Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity.

Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts, and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a buffer modification workflow (BMW) in which the same sample is run by LC-MS in both liquid chromatography solvent with 14NH3-acetate buffer and in solvent with the buffer modified with 15NH3-formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Overall, it identified 26% of ∼27 000 liver LC-MS features as putative metabolites, of which ∼2600 showed HMDB or KEGG database formula match. This workflow is well suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.

Identification of compounds from high-fat and extra virgin olive oil-supplemented diets in whole mouse liver extracts and isolated mitochondria using mass spectrometry.

Nonalcoholic steatohepatitis (NASH) is a fatty liver disorder that could be improved with extra virgin olive oil (EVOO) supplementation in diet. We propose the monitoring, in whole mouse liver extracts and in isolated mitochondria, of the absorption of compounds from three different diets: standard (CT), high-fat (HFD) and high-fat supplemented with EVOO (HFSO). Male mice were submitted to one of the following three diets: CT or HFD for 16 weeks or HFD for 8 weeks followed by additional 8 weeks with HFSO. Following this period, liver was extracted for histological evaluation, mitochondria isolation and mass spectrometry analyses. Diets, liver extracts and Percoll-purified mitochondria were analyzed using ESI-MS and the lipidomics approach. Morphological, histological and spectrometric results indicated a decrease in NASH severity with EVOO supplementation in comparison with animals maintained with HFD. Spectrometric data also demonstrated that some compounds presented on the diets are absorbed by the mitochondria. EVOO was shown to be a potential therapeutic alternative in food for NASH. Our results are in accordance with the proposition that the major factor that influences different responses to diets is their composition - and not only calories - especially when it comes to studies on obesity.

Identification of prolyl oligopeptidase as a cyclosporine-sensitive protease by screening of mouse liver extracts.

Cyclosporine A (CsA) is a cyclic undecapeptide well known for its ability to prevent rejection episodes after organ transplantation via gain-of-function. Therefore, biomedical studies on CsA have been focused on both immunosuppressive properties and binding to the biocatalytically-active immune receptors, the cyclophilins. Much less attention has been spent on effects of cyclosporines on the biological function of other proteins. We used a 9-mer fluorescence-quenched peptide library with defined sequences to identify cyclosporine-sensitive proteolysis in mouse liver extracts. A highly soluble [d-Ser]8-CsA derivative was utilized to avoid drug precipitation at extended incubation times. Analysis of the time courses of proteolysis revealed 15 out of 360 peptide sequences where proteolysis exhibited marked sensitivity to the cyclosporine derivative. As a first example, a collagen-derived substrate was selected from those hits to identify the targeted proteolytic pathway. After purification from mouse liver extracts, prolyl oligopeptidase (EC 3.4.21.26) could be identified as a protease sensitive to submicromolar concentrations of cyclosporines. Surprisingly, in a series of cyclosporine derivatives an inverse relationship was found between the inhibition of prolyl oligopeptidase and inhibition of cyclophilin A.

Purification and characterization of a novel histone H2A specific protease (H2Asp) from chicken liver nuclear extract.

The proteolysis of the N- or the C-terminal tails of histones have recently emerged as a novel form of irreversible posttranslational modifications of histones. However, there are very few reports describing purification of a histone specific protease. Here, we report a histone H2A specific protease (H2Asp) activity in the chicken liver nuclear extract. The H2Asp was purified to homogeneity and was found to be a ~10.5kDa protein. It demonstrated high specificity to histone H2A and was an aspartic acid like protease as shown by protease inhibition assay. The H2Asp, in the in vitro cleavage assay generated a single clipped H2A product which comigrated along with histone H4 in the SDS-PAGE and migrated as a single band when single H2A was used as substrates. The expression of H2Asp was independent of age and was tissue specific, which was demonstrated only in the nuclear extracts of chicken liver and not from the same of other tissues like brain, muscles and erythrocytes. It was also seen that H2Asp activity also exists in other classes of vertebrates from Pisces to Mammals. This report forms the first such report describing purification of a histone H2A specific protease.

Cellular uptake and mutagenic potential of metal oxide nanoparticles in bacterial cells.

Extensive production and consumption of nanomaterials such as ZnO and TiO(2) has increased their release and disposal into the environment. The accumulation of nanoparticles (NPs) in ecosystem is likely to pose threat to non-specific targets such as bacteria. The present study explored the effect of ZnO and TiO(2) NPs in a model bacterium, Salmonella typhimurium. The uptake of ZnO and TiO(2) bare NPs in nano range without agglomeration was observed in S. typhimurium. TEM analysis demonstrated the internalization and uniform distribution of NPs inside the cells. Flow cytometry data also demonstrates that both ZnO and TiO(2) NPs were significantly internalized in the S. typhimurium cells in a concentration dependent manner. A significant increase in uptake was observed in the S. typhimurium treated even with 8 and 80 ng mL(-1) of ZnO and TiO(2) NPs with S9 after 60 min, possibly the formation of micelles or protein coat facilitated entry of NPs. These NPs exhibited weak mutagenic potential in S. typhimurium strains TA98, TA1537 and Escherichia coli (WP2uvrA) of Ames test underscoring the possible carcinogenic potential similar to certain mutagenic chemicals. Our study reiterates the need for re-evaluating environmental toxicity of ZnO and TiO(2) NPs presumably considered safe in environment.

Technical and biological variation in UPLC-MS-based untargeted metabolic profiling of liver extracts: application in an experimental toxicity study on galactosamine.

The relative importance of technical versus bio-logical variation in UPLC-MS liver metabolic profiling studies was assessed on liver samples collected as part of an in vivo hepatotoxicity study. Biological variability within and between two treatment groups (three rats treated with galactosamine and three with galactosamine+uridine) was compared with sampling/extraction variability (three portions extracted from each rat liver section) and UPLC-MS platform variability (triplicate injections of each extract) for aqueous and organic extracts. The impact of scaling on error measurement was investigated on replicate injections of a quality control sample, and consequently started log-transformation was used to stabilize the variance across the ion intensity range. For aqueous extracts, technical variability was two to four times lower than within group interanimal variability. Similar results were obtained for organic extracts for the galactosamine group, sampling/extraction variability being more elevated in the galactosamine+uridine group. For both extract types, differences between treatment groups were the principal source of observed variation, and triplicate injections clustered closely in PCA plots and in HCA dendrograms, indicating small instrument variability compared to observed biological variation. This protocol can be applied to investigate differences in liver metabolic profiles between animal groups in toxicology studies and clinical investigations of liver disease.

Isolation, purification and characterization of antioxidant peptidic fractions from a bovine liver sarcoplasmic protein thermolysin hydrolyzate.

Sarcoplasmic proteins isolated from bovine livers were hydrolyzed using the enzyme thermolysin at 37°C for 2h. The hydrolyzates were filtered through molecular weight cut off membranes (MWCO) and filtrates were obtained. The water activity (a(w)) of unhydrolysed sarcoplasmic protein, full hydrolyzates, 10-kDa and 3-kDa filtrates were below the limit necessary for microbial growth. The antioxidant activities of both filtrates and fractions were assessed using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity assay, the ferric ion reducing antioxidant power (FRAP) assay and the Fe(2+) chelating ability assay. RP-HPLC was used for purification of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates. The peptidic content of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates were assessed using the Dumas method and peptide contents of each fraction were characterized using electrospray quadrupole time-of-flight (ESI-Q-TOF) mass spectrometry with the resultant spectrum analysed using the software programmes Protein Lynx Global Server 2.4. and TurboSEQUEST. Similarities between the amino acid composition of characterized peptides from each fraction and previously reported antioxidant peptides were found. This study demonstrates that meat by-product such as liver can be utilised as raw material for the generation of bioactive peptides with demonstrated antioxidant activities in vitro using the enzyme thermolysin. It is significant as it presents a potential opportunity for meat processors to use their waste streams for the generation of bioactive peptides for potential functional food use.

Intact-protein trapping columns for proteomic analysis in capillary high-performance liquid chromatography.

A new type of monolithic trapping columns with high mechanical strength was prepared by thin-layer sol-gel coating method and applied to trapping intact proteins for on-line capillary liquid chromatography. Monolithic trapping columns were fabricated by entrapping C8 reversed-phase particles into the capillary columns through a sol-gel network, which was formed by hydrolysis and polycondensation of methyltriethoxysilane. Hundreds times of trapping/untrapping for intact proteins were carried out. The trapping columns showed long-term stability up to 300 bar. Recovery, loading capacity and reproducibility of trapping columns were evaluated using four proteins. The recovery of four protein mixtures for the C8 monolithic trapping columns was 99.3% on average. The loading capacity of 5 mm × 320 µm i.d. C8 trapping columns for the protein mixtures was 30 µg. Day-to-day relative standard deviation (RSD) values for recoveries of protein mixtures on the same C8 trapping column ranged from 2.34 to 5.87%, column-to-column RSD values were from 3.01 to 6.81%. The C8 trapping columns were used to trap normal mouse liver intact proteins in a capillary liquid chromatography system. Results demonstrated high efficiency of the monolithic trapping columns for trapping intact proteins for proteomic analysis in on-line capillary liquid chromatography system.

[Construction of the dioxin bioassay method based on the clonal expressed aryl hydrocarbon receptor system].

OBJECTIVE: To study the specific binding of the artificial clonal aryl hydrocarbon receptor translocator (ARNT) with the natural aryl hydrocarbon receptor (AhR) and the recolonization by polyclonal antibody. The dose-response relationship with tetrachlo-rodibenzo-dioxin (TCDD) was also studied to develop TCDD detection method and the binding degree related to dose response. METHODS: (1) The target genes including AhR-PAS, AhR-C and ARNT-PAS were amplified by RT-PCR by using the total RNA purified from the liver cells of C57BL/6J mice as templates to construct pGEX-5X1 recombinants. The recombinant plasmids were expressed in E. coli. (2) The rabbits were immuned by the clonal fusion proteins: AhR-PAS, AhR-C to prepare the polyclonal antibody. (3) The natural AhR from the hepatic cytosol of C57BL/6J mice was extracted. The artificial cloning expressed fusion protein:GST-ARNT-PAS and the natural AhR were incubated in different dose of TCDD. The quantity of the heterodimer through affinity adsorption and Western blots were measured. RESULTS: (1) The target proteins including AhR-PAS, AhR-C and ARNT-PAS were successfully cloned and expressed in E. coli. (2) The detection limit of polyclonal antibody AhR-PAS and AhR-C were 5 ng and 1 ng, respectively. (3) The total protein concentration prepared from the liver cells was 60.5 mg/ml. The artificial clonal protein ARNT-PAS could specifically bind to the natural AhR complex with the existence of TCDD. The detection limit of TCDD was 0.25 pmol which was 80 pg approximately. CONCLUSION: A TCDD detection method based on the aryl hydrocarbon receptor system was established and the detection limit might reach pg grade.

Cells extract from fetal liver promotes the hematopoietic differentiation of human embryonic stem cells.

Here, we have now developed a new inducing system to promote the differentiation of human stem cells (hESCs) toward hematopoietic lineages by the treatment with cells extract of human fetal liver tissue (hFLT). The embryoid bodies (EBs) obtained from human H1 embryonic stem cells were exposed to buffer, hFLT cells extract, heated hFLT cell extract, and cell extract of human liver cells lines-LO2. Then, the feature of EBs in different groups was characterized by real-time RT-PCR and colony-forming assays. The results showed the treatment by hFLT cells extract could activate the hematopoietic genes expression and improve the capacity for hematopoietic progenitor development of hEBs. After that, we cocultured hFLT extract treated hEBs on the hFLSCs (human fetal liver stromal cells) feeder to differentiate them into hematopoietic cells. As a control, untreated hEBs were cocultured on hFLSCs feeder with cytokines. The feature of induced cells from hEBs was characterized by flow cytometry, Wright-Giemsa staining, and colony-forming assays. The results demonstrated that hFLT cells extract was capable of inducing hEBs into hematopoietic cells and combing it with hFLSCs feeder could largely promote hematopoietic differentiation of hESCs. This method may supply a new way to substitute the cytokines required in hematopoietic induction of hESCs.

Protein profilings in mouse liver regeneration after partial hepatectomy using iTRAQ technology.

Liver is unique in its capability to regenerate after an injury. Liver regeneration after a 2/3 partial hepatectomy served as a classical model and is adopted frequently to study the mechanism of liver regeneration. In the present study, semiquantitative analysis of protein expression in mouse liver regeneration following partial hepatectomy was performed using an iTRAQ technique. Proteins from pre-PHx control livers and livers regenerating for 24, 48 and 72 h were extracted and inspected using 4-plex isotope labeling, followed by liquid chromatography fractionation, mass spectrometry and statistical differential analysis. A total of 827 proteins were identified in this study. There were 270 proteins for which quantitative information was available at all the time points in both biologically duplicate experiments. Among the 270 proteins, Car3, Mif, Adh1, Lactb2, Fabp5, Es31, Acaa1b and LOC100044783 were consistently down-regulated, and Mat1a, Dnpep, Pabpc1, Apoa4, Oat, Hpx, Hp and Mt1 were up-regulated by a factor of at least 1.5 from that of the controls at one time point or more. The regulation of each differential protein was also demonstrated by monitoring its time-dependent expression changes during the regenerating process. We believe this is the first report to profile the protein changes in liver regeneration utilizing the iTRAQ proteomic technique.

Isolation and characterization of low-molecular-weight chromium-binding substance (LMWCr) from chicken liver.

Chromodulin (also known as low-molecular-weight chromium-binding substance, LMWCr) is a chromium-binding oligopeptide proposed to play a role in insulin signaling and chromium transport in mammals. This laboratory has isolated and purified this material from a non-mammalian source, an avian. Spectroscopic and physical characterization of the isolated material suggests the material is an oligopeptide with a multinuclear chromium assembly bridged via asparatate and glutamate residues very similar to its mammalian counterparts. The isolated material also possesses a biological activity similar to other LMWCr isolates.

Correlation between liver and plasma fatty acid profile of phospholipids and triglycerides in rats.

Considering the changes in the fatty acid profile of liver lipids related to age, gender and nutritional status or occurring in pathological situations, this study aimed at investigating whether such changes could be judged from measurements conducted in plasma lipids. The fatty acid profile of both liver and plasma phospholipids and triglycerides was measured in 16 control animals and 26 rats depleted in long-chain polyunsaturated (n-3) fatty acids. Within each group of rats, significant correlations prevailed between the percentage of each fatty acid in liver versus plasma phospholipids or triglycerides. However, the plasma/liver ratio for the relative content of C20:5(n-3), C22:5(n-3) and C22:6(n-3) in triglycerides displayed abnormally high values in 2 control animals. The fatty acid profile of liver phospholipids and triglycerides can, as a rule, be judged from measurements made in the corresponding plasma lipids. For instance, measurements in plasma phospholipids could help to identify subjects deficient in (n-3) fatty acids and to assess the dietary correction of this defect.

Determination of multiresidue quinolones regulated by the European Union in pig liver samples. High-resolution time-of-flight mass spectrometry versus tandem mass spectrometry detection.

The use of liquid chromatography coupled to orthogonal acceleration time-of-flight mass spectrometry (LC-ToF-MS) provides an attractive alternative to liquid chromatography coupled to quadrupole (LC-MS) or triple quadrupole mass spectrometry (LC-MS/MS) in multiresidue analysis. ToF-MS provides accurate mass information and a significantly higher mass resolution than quadrupole analyzers. In this work, the influential parameters in time-of-flight detection using an electrospray ionization (ESI) source were studied using a central composite design to obtain the main effects and their two-factor interactions. The method developed uses LC-ESI-ToF-MS to determine and characterize quinolones regulated by the EU in pig liver samples below the maximum residue limits (MRLs). Linearity, decision limit, detection capability, detection and quantification limits, precision and recoveries were determined and adequate results were obtained, with quantification limits between 1.5 and 6 microg kg(-1) and recoveries higher than 60% for all quinolones. Limits of detection are lower than 2 microg kg(-1). Results obtained using LC-ESI-ToF-MS were compared with those obtained using LC coupled to a quadrupole and to triple quadrupole mass spectrometer. The work described in this paper illustrates the suitability and excellent confirmatory potential of LC-ToF-MS for multiresidue analysis in food samples.

Thalidomide and thalidomide transformed by pH-dependent hydrolysis or by liver enzyme treatment does Not impede the proliferation of endothelial cells.

Angiogenesis is essential for tumor growth. In the treatment of tumors with thalidomide, a rationale for its use is that it inhibits angiogenesis. To form new blood vessels, endothelial cells must proliferate. The authors were interested in describing some of the circumstances by which thalidomide may influence proliferation of endothelial cells. Human umbilical vein derived endothelial cells (HUVECs) were exposed to 4.0 or 100 microg/ml of thalidomide in dimethylsulfoxide or to 4 microg/ml of thalidomide prepared an aqueous solutions. Proliferation was determined by measuring incorporation of (3)H-thymidine. Regardless of the solvent used to dissolve thalidomide, the HUVECs treated with thalidomide were not inhibited in their ability to incorporate (3)H-thymidine.

Mutagenic potency in Salmonella typhimurium of organic extracts of soil samples originating from urban, suburban, agricultural, forest and natural areas.

The purpose of the present work was to assess the mutagenic potency of soil samples presumably not contaminated by industrial wastes and discharges. A set of 51 soil samples was collected from areas considered as not contaminated by a known industrial activity: 11 urban samples (collected in cities), 15 suburban samples (collected in villages), 7 agricultural samples, and 18 forest or natural samples. Each soil sample was collected at the surface (0-5cm deep), dried, sieved (2mm), homogenized before organic extraction (dichloromethane/acetone 1/1 (v/v), 37 degrees C, 4h, soil/solvent ratio 1/2, m/v), solvent exchange to DMSO and sterilizing filtration. The micro-method adaptation of the standard bacterial mutagenicity test on Salmonella typhimurium strain TA98 was performed with and without a metabolic activation system (rat-liver homogenate S9), and thus detected the effect of pro-mutagens and direct mutagens, respectively. The use of a pre-incubation method increased the sensitivity of the assay. The results obtained showed a wide range of effect levels, from no effect to clear mutagenicity. In particular, the extract of all 11 urban soil samples demonstrated mutagenic activity, while the extracts of 10 of the 15 suburban samples showed mutagenicity. On the other hand, the extract of only one of the 7 agricultural samples studied induced mutations, and none of the 18 natural or forest-soil samples investigated produced mutagenic extracts. These findings seem to indicate the crucial influence of the diffuse pollution originating from different human activities on the mutagenic potency of urban soil samples. These findings make it possible to classify the soils according to their mutagenic potency. No clear correlation was found between the mutagenicity detected in soil extracts and the measured polycyclic aromatic hydrocarbon (PAH) content of the soils investigated.

Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography.

An unbiased method for large-scale depletion of high-abundance proteins and identification of middle- or low-abundance proteins by multidimensional LC (MDLC) was demonstrated in this paper. At the protein level, the MDLC system, coupling the first dimensional strong cation exchange (SCX) chromatography with the second dimensional RP-HPLC, instead of immunoaffinity technology, was used to deplete high-abundance proteins. Sixty-two fractions from SCX were separated further by RPLC. UV absorption spectra were observed to differentiate high-abundance proteins from middle- or low-abundance proteins. After the depletion of high-abundance proteins, middle- or low-abundance proteins were enriched, digested, and separated by online 2D-micro-SCX/cRPLC. The eluted peptides were deposited on the MALDI target and detected by MALDI-TOF/TOF MS. This depletion strategy was applied to the proteome of the normal human liver (NHL) provided by the China Human Liver Proteome Project (CHLPP). In total, 58 high-abundance proteins were depleted in one experiment. The strategy increases greatly the number of identified proteins and around 1213 proteins were identified, which was about 2.7 times as that of the nondepletion method.

Chemical speciation by selective heteronuclear single-quantum coherence spectroscopy: determination of double-bond quantity in unsaturated fatty acid compounds.

A method for identifying fatty acid species based on the number of double bonds contained in a lipid molecule is presented. Common to all polyunsaturated fatty acids are two signature resonances at approximately 5.3 and 2.8 ppm in the proton chemical-shift spectrum of NMR. These resonances are from the vinyl and bis-allyl protons, respectively, and, although they can be readily observed by NMR from lipid extracts of biological samples, direct speciation has never been demonstrated by NMR. By modifying a conventional HSQC pulse sequence with a J-pulse on the spin system of the vinyl group (generalized as an IS spin system) at the beginning of the initial polarization transfer period and selectively inverting the 13C (I) spins with a narrowband sech/tanh inversion pulse, the collection of data in both dimensions can be restricted to a narrow slice of the chemical-shift range. The resolution is subsequently determined by digitizer efficiency, and spectra can be collected optimally from within a very narrow 1 x 6 ppm window of the respective proton and carbon chemical-shift ranges. With this modification it is possible to distinguish at least one resonance each from the multiple shifts expected from the indirectly detected nuclei of the fatty acid species, oleic acid, linoleic acid, linolenic acid and arachidonic acid, which contain one, two, three and four double bonds, respectively. This and similar methods of applied selectivity are of potential interest in characterizing speciation in biological samples where mixtures are often encountered and chemical shifts of the same structural group of similar molecules give rise to complicated overlapping resonances but are important for diagnosis of disease processes such as cancer.

Identification and analysis of alpha1,6-fucosylated proteins in human normal liver tissues by a target glycoproteomic approach.

alpha1,6-Fucose residues within the N-glycan core structures were commonly observed in many glycoproteins. Our previous studies showed that aberrantly alpha1,6-fucosylated glycoproteins might be associated with metastasis of hepatocellular carcinoma (HCC). Little is known about human normal liver tissues (HNLTs) in the literatures. In this study, a target glycoproteomic approach which consists of lectin-affinity chromatography, 2-DE, protein immunoprecipitation and lectin blot, and MALDI-MS/MS, was utilized to screen physiologically alpha1,6-fucosylated glycoproteins. Lens culinaris agglutinin (LCA)-affinity glycoprotein profiles of HNLT were established and analyzed, which allowed identification of 53 proteins by MS analysis, including haptoglobin precursor, alpha-enolase, etc. Gene ontology (GO) annotation proved that these proteins distribute predominately in organelle and play crucial roles in binding and catalytic reactions. The present methodology enabled the identification of all the specific subsets of glycoprotein, and the corresponding data could contribute to the finding of more aberrantly alpha1,6-fucosylated glycoproteins related to liver diseases.

Phosphoproteome profile of human liver Chang's cell based on 2-DE with fluorescence staining and MALDI-TOF/TOF-MS.

Because reversible protein phosphorylation is central to biological regulation, many methods have been developed for the systematic parallel analysis of the phosphorylation status of large sets of proteins. To directly survey the extent of protein phosphorylation and the distribution of phosphoproteins in biological systems, we used a phosphoprotein staining method, Pro-Q Diamond dye, for the high-throughput identification of phosphoproteins. The specificity of the method was validated with protein standards and subsequently applied to an analysis of total protein from human liver Chang's cells. Proteins were separated by 2-DE, then sequentially stained with Pro-Q Diamond and Coomassie Blue G-250. After image analysis, the proteins in gel spots containing phosphoproteins were identified by MALDI-TOF/TOF-MS. A total of 269 phosphoproteins were identified, and 27 were known phosphoproteins in the SwissProt database. By comparing the relative volumes of the phosphoprotein map and the total protein map, the extent of protein phosphorylation was observed. The phosphoprotein staining method combined with 2-DE also detected polymorphisms of the phosphoproteins, and could distinguish highly abundant, but slightly phosphorylated proteins from less abundant, highly phosphorylated ones. We conclude that the phosphoprotein staining method can be used for global, quantitative phosphorylation detection.