Combined in vivo metabolic effects of quetiapine and methadone in brain and blood of rats

Changes in pharmacokinetics and endogenous metabolites may underlie additive biological effects of concomitant use of antipsychotics and opioids. In this study, we employed untargeted metabolomics analysis and targeted analysis to examine the changes in drug metabolites and endogenous metabolites in the prefrontal cortex (PFC), midbrain, and blood of rats following acute co-administration of quetiapine and methadone. Rats were divided into four groups and received cumulative increasing doses of quetiapine (QTP), methadone (MTD), quetiapine + methadone (QTP + MTD), or vehicle (control). All samples were analyzed using liquid chromatography-mass spectrometry (LC-MS). Our findings revealed increased levels of the quetiapine metabolites: Norquetiapine, O-dealkylquetiapine, 7-hydroxyquetiapine, and quetiapine sulfoxide, in the blood and brain when methadone was present. Our study also demonstrated a decrease in methadone and its metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP) in the rat brain when quetiapine was present. Despite these findings, there were only small differences in the levels of 225-296 measured endogenous metabolites due to co-administration compared to single administrations. For example, N-methylglutamic acid, glutaric acid, p-hydroxyphenyllactic acid, and corticosterone levels were significantly decreased in the brain of rats treated with both compounds. Accumulation of serotonin in the midbrain was additionally observed in the MTD group, but not in the QTP + MTD group. In conclusion, this study in rats suggests a few but important additive metabolic effects when quetiapine and methadone are co-administered.

Assessment of XCMS Optimization Methods with Machine-Learning Performance

The metabolomics field is under rapid development. In particular, biomarker identification and pathway analysis are growing, as untargeted metabolomics is usable for discovery research. Frequently, new processing and statistical strategies are proposed to accommodate the increasing demand for robust and standardized data. One such algorithm is XCMS, which processes raw data into integrated peaks. Multiple studies have tried to assess the effect of optimizing XCMS parameters, but it is challenging to quantify the quality of the XCMS output. In this study, we investigate the effect of two automated optimization tools (Autotuner and isotopologue parameter optimization (IPO)) using the prediction power of machine learning as a proxy for the quality of the data set. We show that optimized parameters outperform default XCMS settings and that manually chosen parameters by liquid chromatography-mass spectrometry (LC-MS) experts remain the best. Finally, the machine-learning approach of quality assessment is proposed for future evaluations of newly developed optimization methods because its performance directly measures the retained signal upon preprocessing.

Postprandial PYY increase by resistant starch supplementation is independent of net portal appearance of short-chain fatty acids in pigs

Increased dietary fiber (DF) fermentation and short-chain fatty acid (SCFA) production may stimulate peptide tyrosine-tyrosine (PYY) secretion. In this study, the effects of hindgut SCFA production on postprandial PYY plasma levels were assessed using different experimental diets in a porto-arterial catheterized pig model. The pigs were fed experimental diets varying in source and levels of DF for one week in 3×3 Latin square designs. The DF sources were whole-wheat grain, wheat aleurone, rye aleurone-rich flour, rye flakes, and resistant starch. Postprandial blood samples were collected from the catheters and analyzed for PYY levels and net portal appearance (NPA) of PYY was correlated to NPA of SCFA. No significant effects of diets on NPA of PYY were observed (P > 0.05), however, resistant starch supplementation increased postprandial NPA of PYY levels by 37 to 54% compared with rye-based and Western-style control diets (P = 0.19). This increase was caused by higher mesenteric artery and portal vein PYY plasma levels (P < 0.001) and was independent of SCFA absorption (P > 0.05). The PYY levels were higher in response to the second daily meal compared with the first daily meal (P < 0.001), but similar among diets (P > 0.10). In conclusion, the increased postprandial PYY responses in pigs fed with different levels and sources of DF are not caused by an increased SCFA absorption and suggest that other mechanisms such as neural reflexes and possibly an increased flow of digesta in the small intestine may be involved. The content of DF and SCFA production did not affect PYY levels.

Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach

Knowledge about identity and function of extracellular polymeric substances (EPS) in complex microbial communities is sparse, although these components have a large influence on the function of the microbial communities. We investigated the presence of selected genes potentially involved in EPS production in a 145 Mbp metagenome prepared by Illumina sequencing from a full-scale wastewater treatment plant carrying out enhanced biological phosphorus removal (EBPR). A range of genes involved in alginate production was identified and assigned mainly to bacteria from the phylum Bacteroidetes. Furthermore, several proteins in the EPS matrix were extracted, purified and identified by mass spectrometry. By using the metagenome as a reference for the metaproteomic analysis, more proteins were identified compared to using only publicly available databases. This illustrates the low degree of similarity between the bacteria in the EBPR community and the sequenced bacteria in the public databases. Hence, the combination of metagenomics and metaproteomics presented here is needed to investigate the identity of the proteins in the EPS matrix.

The potato tuber transcriptome: analysis of 6077 expressed sequence tags

This is the first report of the biosynthetic potential of a tuber storage organ investigated by expressed sequence tag sequencing. A cDNA library was generated from the mature tuber of field grown potato (Solanum tuberosum var. Kuras). Partial sequences obtained from 6077 clones were assembled into 828 clusters and 1533 singletons. The average read length was 592 bp, and 2254 clones were full length. 5717 clones showed homology to genes from other organisms. Genes involved in protein synthesis, protein destination and cell defense predominated in tuber compared to stolon, shoot and leaf organs. 1063 clones were unique to tuber. Transcripts of starch metabolizing enzymes showed similar relative levels in tuber and stolon.

Differential activity and structure of highly similar peroxidases. Spectroscopic, crystallographic, and enzymatic analyses of lignifying Arabidopsis thaliana peroxidase A2 and horseradish peroxidase A2

Anionic Arabidopsis thaliana peroxidase ATP A2 was expressed in Escherichia coli and used as a model for the 95% identical commercially available horseradish peroxidase HRP A2. The crystal structure of ATP A2 at 1.45 A resolution at 100 K showed a water molecule only 2.1 A from heme iron [Ostergaard, L., et al. (2000) Plant Mol. Biol. 44, 231-243], whereas spectroscopic studies of HRP A2 in solution at room temperature [Feis, A., et al. (1998) J. Raman Spectrosc. 29, 933-938] showed five-coordinated heme iron, which is common in peroxidases. Presented here, the X-ray crystallographic, single-crystal, and solution resonance Raman studies at room temperature confirmed that the sixth coordination position of heme iron of ATP A2 is essentially vacant. Furthermore, electronic absorption and resonance Raman spectroscopy showed that the heme environments of recombinant ATP A2 and glycosylated plant HRP A2 are indistinguishable at neutral and alkaline pH, from room temperature to 12 K, and are highly flexible compared with other plant peroxidases. Ostergaard et al. (2000) also demonstrated that ATP A2 expression and lignin formation coincide in Arabidopsis tissues, and docking of lignin precursors into the substrate binding site of ATP A2 predicted that coniferyl and p-coumaryl alcohols were good substrates. In contrast, the additional methoxy group of the sinapyl moiety gave rise to steric hindrance, not only in A2 type peroxidases but also in all peroxidases. We confirm these predictions for ATP A2, HRP A2, and HRP C. The specific activity of ATP A2 was lower than that of HRP A2 (pH 4-8), although a steady-state study at pH 5 demonstrated very little difference in their rate constants for reaction with H2O2 (k1 = 1.0 microM(-1) x s(-1). The oxidation of coniferyl alcohol, ferulic, p-coumaric, and sinapic acids by HRP A2, and ATP A2, however, gave modest but significantly different k3 rate constants of 8.7 +/- 0.3, 4.0 +/- 0.2, 0.70 +/- 0.03, and 0.04 +/- 0.2 microM(-1) x s(-1) for HRP A2, respectively, and 4.6 +/- 0.2, 2.3 +/- 0.1, 0.25 +/- 0.01, and 0.01 +/- 0.004 microM(-1) x s(-1) for ATP A2, respectively. The structural origin of the differential reactivity is discussed in relation to glycosylation and amino acid substitutions. The results are of general importance to the use of homologous models and structure determination at low temperatures.

The effect of phosphorus availability on the carbon economy of contrasting common bean (Phaseolus vulgaris L.) genotypes

A common response to low phosphorus availability is increased relative biomass allocation to roots. The resulting increase in root:shoot ratio presumably enhances phosphorus acquisition, but may also reduce growth rates by diverting carbon to the production of heterotrophic rather than photosynthetic tissues. To assess the importance of increased carbon allocation to roots for the adaptation of plants to low P availability, carbon budgets were constructed for four common bean genotypes with contrasting adaptation to low phosphorus availability in the field ("phosphorus efficiency"). Solid-phase-buffered silica sand provided low (1 microM), medium (10 microM), and high (30 microM) phosphorus availability. Compared to the high phosphorus treatment, plant growth was reduced by 20% by medium phosphorus availability and by more than 90% by low phosphorus availability. Low phosphorus plants utilized a significantly larger fraction of their daytime net carbon assimilation on root respiration (c. 40%) compared to medium and high phosphorus plants (c. 20%). No significant difference was found among genotypes in this respect. Genotypes also had similar rates of P absorption per unit root weight and plant growth per unit of P absorbed. However, P-efficient genotypes allocated a larger fraction of their biomass to root growth, especially under low P conditions. Efficient genotypes had lower rates of root respiration than inefficient genotypes, which enabled them to maintain greater root biomass allocation than inefficient genotypes without increasing overall root carbon costs.

The effect of phosphorus availability on the carbon economy of contrasting common bean (Phaseolus vulgaris L.) genotypes

A common response to low phosphorus availability is increased relative biomass allocation to roots. The resulting increase in root:shoot ratio presumably enhances phosphorus acquisition, but may also reduce growth rates by diverting carbon to the production of heterotrophic rather than photosynthetic tissues. To assess the importance of increased carbon allocation to roots for the adaptation of plants to low P availability, carbon budgets were constructed for four common bean genotypes with contrasting adaptation to low phosphorus availability in the field ("phosphorus efficiency"). Solid-phase-buffered silica sand provided low (1 microM), medium (10 microM), and high (30 microM) phosphorus availability. Compared to the high phosphorus treatment, plant growth was reduced by 20% by medium phosphorus availability and by more than 90% by low phosphorus availability. Low phosphorus plants utilized a significantly larger fraction of their daytime net carbon assimilation on root respiration (c. 40%) compared to medium and high phosphorus plants (c. 20%). No significant difference was found among genotypes in this respect. Genotypes also had similar rates of P absorption per unit root weight and plant growth per unit of P absorbed. However, P-efficient genotypes allocated a larger fraction of their biomass to root growth, especially under low P conditions. Efficient genotypes had lower rates of root respiration than inefficient genotypes, which enabled them to maintain greater root biomass allocation than inefficient genotypes without increasing overall root carbon costs.

A single-ring mitochondrial chaperonin (Hsp60-Hsp10) can substitute for GroEL-GroES in vivo

Chaperonins participate in the facilitated folding of a variety of proteins in vivo. To see whether the same spectrum of target proteins can be productively folded by the double-ring prokaryotic chaperonin GroEL-GroES and its single-ring human mitochondrial homolog, Hsp60-Hsp10, we expressed the latter in an Escherichia coli strain engineered so that the groE operon is under strict regulatory control. We found that expression of Hsp60-Hsp10 restores viability to cells that no longer express GroEL-GroES, formally demonstrating that Hsp60-Hsp10 can carry out all essential in vivo functions of GroEL-GroES.

A single ring is sufficient for productive chaperonin-mediated folding in vivo

Facilitated protein folding by the double toroidal bacterial chaperonin, GroEL/GroES, proceeds by a "two-stroke engine" mechanism in which an allosteric interaction between the two rings synchronizes the reaction cycle by controlling the binding and release of cochaperonin. Using chimeric chaperonin molecules assembled by fusing equatorial and apical domains derived from GroEL and its mammalian mitochondrial homolog, Hsp60, we show that productive folding by Hsp60 and its cognate cochaperonin, Hsp10, proceeds in vitro and in vivo without the formation of a two-ring structure. This simpler "one-stroke" engine works because Hsp60 has a different mechanism for the release of its cochaperonin cap and bound target protein.

Fractal geometry of bean root systems: correlations between spatial and fractal dimension

An obstacle to the study of root architecture is the difficulty of measuring and quantifying the three-dimensional configuration of roots in soil. The objective of this work was to determine if fractal geometry might be useful in estimating the three-dimensional complexity of root architecture from more accessible measurements. A set of results called projection theorems predict that the fractal dimension (FD) of a projection of a root system should be identical to the FD of roots in three-dimensional space (three-dimensional FD). To test this prediction we employed SimRoot, an explicit geometric simulation model of root growth derived from empirical measurements of common bean (Phaseolus vulgaris L.). We computed the three-dimensional FD, FD of horizontal plane intercepts (planar FD), FD of vertical line intercepts (linear FD), and FD of orthogonal projections onto planes (projected FD). Three-dimensional FD was found to differ from corresponding projected FD, suggesting that the analysis of roots grown in a narrow space or excavated and flattened prior to analysis is problematic. A log-linear relationship was found between FD of roots and spatial dimension. This log-linear relationship suggests that the three-dimensional FD of root systems may be accurately estimated from excavations and tracing of root intersections on exposed planes.

Molecular cloning of Limulus alpha 2-macroglobulin

The American horseshoe crab Limulus polyphemus contains alpha 2-macroglobulin (alpha 2M) in the hemolymph plasma and hemocytes. alpha 2M from Limulus shows many of the typical characteristics of mammalian alpha 2M, including the presence of an internal thiol-ester, reactivity with a diversity of endopeptidases, a unique proteinase-trapping mechanism, and reactivity with the mammalian alpha 2M receptor. Additionally, Limulus alpha 2M has the unique property that it regulates the limulin-based hemolytic system of the plasma. A cDNA encoding Limulus alpha 2M has been obtained from a hemocyte cDNA library. The open reading frame encodes an N-terminal signal sequence of 25 amino acid residues and a mature protein of 1482 residues. The entire amino acid sequence is similar to those of the mammalian alpha 2Ms (28-29% identity) and contains common features found in mammalian alpha 2Ms. a bait region, an internal thiol-ester site, and a receptor-binding domain. However, the N-terminal portion (positions 24-105) has no sequence similarity with those of mammalian alpha 2Ms, and it is structurally related to that of the human complement factor C8 chain, consistent with a role for Limulus alpha 2M in host defense. The component sugar analysis of Limulus alpha 2M showed the existence of a complex type of oligosaccharide chain similar to those of mammalian alpha 2M. However, unlike mammalian alpha 2M, no sialic acid was detected in Limulus alpha 2M and it contained approximately 3 mol/mol N-acetylgalactosamine, suggesting the presence of O-linked sugar chains, which have not been found in mammalian alpha 2M. Expression of alpha 2M was detected in hemocytes, but not in hepatopancreas, heart, stomach, intestine, coxal gland, brain and skeletal muscle. Furthermore, immunoblotting of large and small granules of the hemocytes with antiserum against alpha 2M indicated the presence of the alpha 2M in large granules. Trypsin-treated Limulus alpha 2M, but not the native alpha 2M, displaced methylamine-treated human 125I-alpha 2M from the human alpha 2M receptor with a Kd of 30 nM, suggesting conservation of the proteinase-clearance mechanisms between mammalian and arthropod evolutionary lineages.

Identification of residues in alpha-macroglobulins important for binding to the alpha2-macroglobulin receptor/Low density lipoprotein receptor-related protein

Variants of the receptor binding domain of both human alpha2-macroglobulin and the corresponding domain of hen egg white ovomacroglobulin have been expressed in Escherichia coli and refolded in vitro. Competition experiments with methylamine-treated alpha2-macroglobulin for binding to the multifunctional alpha2-macroglobulin receptor identify two Lys residues (residues 1370 and 1374 in human alpha2-macroglobulin) spaced by three amino acid residues as crucial for receptor binding. From this result and mutational evidence from other ligands for the alpha2-macroglobulin receptor, a tentative sequence motif for receptor binding is proposed.

Expression and refolding of a high-affinity receptor binding domain from rat alpha 1-macroglobulin

A recombinant version of the receptor binding domain of rat alpha 1-macroglobulin (RBDv) consisting of residues 1319-1474 has been expressed in E. coli. Competition experiments with 125I-labelled methylamine treated human alpha 2-macroglobulin reveal that the alpha 1-macroglobulin-RBDv exhibit the same high affinity for the alpha 2-macroglobulin receptor as the entire 40 kDa light chain from rat alpha 1-macroglobulin. It is therefore concluded, that all determinants for receptor interaction reside in the C-terminal approx. 150 residues of the alpha-macroglobulin subunit.

Receptor-binding domain of human alpha 2-macroglobulin. Expression, folding and biochemical characterization of a high-affinity recombinant derivative

A recombinant version of the receptor binding domain (RBDv) of human alpha 2-macroglobulin (alpha 2M) has been expressed in E. coli and refolded using a novel iterative procedure. RBDv (Val1299-Ala1451) is extended by 15 residues at the N-terminal side of the Lys1313-Glu papain cleavage site in human alpha 2M. RBDv contains the intra-chain bridge Cys1329-Cys1444 and is soluble and monomeric. Competition experiments with 125I-labelled methylamine-treated alpha 2M reveal that RBDv binds to the placental receptor for transformed alpha 2M with a Kd of 8 nM, i.e. the binding affinity of RBDv is of the same order of magnitude as the intrinsic affinity for binding of one domain in transformed alpha 2M to one receptor molecule.

Amino acid sequence of hen ovomacroglobulin (ovostatin) deduced from cloned cDNA

The complete amino acid sequence of the hen ovomacroglobulin (ovostatin) subunit has been determined from cDNA and partial peptide sequence analysis. Ovostatin is a tetrameric member of the alpha-macroglobulin (alpha M) family of proteins. The 4715 nt ovostatin cDNA encodes a 36- or a 16-residue signal peptide and a 1437-residue mature protein (162.2 kDa). At the protein level the overall score of sequence identity between ovostatin and mammalian alpha Ms is 39-44%, indicating an early divergence from the line leading to the mammalian alpha Ms. Ovostatin contains 56 mol glucosamine per mol subunit, and 12 of its Asn-residues are likely to be N-glycosylated. Including carbohydrate, the size of the ovostatin subunit is approx. 185 kDa. The ovostatin subunit is predicted to contain 12 intrachain disulfide bridges, and two subunits are predicted to be disulfide bound by two interchain bridges. One Cys residue may be unpaired or participate in dimer formation as a third interchain disulfide bridge. Ovostatin contains a unique 40-residue bait region. In contrast to other alpha Ms, ovostatin contains no internal beta-Cys-gamma-Glu thiol ester, as a result of a Cys-to-Asn replacement (TGC or TGT to AAT), but the Gln-moiety of the thiol ester is preserved. By comparing the sequences of the receptor binding domain in alpha Ms with the corresponding region of ovostatin possible determinants for receptor recognition of mammalian alpha Ms are proposed.

Evidence from sequence analysis that hen egg-white ovomacroglobulin (ovostatin) is devoid of an internal beta-Cys-gamma-Glu thiol ester

53 residues of the internal sequence from the proteinase-binding hen egg-white ovostatin have been determined. The stretch corresponds to residues 945-997 of human alpha 2-macroglobulin. The degree of conservation of residues of the two stretches is approx. 74%. Cys-949, being one constituent of the internal thiol ester site of members of the family of proteins related to alpha 2-macroglobulin, is an Asn-residue in hen egg-white ovostatin, but the other constituent, Gln-952, is preserved. The Cys-to-Asn substitution forms the chemical basis for the lack of thiol esters in hen egg-white ovostatin.

[Frequency of recurrence after acute herniotomy]

Ninety-one cases of emergency herniotomy are reviewed as regards the short- and long-term results. The review shows that immediate surgery does not involve any increased risk to the patient as regards mortality and recurrence rate. The frequencies of bowel resection and mortality are related to the duration of the history and the type of hernia.