Proton (1H) magnetic resonance spectroscopy: absolute metabolite concentrations in normal aging human brain at 3Tesla

Session - Normal Aging Brain: Computer 90 (Tuesday)OBJECTIVES: Absolute quantitation of metabolite levels of normal aging human brain has rarely been done. But using a 3T scanner, which provides better signal-to-noise ratio, spectrum with higher resolution can be obtained. MRS can explore aging at a molecular level but controversial findings had been reported in previous frontal lobe studies [1,2] In this study, we investigate in the relationship between regional concentrations of …published_or_final_versionThe 19th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM 2011), Montreal, QC., 7-13 May 2011. In Proceedings of the 19th ISMRM, 2011, v. 19, p. 404

Formation and Dissociation of Phosphorylated Peptide Radical Cations

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Fully Automatable Two-dimensional HILIC–RP Liquid Chromatography with Online Tandem Mass Spectrometry for Shotgun Proteomics

Poster PresentationConference theme: Proteomics: Better for lifeMultidimensional liquid chromatography (MDLC) which multiples the resolution power of individual dimension with high orthogonality is a very efficient front-end separation method for analyzing the digests of complex biological samples. Among the existing two dimensional liquid chromatography (2DLC) systems, the combination of hydrophilic interaction liquid chromatography (HILIC) followed by low-pH reversed-phase (RP)LC (HILIC-RP) has very high orthogonality and is a very promising 2DLC method. Herein, a fully automatable two-dimensional (2D) liquid chromatography system was developed for shotgun proteomics analyses, which coupling the hydrophilic interaction liquid chromatography (HILIC) TSKgel Amide 80 (a non-ionic type) with the low-pH reversedphase (RP) chromatography. The performance of the 2D HILIC-RP LC platform was investigated at both pH 6.8 (neutral pH) and pH 2.7 (acidic pH) of the first dimension HILIC column by duplicate analyses of a Rat pheochromocytoma lysates.Online coupling of the neutral-pH HILIC and RP systems outperformedthe acidic HILIC–RP combination,resulting in 18.4% (1914 versus 1617 nonredundant proteins) and 41.6% (12,989 versus 9172unique peptides) increases in the number of identified proteins and peptides. To further test the established 2D HILIC-RP platform, we identified 2648 non-redundant proteins from triplicate analyses of a Saccharomyces cerevisiae lysate, with the detected protein abundances spanning from approximately41 to 106 copies per cell, which contained up to 2164 different validated protein species with a dynamic range of concentrations up to approximately 104. Herein, this studyestablished a fully automated 2D liquid chromatography platform to enable onlinecoupling of different HILIC and RP chromatography systems, thereby expanding the choice and application of multidimensional liquid chromatography for shotgun proteomics.published_or_final_versio

Normal-State Spin Dynamics and Temperature-Dependent Spin Resonance Energy in an Optimally Doped Iron Arsenide Superconductor

The proximity of superconductivity and antiferromagnetism in the phase diagram of iron arsenides, the apparently weak electron-phonon coupling and the "resonance peak" in the superconducting spin excitation spectrum have fostered the hypothesis of magnetically mediated Cooper pairing. However, since most theories of superconductivity are based on a pairing boson of sufficient spectral weight in the normal state, detailed knowledge of the spin excitation spectrum above the superconducting transition temperature Tc is required to assess the viability of this hypothesis. Using inelastic neutron scattering we have studied the spin excitations in optimally doped BaFe1.85Co0.15As2 (Tc = 25 K) over a wide range of temperatures and energies. We present the results in absolute units and find that the normal state spectrum carries a weight comparable to underdoped cuprates. In contrast to cuprates, however, the spectrum agrees well with predictions of the theory of nearly antiferromagnetic metals, without complications arising from a pseudogap or competing incommensurate spin-modulated phases. We also show that the temperature evolution of the resonance energy follows the superconducting energy gap, as expected from conventional Fermi-liquid approaches. Our observations point to a surprisingly simple theoretical description of the spin dynamics in the iron arsenides and provide a solid foundation for models of magnetically mediated superconductivity.Comment: 8 pages, 4 figures, and an animatio

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Acidithiobacillus thiooxidans secretome containing a newly described lipoprotein Licanantase enhances chalcopyrite bioleaching rate

The nature of the mineral–bacteria interphase where electron and mass transfer processes occur is a key element of the bioleaching processes of sulfide minerals. This interphase is composed of proteins, metabolites, and other compounds embedded in extracellular polymeric substances mainly consisting of sugars and lipids (Gehrke et al., Appl Environ Microbiol 64(7):2743–2747, 1998). On this respect, despite Acidithiobacilli—a ubiquitous bacterial genera in bioleaching processes (Rawlings, Microb Cell Fact 4(1):13, 2005)—has long been recognized as secreting bacteria (Jones and Starkey, J Bacteriol 82:788–789, 1961; Schaeffer and Umbreit, J Bacteriol 85:492–493, 1963), few studies have been carried out in order to clarify the nature and the role of the secreted protein component: the secretome. This work characterizes for the first time the sulfur (meta)secretome of Acidithiobacillus thiooxidans strain DSM 17318 in pure and mixed cultures with Acidithiobacillus ferrooxidans DSM 16786, identifying the major component of these secreted fractions as a single lipoprotein named here as Licanantase. Bioleaching assays with the addition of Licanantase-enriched concentrated secretome fractions show that this newly found lipoprotein as an active protein additive exerts an increasing effect on chalcopyrite bioleaching rate

Using haloperidol as an anti-emetic in palliative care: informing practice through evidence from cancer treatment and post-operative contexts

YesNausea and vomiting are common symptoms in palliative care. Haloperidol is often used as an antiemetic in this context, although direct evidence supporting this practice is limited. To evaluate the efficacy and clinical use of haloperidol as an antiemetic in nonpalliative care contexts to inform practice, the authors conducted a rapid review of (i) published evidence to supplement existing systematic reviews, and (ii) practical aspects affecting the use of haloperidol including formulations and doses that are commonly available internationally. In nausea and vomiting related to cancer treatment, haloperidol was superior to control in two small studies. In postoperative nausea and vomiting (PONV), two randomized controlledtrials found treatment with haloperidol comparable to ondansetron. In palliative care, an observational study found a complete response rate of 24% with haloperidol (one in four patients) which would be consistent with a number needed to treat (NNT) of 3 to 5 derived from PONV. There remains insufficient direct evidence to definitively support the use of haloperidol for the management of nausea and vomiting in palliative care. However, generalizing evidence from other clinical contexts may have some validity

The Endogenous Th17 Response in NO<inf>2</inf>-Promoted Allergic Airway Disease Is Dispensable for Airway Hyperresponsiveness and Distinct from Th17 Adoptive Transfer

Severe, glucocorticoid-resistant asthma comprises 5-7% of patients with asthma. IL-17 is a biomarker of severe asthma, and the adoptive transfer of Th17 cells in mice is sufficient to induce glucocorticoid-resistant allergic airway disease. Nitrogen dioxide (NO2) is an environmental toxin that correlates with asthma severity, exacerbation, and risk of adverse outcomes. Mice that are allergically sensitized to the antigen ovalbumin by exposure to NO2 exhibit a mixed Th2/Th17 adaptive immune response and eosinophil and neutrophil recruitment to the airway following antigen challenge, a phenotype reminiscent of severe clinical asthma. Because IL-1 receptor (IL-1R) signaling is critical in the generation of the Th17 response in vivo, we hypothesized that the IL-1R/Th17 axis contributes to pulmonary inflammation and airway hyperresponsiveness (AHR) in NO2-promoted allergic airway disease and manifests in glucocorticoid-resistant cytokine production. IL-17A neutralization at the time of antigen challenge or genetic deficiency in IL-1R resulted in decreased neutrophil recruitment to the airway following antigen challenge but did not protect against the development of AHR. Instead, IL-1R-/- mice developed exacerbated AHR compared to WT mice. Lung cells from NO2-allergically inflamed mice that were treated in vitro with dexamethasone (Dex) during antigen restimulation exhibited reduced Th17 cytokine production, whereas Th17 cytokine production by lung cells from recipient mice of in vitro Th17-polarized OTII T-cells was resistant to Dex. These results demonstrate that the IL-1R/Th17 axis does not contribute to AHR development in NO2-promoted allergic airway disease, that Th17 adoptive transfer does not necessarily reflect an endogenously-generated Th17 response, and that functions of Th17 responses are contingent on the experimental conditions in which they are generated. © 2013 Martin et al

Survey of CF mutations in the clinical laboratory

BACKGROUND: Since it is impossible to sequence the complete CFTR gene routinely, clinical laboratories must rely on test systems that screen for a panel of the most frequent mutations causing disease in a high percentage of patients. Thus, in a cohort of 257 persons that were referred to our laboratory for analysis of CF gene mutations, reverse line probe assays for the most common CF mutations were performed. These techniques were evaluated as routine first-line analyses of the CFTR gene status. METHODS: DNA from whole blood specimens was extracted and subjected to PCR amplification of 9 exons and 6 introns of the CFTR gene. The resulting amplicons were hybridised to probes for CF mutations and polymorphisms, immobilised on membranes supplied by Roche Molecular Systems, Inc. and Innogenetics, Inc.. Denaturing gradient gel electrophoresis and sequencing of suspicious fragments indicating mutations were done with CF exon and intron specific primers. RESULTS: Of the 257 persons tested over the last three years (referrals based on 1) clinical symptoms typical for/indicative of CF, 2) indication for in vitro fertilisation, and 3) gene status determination because of anticipated parenthood and partners or relatives affected by CF), the reverse line blots detected heterozygote or homozygote mutations in the CFTR gene in 68 persons (26%). Eighty-three percent of those affected were heterozygous (47 persons) or homozygous (10 persons) for the ΔF508 allele. The only other CF-alleles that we found with these tests were the G542X allele (3 persons), the G551D allele (3 persons), the 3849+10kb C-T allele (2 persons) the R117H allele (2 persons) and the 621+1G-T allele (1 person). Of the fifteen IVS8-5T-polymorphisms detected in intron 8, seven (47%) were found in males referred to us from IVF clinics. These seven 5T-alleles were all coupled with a heterozygous ΔF508 allele, they make up 35% of the males with fertility problems (20 men) referred to us. CONCLUSIONS: In summary, the frequency of CF chromosomes in the cohort examined with these tests was 26%, with the ΔF508 allele affecting 83% of the CF chromosomes. It is a substantial improvement for routine CF diagnostics to have available a test system for 30 mutations plus the polypyrimidine length variants in intron 8. Our results show that this test system allows a routine first-line analyses of the CFTR gene status