溱潼凹陷低熟油生物标记物特征及成因机理探讨

根据溱潼凹陷原油和油砂岩抽提物中饱和烃、芳烃化合物的生物标志物组成特征进行了低熟油形成的沉积环境、油及烃源岩成熟度界定等分析研究,并对低熟油的成因机理进行了探讨。研究表明低熟油生源构成体现了多源复合型特征,而高等植物和菌藻类微生物是低熟原油最为重要的成烃母质。低熟油总体体现了微咸水-半咸水的沉积环境。     

Application of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry to biomarker characterization in Brazilian oils

The variety of chemical classes present in oils, as well as possible co-elutions in conventional chromatographic separations, makes the identification of biomarkers a difficult task. Comprehensive two-dimensional gas chromatography (GC × GC) coupled to time-of-flight mass spectrometry (TOFMS) is a powerful tool for overcoming these problems and limitations, since it (i) separates substances using two interconnected capillary columns containing different stationary phases and (ii) uses the fast data acquisition of time-of-flight analyser as a robust registry for GC × GC. In this work, biomarkers present in Brazilian oils were identified both individually and in groups by GC × GC-TOFMS much better than in previous works using one-dimensional GC. In the extracted ion chromatograms (EIC) for ions of mass-to-charge ratio (m/z) 191, co-elutions between tri- and pentacyclic terpanes were resolved in the second column. Noteworthy separation between the C30 hopane and C30R demethylated homohopane was observed. Overlap of hopanes with steranes in the m/z 217 EIC was eliminated. Besides hopanes, demethylated tri- and tetracyclic terpanes were identified and reported for the first time in Brazilian oil samples. These results indicate the superiority of GC × GC-TOFMS as a technique for separation and identification of biomarkers in oils.     

Use of biomarkers to show sub-cellular effects in meadow voles (Microtus pennsylvanicus) living on an abandoned gold mine site

Run-off from mine tailings ponds constitutes the main anthropogenic release of arsenic in Canada. As a potential consequence, wildlife not normally exposed to arsenic under other circumstances may receive toxicologically relevant concentrations of arsenic compounds in their food and water. To test this hypothesis, and to determine if arsenic is being transported through trophic levels, the arsenic concentrations in members of a short food chain (soil-plant-meadow vole) were measured. Arsenic concentrations were higher in exposed organisms compared with those from a reference location. However, elevated concentrations of arsenic do not necessarily indicate impact, and consequently a biomonitoring study was undertaken to determine if there were sub-cellular effects of exposure in meadow voles (Microtus pennsylvanicus) as a consequence of arsenic exposure. In this work, adenosine triphosphate (ATP) and liver glutathione (GSH) levels were used as biomarkers of exposure and the frequency of red blood cell micronuclei (mono- and polychromatic) was used as a biomarker of effect. ATP results were not conclusive but there was a statistically significant relationship between a reduction of GSH in vole livers and increased liver arsenic concentrations. A statistically significant relationship was also observed between increased micronucleated monochromatic red blood cells in voles from arsenic contaminated sites compared to a background location. The results of the GSH and monochromatic red blood cell investigations suggest that there are possible sub-cellular effects on these voles as a consequence of dietary arsenic exposure. This is the first field study in which such effects have been observed in voles living near mine tailings.     

Botanical discrimination and classification of honey samples applying gas chromatography/mass spectrometry fingerprinting of headspace volatile compounds

A validated method for the discrimination and classification of honey samples performing GC/MS fingerprinting of headspace volatile compounds was developed. Combined mass spectra of honey samples originated from different plants and geographical regions of Greece were subjected to orthogonal partial least squares-discriminant analysis™ (OPLS™-DA), soft independent modelling of class analogy (SIMCA), and OPLS™-hierarchical cluster analysis (OPLS™-HCA). Analyses revealed an excellent separation between honey samples according to their botanical origin with the percentage of misclassification to be as low as 1.3% applying OPLS™-HCA. Fragments (m/z) responsible for the observed separation were assigned to phenolic, terpenoid, and aliphatic compounds present in the headspace of unifloral honeys. On the other hand, a variable classification for citrus and thyme honeys according to their geographical origin could be achieved. Results suggested that the developed methodology is robust and reliable for the botanical classification of honey samples, and the study of differences in their chemical composition.     

Novel Non-Protein Biomarkers for Early Detection of Hepatocellular Carcinoma

Early detection of hepatocellular carcinoma (HCC) while in its early stages is critical for reducing HCC mortality in high-risk patients. However, highly sensitive and specific surveillance biomarkers for early-stage HCC detection are still lacking. In recent years, great efforts have been made to research tumor-derived molecular features that are detectable in circulation, such as circulating tumor deoxyribonucleic acid and circulating tumor ribonucleic acid, in order to explore their potential as non-invasive biomarker candidates in many tumor types. In this review, we summarize current studies on these new approaches and their application in early HCC detection.     

Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.     

Polymethylene-interrupted fatty acids: Biomarkers for native and exotic mussels in the Laurentian Great Lakes

Freshwater organisms synthesize a wide variety of fatty acids (FAs); however, the ability to synthesize and/or subsequently modify a particular FA is not universal, making it possible to use certain FAs as biomarkers. Herein we document the occurrence of unusual FAs (polymethylene-interrupted fatty acids; PMI-FAs) in select freshwater organisms in the Laurentian Great Lakes. We did not detect PMI-FAs in: (a) natural seston from Lake Erie and Hamilton Harbor (Lake Ontario), (b) various species of laboratory-cultured algae including a green alga (Scenedesmus obliquus), two cyanobacteria (Aphanizomenon flos-aquae and Synechococystis sp.), two diatoms (Asterionella formosa, Diatoma elongatum) and a chrysophyte (Dinobryon cylindricum) or, (c) zooplankton (Daphnia spp., calanoid or cyclopoid copepods) from Lake Ontario, suggesting that PMI-FAs are not substantively incorporated into consumers at the phytoplankton-zooplankton interface. However, these unusual FAs comprised 4-6% of total fatty acids (on a dry tissue weight basis) of native fat mucket (Lampsilis siliquoidea) and plain pocketbook (L. cardium) mussels and in invasive zebra (Dreissena polymorpha) and quagga (D. bugensis) mussels. We were able to clearly partition Great Lakes' mussels into three separate groups (zebra, quagga, and native mussels) based solely on their PMI-FA profiles. We also provide evidence for the trophic transfer of PMI-FAs from mussels to various fishes in Lakes Ontario and Michigan, further underlining the potential usefulness of PMI-FAs for tracking the dietary contribution of mollusks in food web and contaminant-fate studies.     

Diagnostic biomarkers differentiating metastatic melanoma patients from healthy controls identified by an integrated MALDI-TOF mass spectrometry/bioinformatic approach

The prognosis of advanced metastatic melanoma (American Joint Committee on Cancer (AJCC) stage IV) remains dismal with a 5-year survival rate of 6-18%. In the present study, an integrated MALDI mass spectrometric approach combined with artificial neural networks (ANNs) analysis and modeling has been used for the identification of biomarker ions in serum from stage IV melanoma patients allowing the discrimination of metastatic disease from healthy status with high specificities of 92% for protein ions and 100% for peptide biomarkers. Our ANNs model also correctly classified 98% of a blind validation set of AJCC stage I melanoma samples as nonstage IV samples, emphasizing the power of the newly defined biomarkers to identify patients with late-stage metastatic melanoma. Sequence analysis identified peptides derived from metastasis-associated proteins; alpha 1-acid glycoprotein precursor-1/2 (AAG-1/2) and complement C3 component precursor-1 (CCCP-1). Furthermore, quantitation of serum AAG by an immunoassay showed a significant (p<0.001) increase in AAG serum concentration in stage IV patients in comparison with healthy volunteers; moreover; the quantity of AAG plotted against MALDI-MS peak intensity classified the groups into two distinct clusters. Ongoing studies of other disease stages will provide evidence whether our strategy is sufficiently robust to give rise to stage-specific protein/peptide signatures in melanoma.     

Proteomic profiling of heat shock proteins: An emerging molecular approach with direct pathophysiological and clinical implications

The HSP family is one of the most ancient and evolutionarily conserved protective protein families found in nature. Originally discovered as inducible molecules capable of maintaining cellular homeostasis against abrupt temperature changes, HSPs were later determined to represent an adaptive physiological response that copes with a variety of different cellular proteotoxic stresses. These physiological molecular chaperones facilitate the synthesis, folding, assembly, trafficking and secretion of specific proteins in various cellular compartments. Most importantly, these proteins guard the whole cell proteome against misfolding and inappropriate aggregation. A series of diversified proteotoxic stresses, including heat, hypoxia/ischemia, free radicals, acidosis, ATP depletion and toxins are capable of inducing a typical cellular stress response characterised by rapid inhibition of overall protein synthesis, with a concomitant dramatic increase in HSP expression. From a pathophysiological point of view, HSP induction has been observed in a wide spectrum of inflammatory and degenerative diseases (from cancer to prion disease by passing to infective and autoimmune diseases) and, intriguingly, overexpression monitoring seems to have potential implications in terms of diagnosis, prognosis and, above all, therapy. Proteomics studies, identifying a series of modification of HSP expression patterns in different diseases, are confirming these promising clinical applications.