Benefit and Risk Evaluation of Biased μ-Receptor Agonist Oliceridine versus Morphine.

Background: To improve understanding of the respiratory behavior of oliceridine, a μ-opioid receptor agonist that selectively engages the G-protein-coupled signaling pathway with reduced activation of the β-arrestin pathway, the authors compared its utility function with that of morphine. It was hypothesized that at equianalgesia, oliceridine will produce less respiratory depression than morphine and that this is reflected in a superior utility.

Methods: Data from a previous trial that compared the respiratory and analgesic effects of oliceridine and morphine in healthy male volunteers (n = 30) were reanalyzed.

Quantitative metabolomics using ID-MS.

Quantitative intracellular metabolite measurements are essential for systems biology and modeling of cellular metabolism. The MS-based quantification is error prone because (1) several sampling processing steps have to be performed, (2) the sample contains a complex mixture of partly compounds with the same mass and similar retention time, and (3) especially salts influence the ionization efficiency. Therefore internal standards are required, best for each measured compound.

Conservatism and adaptability during squirrel radiation: what is mandible shape telling us?

Both functional adaptation and phylogeny shape the morphology of taxa within clades. Herein we explore these two factors in an integrated way by analyzing shape and size variation in the mandible of extant squirrels using landmark-based geometric morphometrics in combination with a comparative phylogenetic analysis. Dietary specialization and locomotion were found to be reliable predictors of mandible shape, with the prediction by locomotion probably reflecting the underlying diet.

The cellulose resource matrix.

The emerging biobased economy is causing shifts from mineral fossil oil based resources towards renewable resources. Because of market mechanisms, current and new industries utilising renewable commodities, will attempt to secure their supply of resources. Cellulose is among these commodities, where large scale competition can be expected and already is observed for the traditional industries such as the paper industry.

Sustainability, polysaccharide science, and bio-economy.

At the opening of the 2nd EPNOE conference the role and responsibility of polysaccharide scientists was reflected upon and placed in the context of actual global issues like the transition process towards "sustainable bio-economy". Difficulties in the chain of communication between the different parties involved and towards the wider public was addressed. The need for change in the relations between science and the public and to go beyond the horizon of the specialization was discussed.

Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions.

Background: Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression of recombinant proteins in Pichia pastoris growing on glucose. Furthermore, transcriptional profiling analyses revealed that oxygen availability was strongly affecting ergosterol biosynthesis, central carbon metabolism and stress responses, in particular the unfolded protein response.

Galacturonic acid inhibits the growth of Saccharomyces cerevisiae on galactose, xylose, and arabinose.

The efficient fermentation of mixed substrates is essential for the microbial conversion of second-generation feedstocks, including pectin-rich waste streams such as citrus peel and sugar beet pulp. Galacturonic acid is a major constituent of hydrolysates of these pectin-rich materials. The yeast Saccharomyces cerevisiae, the main producer of bioethanol, cannot use this sugar acid.

Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes.

Our quantitative knowledge of carbon fluxes in the long slender bloodstream form (BSF) Trypanosoma brucei is mainly based on non-proliferating parasites, isolated from laboratory animals and kept in buffers. In this paper we present a carbon balance for exponentially growing bloodstream form trypanosomes. The cells grew with a doubling time of 5.

Development of quantitative metabolomics for Pichia pastoris.

Accurate, reliable and reproducible measurement of intracellular metabolite levels has become important for metabolic studies of microbial cell factories. A first critical step for metabolomic studies is the establishment of an adequate quenching and washing protocol, which ensures effective arrest of all metabolic activity and removal of extracellular metabolites, without causing leakage of metabolites from the cells. Five different procedures based on cold methanol quenching and cell separation by filtration were tested for metabolomics of Pichia pastoris regarding methanol content and temperature of the quenching solution as key parameters.

Lignin depolymerisation in supercritical carbon dioxide/acetone/water fluid for the production of aromatic chemicals.

Valorisation of lignin plays a key role in further development of lignocellulosic biorefinery processes the production of biofuels and bio-based materials. In the present study, organosolv hardwood and wheat straw lignins were converted in a supercritical fluid consisting of carbon dioxide/acetone/water (300-370°C, 100bar) to a phenolic oil consisting of oligomeric fragments and monomeric aromatic compounds with a total yield of 10-12% based on lignin. These yields are similar to the state-of-the-art technologies such as base-catalysed thermal processes applied for lignin depolymerisation.

Late Miocene insular mice from the Tusco-Sardinian palaeobioprovince provide new insights on the palaeoecology of the Oreopithecus faunas.

Oreopithecus bambolii is one of the few hominoids that evolved under insular conditions, resulting in the development of unique adaptations that have fueled an intensive debate. The palaeoenvironment associated with this great ape has been the subject of great controversy as well. On the one hand, palaeobotanical data indicate that Oreopithecus likely inhabited mixed mesophytic forests interrupted by swamps; on the other hand, an abundance of hypsodont bovids points towards the existence of dry and open environments.

Analysis of glycolytic intermediates with ion chromatography- and gas chromatography-mass spectrometry.

In this chapter, we describe a method for the quantitative analysis of glycolytic intermediates using ion chromatography-mass spectrometry (IC-MS) and gas chromatography (GC)-MS as complementary methods. With IC-MS-MS, pyruvate, glucose-6-phosphate, fructuse-6-phosphate, fructose-1,6-bisphosphate, phosphoenolpyruvate, and the sum of 2-phosphoglyceraldehyde + 3-phosphoglyceraldehyde can be quantified. With GC-MS using selected ion monitoring, glyceraldehyde-3-phosphate, dihydroxyacetonephosphate, 2-phosphoglyceraldehyde, and 3-phosphoglyceraldehyde can be analyzed.

Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics.

Accurate determination of intracellular metabolite levels requires well-validated procedures for sampling and sample treatment. Several methods exist for metabolite extraction, but the literature is contradictory regarding the adequacy and performance of each technique. Using a strictly quantitative approach, we have re-evaluated five methods (hot water, HW; boiling ethanol, BE; chloroform-methanol, CM; freezing-thawing in methanol, FTM; acidic acetonitrile-methanol, AANM) for the extraction of 44 intracellular metabolites (phosphorylated intermediates, amino acids, organic acids, nucleotides) from S.

A comprehensive method for the quantification of the non-oxidative pentose phosphate pathway intermediates in Saccharomyces cerevisiae by GC-IDMS.

A gas chromatography isotope dilution mass spectrometry (GC-IDMS) method was developed for the quantification of the metabolites of the non-oxidative part of pentose phosphate pathway (PPP). A mid-polar GC column (Zebron ZB-AAA, 10m, film composition 50% phenyl 50% dimethyl polysiloxane) was used for the chromatographic separation of the intermediates. The optimized GC-MS procedure resulted in improved separation performances and higher sensitivities compared to previous methods.

Simultaneous quantification of free nucleotides in complex biological samples using ion pair reversed phase liquid chromatography isotope dilution tandem mass spectrometry.

A new sensitive and accurate analytical method has been developed for quantification of intracellular nucleotides in complex biological samples from cultured cells of different microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Penicillium chrysogenum. This method is based on ion pair reversed phase liquid chromatography electrospray ionization isotope dilution tandem mass spectrometry (IP-LC-ESI-ID-MS/MS. A good separation and low detection limits were observed for these compounds using dibutylamine as volatile ion pair reagent in the mobile phase of the LC.

Development and application of a differential method for reliable metabolome analysis in Escherichia coli.

Quantitative metabolomics of microbial cultures requires well-designed sampling and quenching procedures. We successfully developed and applied a differential method to obtain a reliable set of metabolome data for Escherichia coli K12 MG1655 grown in steady-state, aerobic, glucose-limited chemostat cultures. From a rigorous analysis of the commonly applied quenching procedure based on cold aqueous methanol, it was concluded that it was not applicable because of release of a major part of the metabolites from the cells.

Quantitative analysis of metabolites in complex biological samples using ion-pair reversed-phase liquid chromatography-isotope dilution tandem mass spectrometry.

A rapid, sensitive and selective ion-pair reversed-phase liquid chromatography-electrospray ionization isotope dilution tandem mass spectrometry (IP-LC-ESI-ID-MS/MS) was developed for quantitative analysis of free intracellular metabolites in cell cultures. As an application a group of compounds involved in penicillin biosynthesis pathway of Penicillium chrysogenum cells, such as penicillin G (PenG), 6-aminopenicillanic acid (6-APA), benzylpenicilloic acid (PIO), ortho-hydroxyphenyl acetic acid (o-OH-PAA), phenylacetic acid (PAA), 6-oxopipeidine-2-carboxylic acid (OPC), 8-hydroxypenicillic acid (8-HPA), L-alpha-(delta-aminoadipyl)-L-alpha-cystenyl-D-alpha-valine (ACV) and isopenicillin N (IPN) were chosen. (13)C-labeled analogs of the metabolites were added to the sample solutions as internal standards (I.

Development of a TLD mailed system for remote dosimetry audit for (192)Ir HDR and PDR sources.

Background And Purpose: In the framework of an ESTRO ESQUIRE project, the BRAPHYQS Physics Network and the EQUAL-ESTRO laboratory have developed a procedure for checking the absorbed dose to water in the vicinity of HDR or PDR sources using a mailed TLD system. The methodology and the materials used in the procedure are based on the existing EQUAL-ESTRO external radiotherapy dose checks.

Materials And Methods: A phantom for TLD postal dose assurance service, adapted to accept catheters from different HDR afterloaders, has been developed.

Long-period astronomical forcing of mammal turnover.

Mammals are among the fastest-radiating groups, being characterized by a mean species lifespan of the order of 2.5 million years (Myr). The basis for this characteristic timescale of origination, extinction and turnover is not well understood.

Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse.

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O(2) uptake and CO(2) evolution.

The EQUAL-ESTRO audit on geometric reconstruction techniques in brachytherapy.

Background And Purpose: A geometric check procedure of the reconstruction techniques used in brachytherapy treatment planning systems was developed by the EQUAL (European Quality Laboratory) Laboratory in the framework of the ESTRO's (European Society for Therapeutic Radiology and Oncology) project 'ESQUIRE' (Education Science and QUality assurance In Radiotherapy in Europe [Baumann M, Brada M. Towards equity in turbulent Europe ESTRO, European cooperation and the European Commission. Radiother Oncol 2005;75:251-2.

In vivo kinetics of primary metabolism in Saccharomyces cerevisiae studied through prolonged chemostat cultivation.

In this study, prolonged chemostat cultivation is applied to investigate in vivo enzyme kinetics of Saccharomyces cerevisiae. S. cerevisiae was grown in carbon-limited aerobic chemostats for 70-95 generations, during which multiple steady states were observed, characterized by constant intracellular fluxes but significant changes in intracellular metabolite concentrations and enzyme capacities.

Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites.

Metabolic-flux analyses in microorganisms are increasingly based on (13)C-labeling data. In this paper a new approach for the measurement of (13)C-label distributions is presented: rapid sampling and quenching of microorganisms from a cultivation, followed by extraction and detection by liquid chromatography-mass spectrometry of free intracellular metabolites. This approach allows the direct assessment of mass isotopomer distributions of primary metabolites.

Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards.

A novel method was developed for the quantitative analysis of the microbial metabolome using a mixture of fully uniformly (U) (13)C-labeled metabolites as internal standard (IS) in the metabolite extraction procedure the subsequent liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. This mixture of fully U (13)C-labeled metabolites was extracted from biomass of Saccharomyces cerevisiae cultivated in a fed-batch fermentation on fully U (13)C-labeled substrates. The obtained labeled cell extract contained, in principle, the whole yeast metabolome, allowing the quantification of any intracellular metabolite of interest in S.

Analysis of in vivo kinetics of glycolysis in aerobic Saccharomyces cerevisiae by application of glucose and ethanol pulses.

This article presents the dynamic responses of several intra- and extracellular components of an aerobic, glucose-limited chemostat culture of Saccharomyces cerevisiae to glucose and ethanol pulses within a time window of 75 sec. Even though the ethanol pulse cannot perturb the glycolytic pathway directly, a distinct response of the metabolites at the lower part of glycolysis was found. We suggest that this response is an indirect effect, caused by perturbation of the NAD/NADH ratio, which is a direct consequence of the conversion of ethanol into acetaldehyde.