Examining the biological pathways underlying clinical heterogeneity in Sjogren's syndrome: proteomic and network analysis.

OBJECTIVES: Stratification approaches are vital to address clinical heterogeneity in Sjogren's syndrome (SS). We previously described that the Newcastle Sjogren's Stratification Tool (NSST) identified four distinct clinical subtypes of SS. We performed proteomic and network analysis to analyse the underlying pathobiology and highlight potential therapeutic targets for different SS subtypes. METHOD: We profiled serum proteins using O-link technology of 180 SS subjects. We used 5 O-link proteomics panels which included a total of 454 unique proteins. Network reconstruction was performed using the ARACNE algorithm, with differential expression estimates overlaid on these networks to reveal the key subnetworks of differential expression. Furthermore, data from a phase III trial of tocilizumab in SS were reanalysed by stratifying patients at baseline using NSST. RESULTS: Our analysis highlights differential expression of chemokines, cytokines and the major autoantigen TRIM21 between the SS subtypes. Furthermore, we observe differential expression of several transcription factors associated with energy metabolism and redox balance namely APE1/Ref-1, FOXO1, TIGAR and BACH1. The differentially expressed proteins were inter-related in our network analysis, supporting the concept that distinct molecular networks underlie the clinical subtypes of SS. Stratification of patients at baseline using NSST revealed improvement of fatigue score only in the subtype expressing the highest levels of serum IL-6. CONCLUSIONS: Our data provide clues to the pathways contributing to the glandular and non-glandular manifestations of SS and to potential therapeutic targets for different SS subtypes. In addition, our analysis highlights the need for further exploration of altered metabolism and mitochondrial dysfunction in the context of SS subtypes.

Mechanisms underlying detection of seed dormancy by a scatter-hoarding rodent.

The mechanism underlying detection of seed dormancy by scatter-hoarding rodents is unclear, although previous work suggests that the pericarp plays an important role in signaling dormancy status. Eastern gray squirrels (Sciurus carolinensis) consume early germinating seeds as they are more likely to perish immediately, whereas dormant seeds tend to be cached. To examine the mechanisms underlying dormancy detection, we characterized physical and chemical differences between germinating and dormant pericarps of northern red oak (Quercus rubra), American chestnut (Castanea dentata) and the BC3 hybrid of Chinese chestnut and American chestnut (Castanea mollissima × C. dentata) using scanning electron microscopy and gas chromatography- mass spectrometry. We found that, as seeds break dormancy, the wax layer on the pericarp degrades and is accompanied by the escape of lower molecular weight kernel compounds or lipid metabolism byproducts. Our field experiments showed that squirrels were 4-8 times more likely to consume seeds that were altered to remove pericarp wax coating or that were sprayed with seed chemicals. We argue that dormancy detection by scatter-hoarding rodents is a complex process involving physical cues such as loss of pericarp wax and chemical cues such as emission of olfactory cues.

A Comparative In Vivo Study of Albumin-Coated Paclitaxel Nanocrystals and Abraxane.

Nanoparticulate drug carriers exploit the enhanced permeability of tumor vasculature to achieve selective delivery of chemotherapeutic drugs. For this purpose, nanoparticles (NPs) need to circulate with a long half-life, enter tumors via the permeable vasculature and stay in tumors via favorable interactions with tumor cells. To fulfill these requirements, albumin-coated nanocrystal formulation of paclitaxel (PTX), Cim-F-alb, featuring high drug loading content, physical stability in serum, and surface-bound albumin in its native conformation is prepared. The pharmacokinetic and biodistribution (PK/BD) profiles of Cim-F-alb in a mouse model of B16F10 melanoma show that Cim-F-alb exhibits a longer plasma half-life and a greater PTX deposition in tumors than Abraxane by ≈1.5 and ≈4.6 fold, respectively. Biolayer interferometry analysis indicates that Cim-F-alb has less interaction with serum proteins than nanocrystals lacking albumin coating, indicating the protective effect of the surface-bound albumin against opsonization in the initial deposition phase. With the advantageous PK/BD profiles, Cim-F-alb shows greater and longer-lasting anticancer efficacy than Abraxane at the equivalent dose. This study demonstrates the significance of controlling circulation stability and surface property of NPs in efficient drug delivery to tumors and enhanced anticancer efficacy.

Chlorine/UV Process for Decomposition and Detoxification of Microcystin-LR.

Microcystin-LR (MC-LR) is a potent hepatotoxin that is often associated with blooms of cyanobacteria. Experiments were conducted to evaluate the efficiency of the chlorine/UV process for MC-LR decomposition and detoxification. Chlorinated MC-LR was observed to be more photoactive than MC-LR. LC/MS analyses confirmed that the arginine moiety represented an important reaction site within the MC-LR molecule for conditions of chlorination below the chlorine demand of the molecule. Prechlorination activated MC-LR toward UV254 exposure by increasing the product of the molar absorption coefficient and the quantum yield of chloro-MC-LR, relative to the unchlorinated molecule. This mechanism of decay is fundamentally different than the conventional view of chlorine/UV as an advanced oxidation process. A toxicity assay based on human liver cells indicated MC-LR degradation byproducts in the chlorine/UV process possessed less cytotoxicity than those that resulted from chlorination or UV254 irradiation applied separately. MC-LR decomposition and detoxification in this combined process were more effective at pH 8.5 than at pH 7.5 or 6.5. These results suggest that the chlorine/UV process could represent an effective strategy for control of microcystins and their associated toxicity in drinking water supplies.

UV-induced effects on chlorination of creatinine.

Ultraviolet (UV) irradiation is commonly employed for water treatment in swimming pools to complement conventional chlorination, and to reduce the concentration of inorganic chloramine compounds. The approach of combining UV irradiation and chlorination has the potential to improve water quality, as defined by microbial composition. However, relatively little is known about the effects of this process on water chemistry. To address this issue, experiments were conducted to examine the effects of sequential UV254 irradiation/chlorination, as will occur in recirculating system of swimming pools, on disinfection byproduct (DBP) formation. Creatinine, which is present in human sweat and urine, was selected as the target precursor for these experiments. Enhanced formation of dichloromethylamine (CH3NCl2) and inorganic chloramines was observed to result from post-chlorination of UV-irradiated samples. Chlorocreatinine was found to be more sensitive to UV254 irradiation than creatinine; UV254 irradiation of chlorocreatinine resulted in opening of the ring structure, thereby yielding a series of intermediates that were more susceptible to free chlorine attack than their parent compound. The quantum yields for photodegradation of creatinine and chlorocreatinine at 254 nm were estimated at 0.011 ± 0.002 mol/E and 0.144 ± 0.011 mol/E, respectively. The N-Cl bond was found to be common to UV-sensitive chlorinated compounds (e.g., inorganic chloramines, CH3NCl2, and chlorocreatinine); compounds that were less susceptible to UV-based attack generally lacked the N-Cl bond. This suggested that the N-Cl bond is susceptible to UV254 irradiation, and cleavage of the N-Cl bond appears to open or promote reaction pathways that involve free chlorine, thereby enhancing formation of some DBPs and promoting loss of free chlorine. Proposed reaction mechanisms to describe this behavior based on creatinine as a precursor are presented.

Structural analysis of succinoglycan oligosaccharides from Sinorhizobium meliloti strains with different host compatibility phenotypes.

Sinorhizobium meliloti NRG247 has a Fix(+) phenotype on Medicago truncatula A20 and is Fix(-) on M. truncatula A17, and the phenotype is reversed with S. meliloti NRG185. As the succinoglycan was shown to impact host specificity, an analysis of the succinoglycan oligosaccharides produced by each strain was conducted. The symbiotically active succinoglycan trimeric oligosaccharides (STOs) from the two S. meliloti strains were compared by chromatography and mass spectrometry, and the analysis of the S. meliloti NRG247 oligosaccharides showed that this strain produces an abundance of STO trimer 1 (T1), containing no succinate (i.e., three nonsuccinylated repeats), yet the low-molecular-weight pool contained no nonsuccinylated monomers (potential repeats). This showed that STO T1 is likely to be the active signal on M. truncatula A20 and that the biosynthesis of the STOs is not a random polymerization of the monomer population. The results also suggest that the fully succinylated STO T7 is required for the infection of M. truncatula A17.

Quantitative and qualitative analyses of human salivary NEFA with gas-chromatography and mass spectrometry.

Salivary non-esterified fatty acids (NEFA) are proposed to play a role in oral health, oral fat detection, and they may hold diagnostic and prognostic potential. Yet, little is known about the array and concentrations of NEFA in saliva. The aim of the study was to conduct qualitative and quantitative analyses of salivary NEFA in healthy humans and to present a new, efficient protocol to perform such analyses. Resting saliva samples from fifteen participants were collected. The salivary lipids were extracted using a modified Folch extraction. The NEFA in the extracted lipids were selectively subjected to pentafluorobenzyl bromide (PFB) derivatization and qualitatively and quantitatively analyzed using gas chromatography-mass spectrometry (GC-MS). A total of 16 NEFA were identified in resting saliva. The four major NEFA were palmitic, linoleic, oleic, and stearic acids. Their concentrations ranged from 2 to 9 µM. This is the first study to characterize individual human salivary NEFA and their respective concentrations. The method used in the study is sensitive, precise, and accurate. It is specific to fatty acids in non-esterified form and hence enables analysis of NEFA without their separation from other lipid classes. Thus, it saves time, reagents and prevents loss of sample. These properties make it suitable for large scale analysis of salivary NEFA.

Accidental amplification and inactivation of a methyltransferase gene eliminates cytosine methylation in Mycosphaerella graminicola.

A de novo search for repetitive elements in the genome sequence of the wheat pathogen Mycosphaerella graminicola identified a family of repeats containing a DNA cytosine methyltransferase sequence (MgDNMT). All 23 MgDNMT sequences identified carried signatures of repeat induced point mutation (RIP). All copies were subtelomeric in location except for one on chromosome 6. Synteny with M. fijiensis implied that the nontelomeric copy on chromosome 6 served as a template for subsequent amplifications. Southern analysis revealed that the MgDNMT sequence also was amplified in 15 additional M. graminicola isolates from various geographical regions. However, this amplification event was specific to M. graminicola; a search for MgDNMT homologs identified only a single, unmutated copy in the genomes of 11 other ascomycetes. A genome-wide methylation assay revealed that M. graminicola lacks cytosine methylation, as expected if its MgDNMT gene is inactivated. Methylation was present in several other species tested, including the closest known relatives of M. graminicola, species S1 and S2. Therefore, the observed changes most likely occurred within the past 10,500 years since the divergence between M. graminicola and S1. Our data indicate that the recent amplification of a single-copy MgDNMT gene made it susceptible to RIP, resulting in complete loss of cytosine methylation in M. graminicola.

Metabolic fingerprint of Brazilian maize landraces silk (stigma/styles) using NMR spectroscopy and chemometric methods.

Aqueous extract from maize silks is used by traditional medicine for the treatment of several ailments, mainly related to the urinary system. This work focuses on the application of NMR spectroscopy and chemometric analysis for the determination of metabolic fingerprint and pattern recognition of silk extracts from seven maize landraces cultivated in southern Brazil. Principal component analysis (PCA) of the (1)H NMR data set showed clear discrimination among the maize varieties by PC1 and PC2, pointing out three distinct metabolic profiles. Target compounds analysis showed significant differences (p < 0.05) in the contents of protocatechuic acid, gallic acid, t-cinnamic acid, and anthocyanins, corroborating the discrimination of the genotypes in this study as revealed by PCA analysis. Thus the combination of (1)H NMR and PCA is a useful tool for the discrimination of maize silks in respect to their chemical composition, including rapid authentication of the raw material of current pharmacological interest.

Addition of nimesulide to small intestinal submucosa biomaterial inhibits postsurgical adhesiogenesis in rats.

Adhesion formation is a common complication in abdominal surgery with incidence as high as 93% and small bowel obstruction a common complication. Because the extracellular matrix material, small intestinal submucosa (SIS), is commonly used in various surgical procedures, methods to inhibit adhesiogenesis are of great interest. This study was undertaken to determine if incorporation of nimesulide (NM), a selective cyclooxygenase (COX)-2 inhibitor, could reduce the extent and tenacity of intraabdominal adhesion formation associated with SIS implantation. Female Sprague-Dawley rats underwent a cecal abrasion surgical procedure to induce adhesiogenesis. Rats were either left untreated or treated by direct application over the injured cecum with polypropylene mesh (PPM); SIS; SIS containing a low dose of NM; or SIS containing a high dose of NM. Rats were euthanized 21 days later, and adhesion extent and tenacity were evaluated using standard scales (0 = minimal adhesiogenesis; 4 = severe adhesiogenesis). Addition of NM to SIS resulted in a significant (p < 0.05) reduction in adhesion extent and in a similar reduction in adhesion tenacity for SIS containing a low dose of NM. Adhesions typically extended from the abraded cecal surface to the body wall and were characterized histologically by fibrous tissue adherent to the cecal wall. In conclusion, addition of the nonsteroidal anti-inflammatory, COX-2 selective drug, NM, to SIS attenuates adhesion extent and tenacity when compared with surgical placement of SIS or PPM alone.

Metabolomic analysis of Ocotea odorifera cell cultures: a model protocol for acquiring metabolite data.

Metabolomics constitutes a quantitative and qualitative survey of the whole metabolites of an organism as well as a tissue, reflecting the genome and proteome of a sample as analyzed. Advanced analytical spectroscopic and chromatographic techniques are used along with uni- or multivariate statistical data analysis, rapidly identifying up- or down-regulated metabolites in complex matrices. In this chapter, protocols for the analysis of target compounds (protocol I) and metabolomics (protocol II) of Ocotea odorifera cell cultures are described. In the first case, the target compound safrole, an aromatic ether used as a flavoring agent and also in the manufacture of insecticides, is analyzed in the organosolvent fraction of stable prototrophic cell lines of O. odorifera by gas chromatography-mass spectrometry. For metabolomics studies the protocol is designed to detect and quantify metabolites in the aqueous extract of O. odorifera cell lines by using high-resolution 1D- and 2D-nuclear magnetic resonance spectroscopy, followed by chemometric analysis of the 1H NMR spectra dataset. Protocol I has been successfully used, for example, in screening studies of cell lines able of producing safrole. Protocol II is suitable to detect the chemical features of a number of metabolite compounds in aqueous extracts of O. odorifera cell lines cultured under certain conditions, leading to new insights into metabolomics of that species.

Solid-phase synthesis of alpha-glucosamine sulfoforms with fragmentation analysis by tandem mass spectrometry.

Sulfated epitopes of alpha-glucosamine (GlcN sulfoforms) were prepared by solid-phase synthesis as models of internal glucosamines within heparan sulfate. An orthogonally protected 2'-hydroxyethyl GlcN derivative was immobilized on a trityl resin support and subjected to regioselective deprotection and sulfonation conditions, which were optimized with the aid of on-resin infrared or Raman analysis. The sulfoforms were cleaved from the resin under mild Lewis acid conditions without affecting the O- or N-sulfate groups and purified by reversed-phase high-performance liquid chromatography (HPLC). The alpha-GlcN sulfoforms and their 4- O-benzyl ethers were examined by electrospray ionization tandem mass spectrometry (ESI-MS/MS), with product ion spectra produced by collision-induced dissociation (CID). ESI-MS/MS revealed significant differences in parent ion stabilities and fragmentation rates as a function of sulfate position. Ion fragmentation by CID resulted in characteristic mass losses with strong correlation to the positions of both free hydroxyl groups and sulfate ions. Most of these fragmentation patterns are consonant with elimination pathways, and suggest possible strategies for elucidating the structures of glucosamine-derived sulfoforms with identical m/ z ratios. In particular, fragmentation analysis can easily distinguish GlcN sulfoforms bearing the relatively rare 3- O-sulfate from isomers with the more common 6- O-sulfate.

Methionine sulfoxide reductase A protects dopaminergic cells from Parkinson's disease-related insults.

Parkinson's disease (PD) is a neurologic disorder characterized by dopaminergic cell death in the substantia nigra. PD pathogenesis involves mitochondrial dysfunction, proteasome impairment, and alpha-synuclein aggregation, insults that may be especially toxic to oxidatively stressed cells including dopaminergic neurons. The enzyme methionine sulfoxide reductase A (MsrA) plays a critical role in the antioxidant response by repairing methionine-oxidized proteins and by participating in cycles of methionine oxidation and reduction that have the net effect of consuming reactive oxygen species. Here, we show that MsrA suppresses dopaminergic cell death and protein aggregation induced by the complex I inhibitor rotenone or mutant alpha-synuclein, but not by the proteasome inhibitor MG132. By comparing the effects of MsrA and the small-molecule antioxidants N-acetylcysteine and vitamin E, we provide evidence that MsrA protects against PD-related stresses primarily via methionine sulfoxide repair rather than by scavenging reactive oxygen species. We also demonstrate that MsrA efficiently reduces oxidized methionine residues in recombinant alpha-synuclein. These findings suggest that enhancing MsrA function may be a reasonable therapeutic strategy in PD.

Hydrolysis of thioesters in an ion trap.

The alkenyldiarylmethanes are a class of non-nucleoside reverse transcriptase inhibitors that are currently being developed as potential antivirals for the treatment of HIV infection and AIDS. As part of our continuing investigations on the alkenyldiarylmethanes, a series of thioester analogues were prepared in an effort to improve upon the metabolic stability of the parent lead compound. Hydrolysis of the thioester moieties was consistently observed during ion trap electrospray ionization (ESI) mass spectrometry to the extent that the parent molecular ion was weak in intensity or simply could not be detected. The same hydrolysis observations were also made when the analogues were analyzed by ion trap electron impact (EI) ionization, indicating the hydrolysis event was the result of the ion trap and not ionization technique. Ion-trap-mediated hydrolysis has been observed previously in prior alkenyldiarylmethane studies and prevented characterization of certain intermediates; thus, we wished to investigate whether modifying instrument parameters and protocols affected the instrument-mediated hydrolysis event. Unfortunately, varying the maximum injection time and the number of microscans performed, independent of each other, had little effect on the intensities of the parent ions [MH(+)] or the hydrolysis products] MH(+) -HSCH(3)].

Identification and quantitation of novel vitamin E metabolites, sulfated long-chain carboxychromanols, in human A549 cells and in rats.

The metabolism of vitamin E involves oxidation of the phytyl chain to generate the terminal metabolite 7,8-dimethyl-2-(beta-carboxyethyl)-6-hydroxychroman (CEHC) via intermediate formation of 13'-hydroxychromanol and long-chain carboxychromanols. Conjugated (including sulfated) metabolites were reported previously but were limited to CEHCs. Here, using electrospray and inductively coupled plasma mass spectrometry, we discovered that gamma-tocopherol (gamma-T) and delta-T were metabolized to sulfated 9'-, 11'-, and 13'-carboxychromanol (9'S, 11'S, and 13'S) in human A549 cells. To further study the metabolites, we developed a HPLC assay with fluorescence detection that simultaneously analyzes sulfated and nonconjugated intermediate metabolites. Using this assay, we found that sulfated metabolites were converted to nonconjugated carboxychromanols by sulfatase digestion. In cultured cells, approximately 45% long-chain carboxychromanols from gamma-T but only 10% from delta-T were sulfated. Upon supplementation with gamma-T, rats had increased tissue levels of 9'S, 11'S, and 13'S, 13'-hydroxychromanol, 13'-carboxychromanol, and gamma-CEHC. The plasma concentrations of combined sulfated long-chain metabolites were comparable to or exceeded those of CEHCs and increased proportionally with the supplement dosages of gamma-T. Our study identifies sulfated long-chain carboxychromanols as novel vitamin E metabolites and provides evidence that sulfation may occur parallel with beta-oxidation. In addition, the HPLC fluorescence assay is a useful tool for the investigation of vitamin E metabolism.

High-throughput analysis of catechins and theaflavins by high performance liquid chromatography with diode array detection.

Increased interest in potential health-protective activities of flavonoid-rich tea has created the need to take advantage of HPLC column and system advances in order to optimize methodologies for flavonoid analysis. Two new RP-C18 methods for HPLC-DAD analysis of tea flavonoids were developed to facilitate separation of catechins within 5 min and separation of catechins and theaflavins within 10 min total analysis time. Calibration results indicate that these methods have on-column limits of detection on the order of 1-10 pmol for most tea catechins, and method replication generally resulted in intraday and interday peak area variation of <5% for catechins and <9% for theaflavins in green and black tea infusions. These new methods are therefore sensitive, reproducible, and represent a 2-4-fold reduction in HPLC analysis time from existing analytical methods. These improvements are readily achievable with commonly used HPLC equipment, thus facilitating increased sample throughput and efficiency across a broad range of experimental applications.

Measuring calcium absorption and utilization in humans.

PURPOSE OF REVIEW: Calcium metabolism is comprised primarily of absorption, urinary excretion, endogenous secretion and bone turnover. This review evaluates recent findings relating to the role of genetic and environmental factors, especially diet, on perturbing parameters of calcium metabolism. Calcium dynamics are studied with the use of isotopic tracers. We also cover state-of-the-art methods for stable calcium isotope ratio analysis and offer insights on experimental design. RECENT FINDINGS: Some progress has been made identifying genetic and hormonal regulators of calcium absorption. Much progress has been made in understanding the role of diet on influencing calcium retention, especially with regard to dietary protein and salt. Long-held views on dietary factors thought to contribute to bone loss through urinary calcium loss have been shown to have no impact on net calcium retention because of compensatory changes in other aspects of calcium metabolism. SUMMARY: Much more work needs to be done on understanding genetic regulators of calcium metabolism. Despite recent advances in our knowledge of dietary influences on calcium metabolism, more studies are needed on the role of environmental factors, especially physical activity.

Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation.

We have isolated and characterized Petunia hybrida cv. Mitchell phenylacetaldehyde synthase (PAAS), which catalyzes the formation of phenylacetaldehyde, a constituent of floral scent. PAAS is a cytosolic homotetrameric enzyme that belongs to group II pyridoxal 5'-phosphate-dependent amino-acid decarboxylases and shares extensive amino acid identity (approximately 65%) with plant L-tyrosine/3,4-dihydroxy-L-phenylalanine and L-tryptophan decarboxylases. It displays a strict specificity for phenylalanine with an apparent Km of 1.2 mM. PAAS is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts.

Metabolic engineering of the phenylpropanoid pathway in Saccharomyces cerevisiae.

Flavonoids are valuable natural products derived from the phenylpropanoid pathway. The objective of this study was to create a host for the biosynthesis of naringenin, the central precursor of many flavonoids. This was accomplished by introducing the phenylpropanoid pathway with the genes for phenylalanine ammonia lyase (PAL) from Rhodosporidium toruloides, 4-coumarate:coenzyme A (CoA) ligase (4CL) from Arabidopsis thaliana, and chalcone synthase (CHS) from Hypericum androsaemum into two Saccharomyces cerevisiae strains, namely, AH22 and a pad1 knockout mutant. Each gene was cloned and inserted into an expression vector under the control of a separate individual GAL10 promoter. Besides its PAL activity, the recombinant PAL enzyme showed tyrosine ammonia lyase activity, which enabled the biosynthesis of naringenin without introducing cinnamate 4-hydroxylase (C4H). 4CL catalyzed the conversion of both trans-cinnamic acid and p-coumaric acid to their corresponding CoA products, which were further converted to pinocembrin chalcone and naringenin chalcone by CHS. These chalcones were cyclized to pinocembrin and naringenin. The yeast AH22 strain coexpressing PAL, 4CL, and CHS produced approximately 7 mg liter(-1) of naringenin and 0.8 mg liter(-1) of pinocembrin. Several by-products, such as 2',4',6'-trihydroxydihydrochalcone and phloretin, were also identified. Precursor feeding studies indicated that metabolic flux to the engineered flavonoid pathway was limited by the flux to the precursor l-tyrosine.

New approach for analysis of the phosphotyrosine proteome and its application to the chicken B cell line, DT40.

In this study, we have begun to analyze phosphotyrosyl and associated proteins present in a DT40 chicken B cell line overexpressing the nonreceptor protein-tyrosine kinase, Syk. An anti-phosphotyrosine antibody was used to select tyrosine-phosphorylated proteins. After tryptic digestion, peptides were subjected to a beta-elimination reaction and phosphotyrosine-containing peptides were enriched via immobilized metal affinity chromatography. Several known substrates and candidate substrates for Syk and the location of 22 tyrosine phosphorylation sites were identified.