mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

<p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.</p> <p>Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.</p&gt

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

<p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.</p> <p>Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.</p&gt

Alternate Heegaard genus bounds distance

Suppose M is a compact orientable irreducible 3-manifold with Heegaard splitting surfaces P and Q. Then either Q is isotopic to a possibly stabilized copy of P or the Hempel distance of the splitting P is no greater than twice the genus of Q. More generally, if P and Q are bicompressible but weakly incompressible connected closed separating surfaces in M then either a) P and Q can be well-separated or b) P and Q are isotopic or c) the Hempel distance of P is no greater than twice the genus of Q.Comment: This is the version published by Geometry & Topology on 4 May 2006 (V4: typesetting correction

Isotope Labelling for Reaction Mechanism Analysis in DBD Plasma Processes

Dielectric barrier discharge (DBD) plasmas and plasma catalysis are becoming an alternative procedure to activate various gas phase reactions. A low-temperature and normal operating pressure are the main advantages of these processes, but a limited energy efficiency and little selectivity control hinder their practical implementation. In this work, we propose the use of isotope labelling to retrieve information about the intermediate reactions that may intervene during the DBD processes contributing to a decrease in their energy efficiency. The results are shown for the wet reforming reaction of methane, using D2O instead of H2O as reactant, and for the ammonia synthesis, using NH3/D2/N2 mixtures. In the two cases, it was found that a significant amount of outlet gas molecules, either reactants or products, have deuterium in their structure (e.g., HD for hydrogen, CDxHy for methane, or NDxHy for ammonia). From the analysis of the evolution of the labelled molecules as a function of power, useful information has been obtained about the exchange events of H by D atoms (or vice versa) between the plasma intermediate species. An evaluation of the number of these events revealed a significant progression with the plasma power, a tendency that is recognized to be detrimental for the energy efficiency of reactant to product transformation. The labelling technique is proposed as a useful approach for the analysis of plasma reaction mechanisms

Dual stable isotope abundances unravel trophic position of estuarine nematodes

The role and quantitative importance of free-living nematodes in marine and estuarine soft sediments remain enigmatic for lack of empirical evidence on the feeding habits and trophic position of most nematode species. Here we use natural abundances of carbon and nitrogen stable isotopes of some abundant nematode species/genera from estuarine intertidal sediments to assess their trophic level and major food sources. In all stations, d15N of different dominant nematode species/genera spanned a range of 3.6 to 6.3 ppt, indicating that at least two trophic levels were represented. The large nematodes Enoplus brevis, Enoploides longispiculosus and Adoncholaimus fuscus consistently had high d15N, in line with mouth-morphology based predictions and empirical evidence on their predacious feeding modes. Daptonema sp., Metachromadora remanei, Praeacanthonchus punctatus and ‘Chromadoridae’ (dominated by Ptycholaimellus ponticus) had comparatively lower d15N, and d13C suggesting that microphytobenthos (MPB) is their major carbon source, although freshly sedimented particulate organic matter may also contribute to their nutrition in silty sediments. The trophic position of Sphaerolaimus sp., a genus with documented predacious feeding mode, was ambiguous. Ascolaimus elongatus had d15N signatures indicating a predacious ecology, which is at variance with expectations from existing feeding type classifications. Our study shows that—despite limitations imposed by the biomass requirements for EA-IRMS (elemental analyser—isotope ratio mass spectrometry) natural isotope abundances of carbon and nitrogen are powerful tools to unravel trophic structure within nematode communities. At the same time, the prominence of different trophic levels results in a large span of d15N, largely invalidating the use of nitrogen isotope abundances to assess food sources and trophic level of whole nematode communities

Quantum SU(2) faithfully detects mapping class groups modulo center

The Jones-Witten theory gives rise to representations of the (extended) mapping class group of any closed surface Y indexed by a semi-simple Lie group G and a level k. In the case G=SU(2) these representations (denoted V_A(Y)) have a particularly simple description in terms of the Kauffman skein modules with parameter A a primitive 4r-th root of unity (r=k+2). In each of these representations (as well as the general G case), Dehn twists act as transformations of finite order, so none represents the mapping class group M(Y) faithfully. However, taken together, the quantum SU(2) representations are faithful on non-central elements of M(Y). (Note that M(Y) has non-trivial center only if Y is a sphere with 0, 1, or 2 punctures, a torus with 0, 1, or 2 punctures, or the closed surface of genus = 2.) Specifically, for a non-central h in M(Y) there is an r_0(h) such that if r>= r_0(h) and A is a primitive 4r-th root of unity then h acts projectively nontrivially on V_A(Y). Jones' [J] original representation rho_n of the braid groups B_n, sometimes called the generic q-analog-SU(2)-representation, is not known to be faithful. However, we show that any braid h not= id in B_n admits a cabling c = c_1,...,c_n so that rho_N (c(h)) not= id, N=c_1 + ... + c_n.Comment: Published by Geometry and Topology at http://www.maths.warwick.ac.uk/gt/GTVol6/paper18.abs.html Version 4: Sentence added to proof of lemma 4.1, page 536, lines 7-