ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.

MOTIVATION: Effective use of proteomics data, specifically mass spectrometry data, relies on the ability to read and write the many mass spectrometer file formats. Even with mass spectrometer vendor-specific libraries and vendor-neutral file formats, such as mzXML and mzData it can be difficult to extract raw data files in a form suitable for batch processing and basic research. Introduced here are the ProteomeCommons.org Input and Output Framework, abbreviated to IO Framework, which is designed to abstractly represent mass spectrometry data. This project is a public, open-source, free-to-use framework that supports most of the mass spectrometry data formats, including current formats, legacy formats and proprietary formats that require a vendor-specific library in order to operate. The IO Framework includes an on-line tool for non-programmers and a set of libraries that developers may use to convert between various proteomics file formats. AVAILABILITY: The current source-code and documentation for the ProteomeCommons.org IO Framework is freely available at http://www.proteomecommons.org/current/531/

ProteomeCommons.org JAF: reference information and tools for proteomics.

SUMMARY: Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids and ion masses that directly correspond to known amino acid sequences. The Java Analysis Framework (JAF) for proteomics provides a freely usable, open-source library of Java code that abstracts all of the aforementioned data, enabling more rapid development of proteomics tools. The JAF also includes several user tools that can be run directly from a web browser. AVAILABILITY: The current version and an archive of all older versions of the Java Analysis Framework for Proteomics is freely available, including complete source-code, at http://www.proteomecommons.org/current/511/.

C60 in water: nanocrystal formation and microbial response.

Upon contact with water, under a variety of conditions, C60 spontaneously forms a stable aggregate with nanoscale dimensions (d = 25-500 nm), termed here "nano-C60". The color, hydrophobicity, and reactivity of individual C60 are substantially altered in this aggregate form. Herein, we provide conclusive lines of evidence demonstrating that in solution these aggregates are crystalline in order and remain as underivatized C60 throughout the formation/stabilization process that can later be chemically reversed. Particle size can be affected by formation parameters such as rates and the pH of the water addition. Once formed, nano-C60 remains stable in solution at or below ionic strengths of 0.05 I for months. In addition to demonstrating aggregate formation and stability over a wide range of conditions, results suggest that prokaryotic exposure to nano-C60 at relatively low concentrations is inhibitory, indicated by lack of growth (> or = 0.4 ppm) and decreased aerobic respiration rates (4 ppm). This work demonstrates the fact that the environmental fate, distribution, and biological risk associated with this important class of engineered nanomaterials will require a model that addresses not only the properties of bulk C60 but also that of the aggregate form generated in aqueous media.

Adsorption of cadmium on anatase nanoparticles-effect of crystal size and pH.

The adsorption and desorption of Cd(2+) to large and nanometer-scale anatase crystals have been studied to determine the relationship between heavy metal adsorption properties and anatase particle size. A solvothermal method was used to synthesize very fine anatase nanocrystals with average grain sizes ranging from 8 to 20 nm. On a surface area basis, it was found that large and nanometer-scale anatase particles had similar maximum Cd(2+) adsorption capacities, while their adsorption slopes differed by more than 1 order of magnitude. The particle-size effect on adsorption is constant over a pH range of 4-7.5. The desorption of Cd(2+) from both particle sizes is completely reversible. The adsorption data have been modeled by the Basic Stern model using three monodentate surface complexes. It is proposed that intraparticle electrostatic repulsion may reduce the adsorption free energy significantly for nanometer-sized particles.

Tissue-specific cytokine production during experimental acute pancreatitis. A probable mechanism for distant organ dysfunction.

Our purpose was to determine if cytokines are produced systemically during acute pancreatitis. Proinflammatory cytokines are elevated during acute pancreatitis and have been implicated in the progression of pancreatitis-associated multiple organ dysfunction. Whether these mediators are produced within all tissues or very few specific organs is not known. Edematous pancreatitis was induced in adult male mice by IP injection of cerulein. Necrotizing pancreatitis was induced in young female mice by feeding a choline-deficient, ethionine supplemented diet. Animals were sacrificed as pancreatitis worsened, with multiple organs prepared for tissue mRNA and protein analysis by RT-PCR and immunoblotting. Pancreatitis severity was established by histologic grading and serum amylase and lipase. There was no cytokine mRNA or protein detectable prior to the induction of pancreatitis. Tumor necrosis factor-alpha (TNF-alpha) and interleukin-1-beta (IL-1 beta) mRNA and protein were detected within the pancreas early in the course of pancreatitis in both models, coinciding with the development of hyperamylasemia (both P < 0.001). Interleukin-6 was produced in the pancreas after pancreatitis was more fully developed (P < 0.001). IL-1 beta and TNF-alpha were subsequently produced in large amounts in lung, liver, and spleen but never within kidney, cardiac muscle, or skeletal muscle. A significant delay between pancreatic and distant organ cytokine production was always observed. It is concluded that proinflammatory cytokines are produced within the pancreas and within organs known to develop dysfunction during severe pancreatitis. Cytokine production is tissue specific, correlates with disease severity, and occurs within the pancreas first and subsequently within distant organs.