A prostate cancer tissue specific spectral library for targeted proteomic analysis

Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.     

Copper isotopes as possible neoplasia biomarkers in captive wild felids

The longevity of zoo animals is increasing due to continuous improvement in husbandry and veterinary medicine. However, increasing age is correlated to a higher prevalence of neoplasia. Despite tremendous improvement in diagnoses and monitoring capacities, cancers are still a challenge for veterinarians within the global zoo community. The recent use of copper isotopes as biomarkers for neoplasia in both human and veterinary medicine is a promising and cost‐effective diagnostic tool. Two hundred and twenty‐nine serum samples from 10 different species of wild felids under human care were processed through mass spectrometry to determine the ratio of heavy and light copper isotopes (⁶⁵Cu/⁶³Cu). The results of this preliminary study exhibit an important variability between felid species, with a ratio ranging between ?1.71 and 0.63. Additionally, copper isotopes seem to be a promising diagnostic tool in monitoring cancer in wild animals, as in human medicine, where the isotopic ratio decreases significantly with time in the presence of a tumor.     

Apical membrane localization of the adenomatous polyposis coli tumor suppressor protein and subcellular distribution of the beta-catenin destruction complex in polarized epithelial cells

The adenomatous polyposis coli (APC) protein is implicated in the majority of hereditary and sporadic colon cancers. APC is known to function as a tumor suppressor through downregulation of beta-catenin as part of a high molecular weight complex known as the beta-catenin destruction complex. The molecular composition of the intact complex and its site of action in the cell are still not well understood. Reports on the subcellular localization of APC in various cell systems have differed significantly and have been consistent with an association with a cytosolic complex, with microtubules, with the nucleus, or with the cortical actin cytoskeleton. To better understand the role of APC and the destruction complex in colorectal cancer, we have begun to characterize and isolate these complexes from confluent polarized human colon epithelial cell monolayers and other epithelial cell types. Subcellular fractionation and immunofluorescence microscopy reveal that a predominant fraction of APC associates tightly with the apical plasma membrane in a variety of epithelial cell types. This apical membrane association is not dependent on the mutational status of either APC or beta-catenin. An additional pool of APC is cytosolic and fractionates into two distinct high molecular weight complexes, 20S and 60S in size. Only the 20S fraction contains an appreciable portion of the cellular axin and small but detectable amounts of glycogen synthase kinase 3beta and beta-catenin. Therefore, it is likely to correspond to the previously characterized beta-catenin destruction complex. Dishevelled is almost entirely cytosolic, but does not significantly cofractionate with the 20S complex. The disproportionate amount of APC in the apical membrane and the lack of other destruction complex components in the 60S fraction of APC raise questions about whether these pools of APC take part in the degradation of beta-catenin, or alternatively, whether they could be involved in other functions of the protein that still must be determined.     

Fractionation of phosphate in sediments of four representative mangrove stages (French Guiana)

Phosphate was fractionated in Guianese mangrove sediments. Fe(OOH)P was extracted using a Ca-EDTA + Na-dithionite solution buffered at pH 8. CaCO₃P was extracted using Na₂-EDTA solution at pH 4.5. Next, Acid Soluble Organic Phosphate (ASOP) was extracted by H₂SO₄ 0.5 N. Finally, Residual Organic Phosphate (ROP) was digested with H₂SO₄ + H₂O₂. Four representative mangrove stages have been studied: sea edge pioneer mangroves, mature coastal mangroves, mixed riverine mangroves, and declining to dead mangroves. The sum of the P-fractions varied between 638 to 804 g g^-1 in pioneer and mixed mangroves respectively. In all the stages, the percentage of inorganic phosphate was larger than 50% of the total P. Fe(OOH)P varied between 221 (pioneer mangrove) to 426 g g^-1 (dead mangrove). CaCO₃P varied between 75 to 102 g g^-1 in mixed, dead or mature mangroves and attained 125 g g^-1 in pioneer mangrove. The sum of the concentrations of organic phosphate (ASOP + ROP) increased markedly from the dead mangrove (189 g g^-1) to the mixed mangrove (380 g g^-1). Guianese mangroves, are relatively rich in total phosphate, possibly because they are narrowly related to the 'Amazon dispersal system. Each mangrove stage can be characterised by a prevailing form of phosphate. The concentrations of these different forms were ascribed to the marked relations with the seawater which controls import or export of suspended matters and to the wave action which controls the resuspension of the sediments and subsequently exchange of phosphate between the suspended matter and the water column.     

Alkenone and alkenoic acid compositions of the membrane fractions of Emiliania huxleyi

The lipid classes and unsaturation ratios of long-chain alkenones (nC37-C39), related alkyl alkenoate compounds (nC37-C38) and alkenoic acids (nC14-C22) were determined in isolated membrane and organelle fractions of Emiliania huxleyi. The percentage distribution of these compounds was predominantly high in the endoplasmic reticulum (ER) and coccolith-producing compartment (CPC)-rich membrane fraction, although alkenones and alkenoates could be detected in all membrane fractions. In particular, the alkenones were mainly located in CPC, since their distribution was closely correlated with that of uronic acids which are markers of CPC. In contrast, the alkenoic acids seemed to be mainly located in chloroplast (thylakoid)-rich fractions. The alkenone unsaturation ratio and the ratio of alkenoates to alkenones were similar in all fractions, while the unsaturation ratio of alkenoic acids in the thylakoid-rich and plasma membrane (PM)/Golgi body-rich fractions was overwhelmingly higher than that in the ER/CPC-rich fractions. Thus, alkenoic acids seemed to be typical membrane-bound lipids, and could be closely related to photosynthesis and involved in regulating membrane fluidity and rigidity in E. huxleyi. It is presumed from these results that the alkenones and alkenoates were membrane-unbound lipids that might be associated with the function of CPC.     

Changes in dissolved lignin-derived phenols, neutral sugars, uronic acids, and amino sugars with depth in forested Haplic Arenosols and Rendzic Leptosols

A major part of the dissolved organic matter produced in the organic layers of forest ecosystems and leached into the mineral soil is retained by the upper subsoil horizons. The retention is selective and thus dissolved organic matter in the subsoils has different composition than dissolved organic matter leached from the forest floor. Here we report on changes in the composition of dissolved organic matter with soil depth based on C-to-N ratios, XAD-8 fractionation, wet-chemical analyses (lignin-derived CuO oxidation products, hydrolysable sugars and amino sugars) and liquid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy. Dissolved organic matter was sampled directly beneath the forest floor using tension-free lysimeters and at 90cm depth by suction cups in Haplic Arenosols under Scots pine (Pinus sylvestris L.) and Rendzic Leptosols under European beech (Fagus sylvatica L.) forest. At both sites, the concentrations of dissolved organic carbon (DOC) decreased but not as strongly as reported for deeply weathered soils. The decrease in DOC was accompanied by strong changes in the composition of dissolved organic matter. The proportion of the XAD-8-adsorbable (hydrophobic) fraction, carboxyl and aromatic C, and the concentrations of lignin-derived phenols decreased whereas the concentrations of sugars, amino sugars, and nitrogen remained either constant or increased. A general feature of the compositional changes within the tested compound classes was that the ratios of neutral to acidic compounds increased with depth. These results indicate that during the transport of dissolved organic matter through the soils, oxidatively degraded lignin-derived compounds were preferentially retained while potentially labile material high in nitrogen and carbohydrates tended to remain dissolved. Despite the studied soils' small capacity to sorb organic matter, the preferential retention of potentially refractory and acidic compounds suggests sorption by the mineral soil matrix rather than biodegradation to govern the retention of dissolved organic matter even in soils with a low sorption capacity.     

Cold ethanol fractionation and heat inactivation of hepatitis a virus during manufacture of albumin from human plasma

The purpose of the present study was to examine the efficacy and mechanism of fraction IV cold ethanol fractionation and pasteurization (60°C heat treatment for 10h), involved in the manufacture of albumin from human plasma, in the removal and/or inactivation of the hepatitis A virus (HAV). Samples from the relevant stages of the production process were spiked with HAV and the amount of virus in each fraction then quantified using a 50% tissue culture infectious dose (TCID₅₀). HAV was effectively partitioned from albumin during the fraction IV cold ethanol fractionation with a log reduction factor of 3.43. Pasteurization was also found to be a robust and effective step in inactivating HAV, where the titers were reduced from an initial titer of 7.60 log TCID₅₀ to undetectable levels within 5 h of treatment. The log reduction factor achieved during pasteurization was≽4.76. Therefore, the current results indicate that the production process for albumin has sufficient HAV reducing capacity to achieve a high margin of virus safety.     

Fine oral filaments in Paramecium: a biochemical and immunological analysis

In Paramecium, several kinds of the oral networks of fine filaments are defined at the ultrastructural level. Using the sodium chloride-treated oral apparatus of Paramecium as an antigen to produce monoclonal antibodies, we have begun to identify the proteins constituting these networks. Immunoblotting showed that all positive antibodies were directed against three bands (70-, 75-and 83-kD), which corresponded to quantitatively minor components of the antigen; there was no antibody specific for the quantitatively major components (58- and 62-kD). Immunolocalization with four of these antibodies directed against one or several of these three bands showed that these proteins are components of the fine filaments supporting the oral area; a decoration of the basal bodies and the outer lattice was also observed on the cortex. Immunofluorescence on interphase cells suggested that the three proteins colocalized on the left side of the oral apparatus, whereas only the 70-kD band was detected on the right side. During division, the antigens of the antibodies were detected at different stages after oral basal body assembly. The antibodies cross-reacted with the tetrins, which are oral filament-forming proteins in Tetrahymena, demonstrating that tetrin-related proteins are quantitatively minor components of the oral and the somatic cytoskeleton of Paramecium.     

Filling of a wetland (Seine estuary,France): natural eutrophication or anthropogenic process? A sedimentological and geochemical study of wetland organic sediments

Hydrobiologia - For over a century the Seine estuary has been highly affected by human activities, resulting in a reduction of the surface of wetland habitat. Several ponds of the Vernier Marsh,...