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 (MS² and MS³ 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, C₉H₁₄O₅ and <i>m</i> / <i>z</i> 215, C₁₀H₁₆O₅), 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 C₉- and C₁₀-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 $k$ is polynomial-time solvable for $k \leq 4$ and NP-complete for $k \geq 5$. 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 $k \geq 7$ and even $k \geq 10$. Moreover, we characterize the biconnected planar multi-graphs admitting 3- and 4-uniform embeddings (in a $k$-uniform embedding all faces have size $k$) 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 $n$ vertices has a representation in $\lceil \sqrt{n/2}+1 \rceil$ planes. In 3 dimensions, we show that there exist graphs with $6n-15$ 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 $r > 1$ countries each. We prove that the problem can be solved in polynomial time using $s$ colours on maps whose underlying adjacency graph has no induced subgraph of average degree larger than $s/r$. However, if $s \geq 3$, the problem is NP-hard even if the graph is a forest of paths of arbitrary lengths (for any $r \geq 2$, provided $s < 2r - \sqrt(2r + 1/4+ 3/2)$. 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 $r \geq 2$, if $3 \leq s \leq 2r-1$ (and polynomial time solvable otherwise). For arbitrary planar graphs we prove NP-hardness if $s<7$ for $r=2$, and $s < 6r-3$, for $r \geq 3$. The result for planar graphs also proves the NP-hardness of colouring with less than 7 colours graphs of thickness two and less than $6r-3$ colours graphs of thickness $r \geq 3$.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