Proteomic analysis of pericardial effusion: Characteristics of tuberculosis-related proteins

The aim of this study has been designed to identify the tuberculosis (TB)-related proteins in pericardial effusion by proteomic approaches. TB is one of the major infectious diseases causing pericardial effusion. This study details protein profiles in pericardial effusion from three TB patients and three heart failure patients. Pericardial effusions were analyzed using 2-DE combined with the nano-HPLC-ESI-MS/MS. Eleven protein spots with differential expression in pericardial effusion were identified between the two groups of TB and heart failure patients (the control group). Seven protein spots were upregulated and four were downregulated. The composition of the pericardial effusion proteome may reflect the pathophysiological conditions affecting the progression of tuberculous pericarditis. The proteins in the tuberculous pericardial effusion with differential expression may serve as new and direct indicators of drug treatment. A possible conclusion is indicated that fibrinogen may play an important role for fibrin assembly in tuberculous pericardial effusion.     

Quantitative proteomics for identification of cancer biomarkers

Quantitative proteomics can be used for the identification of cancer biomarkers that could be used for early detection, serve as therapeutic targets, or monitor response to treatment. Several quantitative proteomics tools are currently available to study differential expression of proteins in samples ranging from cancer cell lines to tissues to body fluids. 2-DE, which was classically used for proteomic profiling, has been coupled to fluorescence labeling for differential proteomics. Isotope labeling methods such as stable isotope labeling with amino acids in cell culture (SILAC), isotope-coded affinity tagging (ICAT), isobaric tags for relative and absolute quantitation (iTRAQ), and (18) O labeling have all been used in quantitative approaches for identification of cancer biomarkers. In addition, heavy isotope labeled peptides can be used to obtain absolute quantitative data. Most recently, label-free methods for quantitative proteomics, which have the potential of replacing isotope-labeling strategies, are becoming popular. Other emerging technologies such as protein microarrays have the potential for providing additional opportunities for biomarker identification. This review highlights commonly used methods for quantitative proteomic analysis and their advantages and limitations for cancer biomarker analysis.     

Challenges and opportunities for cell line secretomes in cancer proteomics

Cancer cell lines are the most widely used experimental models in cancer research. Their advantages of easy growth and manipulation are unfortunately paralleled by their limitations derived from long-term growth in isolation from the rest of the tumor, and hence, lack of tumor microenvironment. We are however currently witnessing novel and transformative advances that are making cell lines more reflective of the human biology and therefore, better experimental models for cancer research. Beyond the experimental model used, the choice of cellular proteome is key in proteomics-based biomarker discovery. Over the last decade, cell line secretomes have been proposed as an alternative for tumor biomarker discovery due to the difficulties posed by plasma in terms of complexity and low abundance of tumor-specific biomarkers. Cell line secretomes are enriched with proteins already linked to tumorigenesis, which also have a good chance of being present in biological fluids. In this review, we will provide an overview of the main technical and biological issues related to cell line secretome analysis, and briefly discuss both the challenges and opportunities in its use for tumor biomarker discovery.     

Gastrointestinal fluids proteomics

Seventy million people suffer from diseases of the gastrointestinal tract annually in US, translating to US$85.5 billion in direct healthcare costs. The debilitating effects of these gastrointestinal (GI) diseases can be circumvented with good biomarkers for early detection of these disorders, which will greatly increase the success of curative treatments. GI fluids represent a potential reservoir of biomarkers for early diagnosis of various GI and systemic diseases since these fluids are the most proximal fluid bathing diseased cells. They are anticipated to have proteomes that closely reflect the ensemble of proteins secreted from the respective GI tissues. Most importantly, the disease markers present in GI fluids should be present in higher concentrations than in sera, thus offering greater sensitivity in their detection. However, proteome analysis of GI fluids can be complex mainly due to the dynamic range of protein content and the numerous PTMs of proteins in each specialized GI compartment. This review attempts to discuss the physiology of the various GI fluids, the special technical considerations required for proteome analysis of each fluid, as well as to summarize the current state of knowledge of biomarker discoveries and clinical utility of GI fluids such as salivary, gastric, pancreatic, and biliary secretions.     

Proteome analysis of human foetal, aged and advanced nuclear cataract lenses

The most complete proteome of human lenses has been compiled using 2-D LC-MS/MS analysis of foetal, aged normal and advanced nuclear cataract lenses. A total of 231 proteins were identified across all lens groups, including 112 proteins that have not been reported previously. Proteins were grouped according to their PANTHER molecular function classification in order to facilitate comparisons. Previously unreported N-terminal acetylation was detected in a number of proteins, with the majority being associated with the prior removal of a methionine residue. This pattern of proteolysis may indicate that methionine aminopeptidase activity is present in human lenses. Acetylation is likely to aid in the stability of proteins that are present in the lens for many decades. Protein sequences were also used to interrogate the three human lens cDNA libraries publicly available. Surprisingly, 84 proteins we identified were not present in the cDNA libraries.     

NanoArrays, The Next Generation Molecular Array Format for High Throughput Proteomics, Diagnostics and Drug Discover.

Biomolecular array technology is an invaluable tool for rapid screening of nucleic acid mixtures. This approach has been tremendously successful both in its breadth of application and its commercial value. Entire genomes, including the human genome, have been screened by molecular array techniques. Arrays are a rapid and now routine method for analysis of expression patterns and their association with physiological states. Such a rapid, high throughput analysis of cellular expression is key to the expansion of our basic knowledge of the relationship between gene expression and organismal function, as well as to the understanding of the genetic component of disease states and the predisposition to disease.Despite the success of array technology for nucleic acid applications, a similar trend for proteins has not occurred. Due, in part, to the difficulties involved in production and labeling of proteins for solid state analysis, solid state arrays of proteins are not widely utilized. Protein function and interaction have been traditionally addressed by the combination of 2D gel electrophoretic separation and mass spectrometry to examine individual protein spots, a slow, tedious and expensive process. Another approach uses in vivo methods for examining protein-protein interactions by the two-hybrid system in yeast and mammalian cells [1]. Although the two-hybrid system has shown some success in finding new interaction between proteins in important cellular pathways, it is far more difficult, costly and time consuming than the solid state methods used for nucleic acids.BioForce Laboratory, Inc., has developed a solid state method for examining the interaction between a wide range of molecules in an array format. This technology involves several key technological innovations.     

Proteomics of nipple aspirate fluid, breast cyst fluid, milk, and colostrum

Proteomic analysis of breast fluids has wide-ranging clinical applications. Protein expression in nipple aspirate fluid and breast cyst fluid may prove valuable for the detection and monitoring of breast cancer, but has been hampered by the lack of a single marker with sufficient breast cancer sensitivity and specificity to be clinically useful. The assessment of multiple proteins may offer a more powerful cancer detection tool. Breast cancer is particularly difficult to detect in women who are lactating. The identification of cancer predicting proteins in milk may prove very helpful in an early cancer detection in this group of women. A better understanding of the protein composition of milk and colostrum should improve infant care and nutrition, and lead to alternatives for individuals with milk allergies.     

Protein content in aqueous humor from patients with pseudoexfoliation (PEX) investigated by capillary LC MALDI‐TOF/TOF MS

Analysis of proteins in human body fluids is challenging since the composition of the sample often is rather complex. Here we present a method for analysis of proteins in aqueous humor from two groups of cataract patients, with and without pseudoexfoliation (PEX). Aqueous humor is an extracellular fluid contained in the anterior chamber of the eye between the cornea and iris. The limited volume of sample requires sophisticated analysis techniques. Our method is based on a total tryptic digestion of the sample followed by capillary LC‐MALDI MS and MS/MS analysis of the peptides. The method is rapid, efficient and suitable as a complement or alternative to more commonly used methods based on gel electrophoretic experiments. With this method we found and unambiguously identified 30 nonredundant proteins. Proteins found include general transport proteins such as albumin and apolipoprotein A1 but also specific proteins involved in immune response, such as complement factors. Cystatin C, clusterin, and crystallins were also found. Although the number of proteins was roughly the same in both groups there was a significant difference in their identities. These findings may give some new insights into the pathophysiology of the PEX syndrome.     

Interfacial configurations and mixing performances of fluids in staggered curved-channel micromixers

We present a parallel laminar micromixer with staggered curved channels for homogeneously mixing two fluids by Dean vortex. The secondary flows are produced in curved rectangular channels by the centrifugal forces; the diffusion distance of two fluids is reduced due to the staggered structures of the flow channels. The mixing strength is increased when one stream is injected into the other. Confocal microscopy and pH indicator have been used to study the mixing. Computational fluid dynamics simulations are utilized to examine the interfacial configurations and the mixing behaviors inside the channels. The interface of the two fluids is heavily distorted and increases the interfacial area because of the unique structures. The mixing index of the staggered curved-channel mixer with tapered channels is higher than those of the other curved-channel mixers. The effects of various Reynolds numbers and channel configurations on mixing performances are investigated in terms of the experimental mixing indices and the computational interfacial patterns. The comparison between the experimental data and numerical results shows a very similar trend.     

Proteomic analysis to improve adequacy of hemo- and peritoneal dialysis: Removal of small and high molecular weight proteins with high- and low-flux filters or a peritoneal membrane

The reduction of morbidity and mortality in patients undergoing hemo- or peritoneal dialysis is strongly related to an efficient and selective clearance of uremic toxins. We used proteomics methods to analyze and further characterize the dialytic removal of still undefined middle and high molecular weigh proteins as a basis for further improvement of dialysis assessment. Dialysates from 26 hemodialysis patients treated with different types of low- (F6HPS?) and high-flux (FX80?, APS650?, FX60?) filters as well as peritoneal fluids from 10 continuous ambulatory peritoneal dialysis (CAPD) patients were analyzed by SELDI-TOF and 2-DE. The protein patterns showed selective differences in the proteins cleared depending on the dialysis method used and the filter membrane. While SELDI analyses of dialysates from the F6HPS revealed almost no protein clearance, high-flux filters and CAPD dialysates showed protein release of different molecular weight ranges. Furthermore, 2-DE and MS analysis identified 48 different proteins from the dialysate of high-flux filters and 21 from peritoneal dialysis fluids. In F6HPS dialysates, however, only few proteins could be identified.     

Proteomic analysis of serum, plasma, and lymph for the identification of biomarkers

Probably no topic has generated more excitement in the world of proteomics than the search for biomarkers. This excitement has been generated by two realities: the constant need for better biomarkers that can be used for disease diagnosis and prognosis, and the recent developments in proteomic technologies that are capable of scanning the individual proteins within varying complex clinical samples. Ideally a biomarker would be assayable from a noninvasively collected sample, therefore, much of the focus in proteomics has been on the analysis of biofluids such as serum, plasma, urine, cerebrospinal fluid, lymph, etc. While the discovery of biomarkers has been elusive, there have been many advances made in the understanding of the proteome content of various biofluids, and in the technologies used for their analysis, that continues to point the research community toward new methods for achieving the ultimate goal of identifying novel disease-specific biomarkers. In this review, we will describe and discuss many of the proteomic approaches taken in an attempt to find novel biomarkers in serum, plasma, and lymph.     

Review of methods for determination of total protein and peptide concentration in biological samples

Clinical proteomics can be defined as the use of proteomic technologies to identify and measure biomarkers in fluids and tissues. The current work is intended to review various methods used for the determination of the total concentration of protein or peptide in fluids and tissues and the application of such methods to clinical proteomics. Specifically, this article considers the approaches to the measurement of total protein concentration, not the measurement of the concentration of a specific protein or group of proteins in a larger mixture of proteins. The necessity of understanding various concepts such as fit-for-use, quality-by-design, and other regulatory elements is discussed, as is the significance of using suitable standards for the protein quality of various samples.     

Clinical application of tear proteomics: Present and future prospects

Human tear fluid is charactered with very small volume and complex protein constitutes with a very large orders of magnitude. The tear proteome analysis provides a unique dataset (i.e., specific protein markers or protein patterns) that may be correlated to more effective diagnosis, prognosis, and response to therapy. Compared to less than 100 tear proteins obtained by the traditional methods, more than 400 proteins have been found in human tear fluid by current proteomic technologies. Many proteomics techniques, such as 2-DE, MALDI-TOF-MS, LC-MS, SELDI-TOF-MS, protein arrays, have been used to perform tear proteome analysis in healthy and/or disease subjects. The clinical application of tear proteomics needs suitable tear collection methods, standard tear handling procedures, and more sensitive and reliable proteomic technologies.     

A straightforward determination of fluid viscosity and density using microcantilevers: From experimental data to analytical expressions

Vibrating microcantilevers are used to measure the density and the viscosity of surrounding fluids. The classical procedure involves experimental acquisition of the deflection spectrum of the beam, but a systematic calibration step is mandatory for obtaining viscosity and density. In the present study, a method is proposed to facilitate these measurements for Newtonian fluids with only one calibration step in air during the cantilever lifetime. Our approach relies on a complete theoretical analysis allowing to approximate semi-analytically the deflection spectrum with a second-order transfer function and to determine an analytical relationship between viscosity, density and the parameters of the transfer function. Fluid parameter determination results are shown for validation and discussed.     

Survival model in oral squamous cell carcinoma based on clinicopathological parameters,molecular markers and support vector machines

The aim of the present study is to find an intelligent and efficient model, based on Support Vector Machines (SVM), able to predict prognosis in patients with oral squamous cell carcinoma (OSCC). A total of 34 clinical and molecular variables were studied in 69 patients suffering from an OSCC. Variables were selected by means of two methods applied in parallel (Non-concave penalty and Newton’s methods). The implementation of a predictive model was performed using the SVM as a classifier algorithm. Finally, its classification ability was evaluated by discriminant analysis. Recurrence, number of recurrences, and TNM stage have been identified as the most relevant prognosis factors with both used methods. Classification rates reached 97.56% and 100% for alive and dead patients, respectively (overall classification rate of 98.55%). SVM techniques build tools able to predict with high accuracy the survival of a patient with OSCC.     

A novel passive micromixer: lamination in a planar channel system

A novel passive micromixer concept is presented. The working principle is to make a controlled 90° rotation of a flow cross-section followed by a split into several channels; the flow in each of these channels is rotated a further 90° before a recombination doubles the interfacial area between the two fluids. This process is repeated until achieving the desired degree of mixing. The rotation of the flow field is obtained by patterning the channel bed with grooves. The effect of the mixers has been studied using computational fluid mechanics and prototypes have been micromilled in poly(methyl methacrylate). Confocal microscopy has been used to study the mixing. Several micromixers working on the principle of lamination have been reported in recent years. However, they require three-dimensional channel designs which can be complicated to manufacture. The main advantage with the present design is that it is relatively easy to produce using standard microfabrication techniques while at the same time obtaining good lamination between two fluids.     

Risk analysis for occupational safety and health in the textile industry: Integration of FMEA,FTA, and BIFPET methods

Identifying and managing health and safety risks that threaten personnel in production systems are vital for the continuity and success of organizations. Many tools are used to accurately analyze and assess risks. Failure mode and effect analysis (FMEA) is one of the most commonly used tools in different industries. However, the accuracy and reliability of FMEA method have been fairly criticized by many researchers in the field. In this study, an approach based on FMEA that integrates the advantages of the fault tree analysis (FTA) method and belief in fuzzy probability estimations of time (BIFPET) algorithm has been proposed in order to improve the performance of the FMEA method. In order to practically apply the proposed method to real life problems, it has been employed to analyze and assess the potential risks for a finishing process in the fabric dyeing department of a textile company. The performance of the proposed FMEA-FTA-BIFPET method has been compared to the results obtained by FMEA-FTA and FMEA-FTA-program evaluation and review technique (PERT) distribution integrated methods. The results of this study show that failure related to fabric trimming adjustment in the tenter has the highest risk priority number. The proposed approach can be used in various industry for risk analysis. In addition, results obtained by the study have indicated that the proposed approach can be implemented in practice to perform comprehensive risk assessment procedures as it reflects real-life dynamics to analyze and assess potential risk.     

Realistic simulation of mixing fluids

Recently, simulation of mixing fluids, for which wide applications can be found in multimedia, computer games, special effects, virtual reality, etc., is attracting more and more attention. Most previous methods focus separately on binary immiscible mixing fluids or binary miscible mixing fluids. Until now, little attention has been paid to realistic simulation of multiple mixing fluids. In this paper, based on the solution principles in physics, we present a unified framework for realistic simulation of liquid–liquid mixing with different solubility, which is called LLSPH. In our method, the mixing process of miscible fluids is modeled by a heat-conduction-based Smooth Particle Hydrodynamics method. A special self-diffusion coefficient is designed to simulate the interactions between miscible fluids. For immiscible fluids, marching-cube-based method is adopted to trace the interfaces between different types of fluids efficiently. Then, an optimized spatial hashing method is adopted for simulation of boundary-free mixing fluids such as the marine oil spill. Finally, various realistic scenes of mixing fluids are rendered using our method.