Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis： A Review

Various methods and specialized software programs are available for processing two- dimensional gel electrophoresis （2-DGE） images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and hor- izontal streaking, fuzzy spots, and background noise, which greatly complicate computational anal- ysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images： Gaussian, Rayleigh, and exponen- tial, with signal-to-noise ratios （SNRs） ranging 8-20 decibels （dB）. We compared the performanceof wavelet, contourlet, total variation （TV）, and wavelet-total variation （WTTV） techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sen- sitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10- 20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best per- formance with any level of Gaussian noise and low levels （20-14 dB） of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.

Differential protein expression in low-grade astrocytomas and peritumoral human brain tissues

Differential protein expression between various pathological grades of glioma has been shown in studies of glioma proteomics. However, very little data is available regarding normal brain tissues and glioma differential protein expression, because normal human brain tissues are difficult to harvest. The present study selected samples from low-grade astrocytomas and peritumoral brain tissues to analyze differential protein expression by two-dimensional （2D） electrophoresis and mass spectrometry techniques. Results revealing 36 protein spots by 2D electrophoresis, including 23 spots revealing increased expression and 13 spots revealing decreased expression. However, 25 differential proteins were identified by mass spectrometry, including 16 proteins with increased expression and 9 with decreased expression. Western blot analysis confirmed the mass spectrometry results, i.e., heat shock protein 70 （HSP70） and human transthyretin （TTR） expressions were increased, but glial fibrillary acidic protein （GFAP） was decreased, in astrocytomas. The present study constructed a 2D electrophoresis pattern between low-grade astrocytomas in the human brain and peritumoral tissues. Results demonstrated that a majority of differential proteins, such as HSP70, TTR, and GFAP, participate in malignant progression of gliomas.

Application of proteomics in environmental science

Proteomics involves the separation of proteins,identification of the amino acid sequence of the interested or target proteins,study of the function of the proteins,modification,structure and ultimate assignments to functional pathways in the cell.The proteomic investigations have contributed greatly to human diseases studies,new drugs discovery researches,and environmental science in recent years.This article provides a review on the development of the main proteomic technologies,including both the gel based and non-gel based technologies,and their applications in environmental science.Proteomic technologies have been utilized in the environmental stresses studies to analyze the induction or reduction of proteins at expression level and identify the target proteins to investigate their function in response to environmental stresses,such as high or low pH,oxidation stress,and toxic chemicals.Such protein responses are also helpful to understand the mechanisms of some cellular activities and the functions of some proteins.