120 research outputs found
Campholenic aldehyde ozonolysis: a mechanism leading to specific biogenic secondary organic aerosol constituents
In the present study, campholenic aldehyde ozonolysis was performed to
investigate pathways leading to specific biogenic secondary organic aerosol
(SOA) marker compounds. Campholenic aldehyde, a known α-pinene
oxidation product, is suggested to be a key intermediate in the formation of
terpenylic acid upon α-pinene ozonolysis. It was reacted with ozone
in the presence and absence of an OH radical scavenger, leading to SOA
formation with a yield of 0.75 and 0.8, respectively. The resulting
oxidation products in the gas and particle phases were investigated
employing a denuder/filter sampling combination. Gas-phase oxidation
products bearing a carbonyl group, which were collected by the denuder, were
derivatised by 2,4-dinitrophenylhydrazine (DNPH) followed by liquid
chromatography/negative ion electrospray ionisation time-of-flight mass
spectrometry analysis and were compared to the gas-phase compounds detected
by online proton-transfer-reaction mass spectrometry. Particle-phase
products were also analysed, directly or after DNPH derivatisation, to
derive information about specific compounds leading to SOA formation. Among
the detected compounds, the aldehydic precursor of terpenylic acid was
identified and its presence was confirmed in ambient aerosol samples from
the DNPH derivatisation, accurate mass data,
and additional mass spectrometry (MS<sup>2</sup> and MS<sup>3</sup>
fragmentation studies). Furthermore, the present investigation sheds light on
a reaction pathway leading to the formation of terpenylic acid, involving
α-pinene, α-pinene oxide, campholenic aldehyde, and
terpenylic aldehyde. Additionally, the formation of diaterpenylic acid
acetate could be connected to campholenic aldehyde oxidation. The present
study also provides insights into the source of other highly functionalised
oxidation products (e.g. <i>m</i> / <i>z</i> 201, C<sub>9</sub>H<sub>14</sub>O<sub>5</sub> and <i>m</i> / <i>z</i> 215,
C<sub>10</sub>H<sub>16</sub>O<sub>5</sub>), which have been observed in ambient aerosol
samples and smog chamber-generated monoterpene SOA. The <i>m</i> / <i>z</i> 201 and 215
compounds were tentatively identified as a C<sub>9</sub>- and
C<sub>10</sub>-carbonyl-dicarboxylic acid, respectively, based on reaction
mechanisms of campholenic aldehyde and ozone, as well as detailed interpretation of
mass spectral data, in conjunction with the formation of corresponding
DNPH derivatives
Characterisation and optimisation of a sample preparation method for the detection and quantification of atmospherically relevant carbonyl compounds in aqueous medium
Carbonyl compounds are ubiquitous in the atmosphere and either emitted primarily from anthropogenic and biogenic sources or they are produced secondarily from the oxidation of volatile organic compounds. Despite a number of studies about the quantification of carbonyl compounds a comprehensive description of optimised methods is scarce for the quantification of atmospherically relevant carbonyl compounds. The method optimisation was conducted for seven atmospherically relevant carbonyl compounds including acrolein, benzaldehyde, glyoxal, methyl glyoxal, methacrolein, methyl vinyl ketone and 2,3-butanedione. O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride (PFBHA) was used as derivatisation reagent and the formed oximes were detected by gas chromatography/mass spectrometry (GC/MS). With the present method quantification can be carried out for each carbonyl compound originating from fog, cloud and rain or sampled from the gas- and particle phase in water. Detection limits between 0.01 and 0.17 μmol L−1 were found, depending on carbonyl compounds. Furthermore, best results were found for the derivatisation with a PFBHA concentration of 0.43 mg mL−1 for 24 h followed by a subsequent extraction with dichloromethane for 30 min at pH = 1. The optimised method was evaluated in the present study by the OH radical initiated oxidation of 3-methylbutanone in the aqueous phase. Methyl glyoxal and 2,3-butanedione were found to be oxidation products in the samples with a yield of 2% for methyl glyoxal and 14% for 2,3-butanedione after a reaction time of 5 h
Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli
BACKGROUND: To maintain populations of microbial cells under controlled conditions of growth and environment for an indefinite duration is a prerequisite for experimentally evolving natural isolates of wild-type species or recombinant strains. This goal is beyond the scope of current continuous culture apparatus because these devices positively select mutants that evade dilution, primarily through attachment to vessel surfaces, resulting in persistent sub-populations of uncontrollable size and growth rate. RESULTS: To overcome this drawback, a device with two growth chambers periodically undergoing transient phases of sterilization was designed. The robustness of this device was assessed by propagating an E. coli strain under permanent thymine starvation for over 880 days, i.e. metabolic conditions notoriously known to lead to cell death and clogging of cultivation vessels. Ten thousand generations were required to obtain a descendant lineage that could resist thymine starvation and had recovered wild-type growth rate. CONCLUSIONS: This approach provides a technological framework for the diversification and improvement of microbial strains by long-term adaptation to inescapable metabolic constraints. An E. coli strain that is totally resistant to thymineless death was selected
Planar Embeddings with Small and Uniform Faces
Motivated by finding planar embeddings that lead to drawings with favorable
aesthetics, we study the problems MINMAXFACE and UNIFORMFACES of embedding a
given biconnected multi-graph such that the largest face is as small as
possible and such that all faces have the same size, respectively.
We prove a complexity dichotomy for MINMAXFACE and show that deciding whether
the maximum is at most is polynomial-time solvable for and
NP-complete for . Further, we give a 6-approximation for minimizing
the maximum face in a planar embedding. For UNIFORMFACES, we show that the
problem is NP-complete for odd and even . Moreover, we
characterize the biconnected planar multi-graphs admitting 3- and 4-uniform
embeddings (in a -uniform embedding all faces have size ) and give an
efficient algorithm for testing the existence of a 6-uniform embedding.Comment: 23 pages, 5 figures, extended version of 'Planar Embeddings with
Small and Uniform Faces' (The 25th International Symposium on Algorithms and
Computation, 2014
Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution
To ensure dosage compensation between the sexes, one randomly chosen X chromosome is silenced in each female cell in the process of X-chromosome inactivation (XCI). XCI is initiated during early development through upregulation of the long non-coding RNA Xist, which mediateschromosome-wide gene silencing. Cell differentiation, Xist upregulation and silencing are thought tobe coupled at multiple levels to ensure inactivation of exactly one out of two X chromosomes. Here we perform an integrated analysis of all three processes through allele-specific single-cellRNA-sequencing. Specifically, we assess the onset of random XCI with high temporal resolution indifferentiating mouse embryonic stem cells, and develop dedicated analysis approaches. By exploitingthe inter-cellular heterogeneity of XCI onset, we identify Nanog downregulation as its main trigger and discover additional putative Xist regulators. Moreover, we confirm several predictions of thestochastic model of XCI where monoallelic silencing is thought to be ensured through negativefeedback regulation. Finally, we show that genetic variation modulates the XCI process at multiplelevels, providing a potential explanation for the long-known Xce effect, which leads to preferentialinactivation of a specific X chromosome in inter-strain crosses. We thus draw a detailed picture of thedifferent levels of regulation that govern the initiation of XCI. The experimental and computationalstrategies we have developed here will allow us to profile random XCI in more physiological contexts,including primary human cells in vivo
Atomic matter wave scanner
We report on the experimental realization of an atom optical device, that
allows scanning of an atomic beam. We used a time-modulated evanescent wave
field above a glass surface to diffract a continuous beam of metastable Neon
atoms at grazing incidence. The diffraction angles and efficiencies were
controlled by the frequency and form of modulation, respectively. With an
optimized shape, obtained from a numerical simulation, we were able to transfer
more than 50% of the atoms into the first order beam, which we were able to
move over a range of 8 mrad.Comment: 4 pages, 4 figure
Planar projections of graphs
We introduce and study a new graph representation where vertices are embedded
in three or more dimensions, and in which the edges are drawn on the
projections onto the axis-parallel planes. We show that the complete graph on
vertices has a representation in planes. In 3
dimensions, we show that there exist graphs with edges that can be
projected onto two orthogonal planes, and that this is best possible. Finally,
we obtain bounds in terms of parameters such as geometric thickness and linear
arboricity. Using such a bound, we show that every graph of maximum degree 5
has a plane-projectable representation in 3 dimensions.Comment: Accepted at CALDAM 202
The Complexity of the Empire Colouring Problem
We investigate the computational complexity of the empire colouring problem
(as defined by Percy Heawood in 1890) for maps containing empires formed by
exactly countries each. We prove that the problem can be solved in
polynomial time using colours on maps whose underlying adjacency graph has
no induced subgraph of average degree larger than . However, if , the problem is NP-hard even if the graph is a forest of paths of arbitrary
lengths (for any , provided .
Furthermore we obtain a complete characterization of the problem's complexity
for the case when the input graph is a tree, whereas our result for arbitrary
planar graphs fall just short of a similar dichotomy. Specifically, we prove
that the empire colouring problem is NP-hard for trees, for any , if
(and polynomial time solvable otherwise). For arbitrary
planar graphs we prove NP-hardness if for , and , for . The result for planar graphs also proves the NP-hardness of colouring
with less than 7 colours graphs of thickness two and less than colours
graphs of thickness .Comment: 23 pages, 12 figure
FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data
<p>Abstract</p> <p>Background</p> <p>Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.</p> <p>Results</p> <p>To help researchers to visualize and interpret integrated genomics data, we present a novel visualization method and bioinformatics software tool called FORG3D that is based on real-time three-dimensional force-directed graphs. FORG3D can be used to visualize integrated networks of genome scale data such as interactions between genes or gene products, signaling transduction, metabolic pathways, functional interactions and evolutionary relationships. Furthermore, we demonstrate its utility by exploring gene network relationships using integrated data sets from a <it>Caenorhabditis elegans </it>Parkinson's disease model.</p> <p>Conclusion</p> <p>We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.</p
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