various experimental conditions. In this dissertation, we present the procedures of differential expression analysis and propose solutions of the missing data problem in the 2d gel electrophoresis experiment. Our differential expression analysis consists of data normalization, variance stabilization, analysis of variance anova , estimation of protein specific variance, adjustment for multiple comparison and chi square tests. A case study of the impact of low dose arsenic and low dose ionizing radiation on human cells is presented.

It shows that anova ajusted with the empirical bayes estimate of protein specific variance combined with pfdr adjustment gives the highest yield of differential protein expression while minimizing the false discovery rate. The proteomics data generated by 2d gel electrophoresis has proven difficult to analyze due to its large proportion of missing data. The missing values can be either generated by random experimental variations or as a result of being below the limit of detection.

We develop a novel statistical technique that uses the customized expectation maximization em algorithm and the adjusted f test to identify the differential expression in the presence of missing data. Simulation studies reveal that our em based approach has better performance in handling missing data compared with the other two traditional methods, discarding missing data and filling with the detection limit. Furthermore, the empirical bayes correction to the variance estimate in the em algorithm is proposed to lessen the variance heterogeneity problem and increase the power of the f test. Simulation studies show that the empirical bayes correction improves the performance of our em based approach and provides less biased parameter estimates. Two dimensional gel electrophoresis3 two dimensional gel electrophoresis in 2d ge the first separation includes ief, allowing separation of intact proteins.

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