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 horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. 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 exponential, with signal-to-noise ratios (SNRs) ranging 8–20 decibels (dB). We compared the performance of 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 sensitive 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 performance 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.

Cancer is a complex and evolving disease that is the leading cause of death in the twenty-first century, and colorectal and liver cancers specifically are in the top 10 cancer types in terms of incidence and mortality; therefore, there has been a shift towards researching prevention strategies, amongst which chemoprevention is key. Coffee is a natural product that has recently gained importance in this area due to its chemopreventive potential and its high level of consumption worldwide. In this review, recent epidemiological and experimental evidence of the chemopreventive effect of coffee against these two types of cancer are presented, and the role of the different compounds present in coffee in cell proliferation, apoptosis and response to oxidative stress are discussed.

The discovery of protein biomarkers that reflect the biological state of the body is of vital importance to disease management. Urine is an ideal source of biomarkers that provides a non-invasive approach to diagnosis, prognosis and prediction of diseases. Consequently, the study of the human urinary proteome has increased dramatically over the last 10 years, with many studies being published. This review focuses on urinary protein biomarkers that have shown potential, in initial studies, for diseases affecting the urogenital tract, specifically chronic kidney disease and prostate cancer, as well as other non-urogenital pathologies such as breast cancer, diabetes, atherosclerosis and osteoarthritis. PubMed was searched for peer-reviewed literature on the subject, published in the last 10 years. The keywords used were "urine, biomarker, protein, and/or prostate cancer/breast cancer/chronic kidney disease/diabetes/atherosclerosis/osteoarthritis". Original studies on the subject, as well as a small number of reviews, were analysed including the strengths and weaknesses, and we summarized the performance of biomarkers that demonstrated potential. One of the biggest challenges found is that biomarkers are often shared by several pathologies so are not specific to one disease. Therefore, the trend is shifting towards implementing a panel of biomarkers, which may increase specificity. Although there have been many advances in urinary proteomics, these have not resulted in similar advancements in clinical practice due to high costs and the lack of large data sets. In order to translate these potential biomarkers to clinical practice, vigorous validation is needed, with input from industry or large collaborative studies.

Introduction: Cardiovascular disease (CVD) is the leading noncommunicable disease and main cause of death worldwide. Traditionally, blood has been the sample of choice for biomarker discovery, however, urine has roused great interest in recent years as a source of biomarkers. Sample collection is simple, non-invasive, and there is the possibility of implementing minimal cost tests in primary care settings. Areas covered: In this review, we systematically searched PubMed for proteomic studies of CVD, with the criteria that urine was included as a biological sample. Based on these criteria, and after manual curation, 47 research papers were included: 8 for coronary artery disease, 5 for angina, 15 for myocardial infarction, 23 for heart failure, and 4 for cerebrovascular disease. Expert commentary: Urinary biomarkers of early, asymptomatic stages of the disease would have a great impact on CVD morbidity and mortality, as widespread screening could be implemented at a reduced cost, allowing high-risk individuals to be identified and treated in a timely manner. An approach involving multiple biomarkers is necessary, as a single biomarker is unlikely to be sensitive/specific enough. By assessing a range of peptides there is the potential to detect changes in many pathways involved in the pathogenesis of CVDs.

Background: Two-dimensional gel electrophoresis (2-DGE) is a commonly used tool for proteomic analysis. This gel-based technique separates proteins in a sample according to their isoelectric point and molecular weight. 2-DGE images often present anomalies due to the acquisition process, such as: diffuse and overlapping spots, and background noise. This study proposes a joint pre-processing framework that combines the capabilities of nonlinear filtering, background correction and image normalization techniques for pre-processing 2-DGE images. Among the most important, joint nonlinear diffusion filtering, adaptive piecewise histogram equalization and multilevel thresholding were evaluated using both synthetic data and real 2-DGE images. Results: An improvement of up to 46% in spot detection efficiency was achieved for synthetic data using the proposed framework compared to implementing a single technique of either normalization, background correction or filtering. Additionally, the proposed framework increased the detection of low abundance spots by 20% for synthetic data compared to a normalization technique, and increased the background estimation by 67% compared to a background correction technique. In terms of real data, the joint pre-processing framework reduced the false positives up to 93%. Conclusions: The proposed joint pre-processing framework outperforms results achieved with a single approach. The best structure was obtained with the ordered combination of adaptive piecewise histogram equalization for image normalization, geometric nonlinear diffusion (GNDF) for filtering, and multilevel thresholding for background correction.

La abeja africanizada es la más común en la apicultura colombiana y a su veneno (apitoxina) se le han atribuido propiedades terapéuticas para diferentes enfermedades, sin mayor soporte científico. Al revisar en la literatura los reportes publicados sobre el análisis proteómico de la apitoxina, se encontraron cuatro métodos distintos para la extracción de proteínas de la apitoxina. El primer método consiste en resuspender la apitoxina en Urea 7 M, precipitar con acetona y finalmente resuspender en Urea 7 M y CHAPS 4 %. Para el segundo método se resuspende la apitoxina en buffer de lisis, se precipita con ácido tricloroacético, y luego se resuspende en Urea 7 M y CHAPS 4 %. El tercer método es igual al anterior, excepto que la precipitación se realiza con acetona en vez de ácido tricloroacético. Finalmente, el cuarto método consiste en resuspender la apitoxina en agua destilada, precipitar con acetona y resuspender en Urea 7 M y CHAPS 4 %. Este trabajo se enfocó en comparar el desempeño de estos cuatro métodos de extracción y determinar el método con el mejor resultado en cuanto a la concentración e integridad obtenida de las proteínas. De los distintos métodos evaluados, se encontró que los mejores resultados en cuanto a concentración de proteínas se obtuvieron con la resuspensión de apitoxina en buffer de lisis y precipitación con acetona (método 3) y con el método de resuspensión de apitoxina en agua destilada y precipitación con acetona (método 4). De estos, el mejor método de extracción en cuanto a integridad de las proteínas y perfil proteómico fue el de resuspensión de apitoxina en buffer de lisis seguido de precipitación con acetona (método 3).