An instrument to measure fast gas phase radical kinetics at hight temperatures and pressures

Fast radical reactions are central to the chemistry of planetary atmospheres and combustion systems. Laser-induced fluorescence is a highly sensitive and selective technique that can be used to monitor a number of radical species in kinetics experiments, but is typically limited to low pressure systems owing to quenching of fluorescent states at higher pressures. The design and characterisation of an instrument is reported using laser-induced fluorescence detection to monitor fast radical kinetics (up to 25,000 s-1) at high temperatures and pressures by sampling from a high pressure reaction region to a low pressure detection region. Kinetics have been characterised at temperatures reaching 740 K and pressures up to 2 atm, with expected maximum operational conditions of up to ~ 900 K and ~ 5 atm. The distance between the point of sampling from the high pressure region and the point of probing within the low pressure region is critical to the measurement of fast kinetics. The instrumentation described in this work can be applied to the measurement of kinetics relevant to atmospheric and combustion chemistry

Measurement of OH reactivity by laser flash photolysis coupled with laser-induced fluorescence spectroscopy

OH reactivity (k’OH) is the total pseudo-first-order loss rate coefficient describing the removal of OH radicals to all sinks in the atmosphere, and is the inverse of the chemical lifetime of OH. Measurements of ambient OH reactivity can be used to discover the extent to which measured OH sinks contribute to the total OH loss rate. Thus, OH reactivity measurements enable determination of the comprehensiveness of measurements used in models to predict air quality and ozone production, and, in conjunction with measurements of OH radical concentrations, to assess our understanding of OH production rates. In this work, we describe the design and characterisation of an instrument to measure OH reactivity using laser flash photolysis coupled to laser-induced fluorescence (LFP-LIF) spectroscopy. The LFP-LIF technique produces OH radicals in isolation, and thus minimises potential interferences in OH reactivity measurements owing to the reaction of HO2 with NO which can occur if HO2 is co-produced with OH in the instrument. Capabilities of the instrument for ambient OH reactivity measurements are illustrated by data collected during field campaigns in London, UK, and York, UK. The instrumental limit of detection for k’OH was determined to be 1.0 s-1 for the campaign in London and 0.4 s-1 for the campaign in York. The precision, determined by laboratory experiment, is typically < 1 s-1 for most ambient measurements of OH reactivity. Total uncertainty in ambient measurements of OH reactivity is ~6 %. We also present the coupling and characterisation of the LFP-LIF instrument to an atmospheric chamber for measurements of OH reactivity during simulated experiments, and provide suggestions for future improvements to OH reactivity LFP-LIF instruments

Pressure-dependent calibration of the OH and HO2 channels of a FAGE HOx instrument using the Highly Instrumented Reactor for Atmospheric Chemistry (HIRAC)

The calibration of field instruments used to measure concentrations of OH and HO2 worldwide has traditionally relied on a single method utilising the photolysis of water vapour in air in a flow tube at atmospheric pressure. Here the calibration of two FAGE (fluorescence assay by gaseous expansion) apparatuses designed for HOx (OH and HO2) measurements have been investigated as a function of external pressure using two different laser systems. The conventional method of generating known concentrations of HOx from H2O vapour photolysis in a turbulent flow tube impinging just outside the FAGE sample inlet has been used to study instrument sensitivity as a function of internal fluorescence cell pressure (1.8-3.8 mbar). An increase in the calibration constants CHO and CHO2 with pressure was observed, and an empirical linear regression of the data was used to describe the trends, with ΔCHO Combining double low line (17 ± 11) % and ΔCHO2 Combining double low line (31.6 ± 4.4)% increase per millibar air (uncertainties quoted to 2σ). Presented here are the first direct measurements of the FAGE calibration constants as a function of external pressure (440-1000 mbar) in a controlled environment using the University of Leeds HIRAC chamber (Highly Instrumented Reactor for Atmospheric Chemistry). Two methods were used: the temporal decay of hydrocarbons for calibration of OH, and the kinetics of the second-order recombination of HO2 for HO2 calibrations. Over comparable conditions for the FAGE cell, the two alternative methods are in good agreement with the conventional method, with the average ratio of calibration factors (conventional : alternative) across the entire pressure range, COH(conv)/COH(alt) Combining double low line 1.19 ± 0.26 and CHO2(conv)/CHO2(alt) Combining double low line 0.96 ± 0.18 (2σ). These alternative calibration methods currently have comparable systematic uncertainties to the conventional method: ∼ 28% and ∼ 41% for the alternative OH and HO2 calibration methods respectively compared to 35% for the H2O vapour photolysis method; ways in which these can be reduced in the future are discussed. The good agreement between the very different methods of calibration leads to increased confidence in HOx field measurements and particularly in aircraft-based HOx measurements, where there are substantial variations in external pressure, and assumptions are made regarding loss rates on inlets as a function of pressure

Implementation of a chemical background method for atmospheric OH measurements by laser-induced fluorescence: characterisation and observations from the UK and China

Hydroxyl (OH) and hydroperoxy (HO2) radicals are central to the understanding of atmospheric chemistry. Owing to their short lifetimes, these species are frequently used to test the accuracy of model predictions and their underlying chemical mechanisms. In forested environments, laser-induced fluorescence–fluorescence assay by gas expansion (LIF–FAGE) measurements of OH have often shown substantial disagreement with model predictions, suggesting the presence of unknown OH sources in such environments. However, it is also possible that the measurements have been affected by instrumental artefacts, due to the presence of interfering species that cannot be discriminated using the traditional method of obtaining background signals via modulation of the laser excitation wavelength (“OHwave”). The interference hypothesis can be tested by using an alternative method to determine the OH background signal, via the addition of a chemical scavenger prior to sampling of ambient air (“OHchem”). In this work, the Leeds FAGE instrument was modified to include such a system to facilitate measurements of OHchem, in which propane was used to selectively remove OH from ambient air using an inlet pre-injector (IPI). The IPI system was characterised in detail, and it was found that the system did not reduce the instrument sensitivity towards OH ( 99 %) without the removal of OH formed inside the fluorescence cell (< 5 %). Tests of the photolytic interference from ozone in the presence of water vapour revealed a small but potentially significant interference, equivalent to an OH concentration of ∼4×105 molec. cm−3 under typical atmospheric conditions of [O3] =50 ppbv and [H2O] =1 %. Laboratory experiments to investigate potential interferences from products of isoprene ozonolysis did result in interference signals, but these were negligible when extrapolated down to ambient ozone and isoprene levels. The interference from NO3 radicals was also tested but was found to be insignificant in our system. The Leeds IPI module was deployed during three separate field intensives that took place in summer at a coastal site in the UK and both in summer and winter in the megacity of Beijing, China, allowing for investigations of ambient OH interferences under a wide range of chemical and meteorological conditions. Comparisons of ambient OHchem measurements to the traditional OHwave method showed excellent agreement, with OHwave vs OHchem slopes of 1.05–1.16 and identical behaviour on a diel basis, consistent with laboratory interference tests. The difference between OHwave and OHchem (“OHint”) was found to scale non-linearly with OHchem, resulting in an upper limit interference of (5.0±1.4) ×106 molec. cm−3 at the very highest OHchem concentrations measured (23×106 molec. cm−3), accounting for ∼14 %–21 % of the total OHwave signal

Development of the electric organ in embryos and larvae of the knifefish, Brachyhypopomus gauderio

This is the final version. Available on open access from Elsevier via the DOI in this recordSouth American Gymnotiform knifefish possess electric organs that generate electric fields for electro-location and electro-communication. Electric organs in fish can be derived from either myogenic cells (myogenic electric organ/mEO) or neurogenic cells (neurogenic electric organ/nEO). To date, the embryonic development of EOs has remained obscure. Here we characterize the development of the mEO in the Gymnotiform bluntnose knifefish, Brachyhypopomus gauderio. We find that EO primordial cells arise during embryonic stages in the ventral edge of the tail myotome, translocate into the ventral fin and develop into syncytial electrocytes at early larval stages. We also describe a pair of thick nerve cords that flank the dorsal aorta, the location and characteristic morphology of which are reminiscent of the nEO in Apteronotid species, suggesting a common evolutionary origin of these tissues. Taken together, our findings reveal the embryonic origins of the mEO and provide a basis for elucidating the mechanisms of evolutionary diversification of electric charge generation by myogenic and neurogenic EOs.Iraq GovernmentBiotechnology and Biological Sciences Research Council (BBSRC)Living Systems Institute Director’s Fun

Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease

We present the first application of the hypothesis-rich mathematical theory to genome-wide association data. The Hamza et al. late-onset sporadic Parkinson's disease genome-wide association study dataset was analyzed. We found a rare, coding, non-synonymous SNP variant in the gene DZIP1 that confers increased susceptibility to Parkinson's disease. The association of DZIP1 with Parkinson's disease is consistent with a Parkinson's disease stem-cell ageing theory.Comment: 14 page

The FU gene and its possible protein isoforms

BACKGROUND: FU is the human homologue of the Drosophila gene fused whose product fused is a positive regulator of the transcription factor Cubitus interruptus (Ci). Thus, FU may act as a regulator of the human counterparts of Ci, the GLI transcription factors. Since Ci and GLI are targets of Hedgehog signaling in development and morphogenesis, it is expected that FU plays an important role in Sonic, Desert and/or Indian Hedgehog induced cellular signaling. RESULTS: The FU gene was identified on chromosome 2q35 at 217.56 Mb and its exon-intron organization determined. The human developmental disorder Syndactyly type 1 (SD1) maps to this region on chromosome 2 and the FU coding region was sequenced using genomic DNA from an affected individual in a linked family. While no FU mutations were found, three single nucleotide polymorphisms were identified. The expression pattern of FU was thoroughly investigated and all examined tissues express FU. It is also clear that different tissues express transcripts of different sizes and some tissues express more than one transcript. By means of nested PCR of specific regions in RT/PCR generated cDNA, it was possible to verify two alternative splicing events. This also suggests the existence of at least two additional protein isoforms besides the FU protein that has previously been described. This long FU and a much shorter isoform were compared for the ability to regulate GLI1 and GLI2. None of the FU isoforms showed any effects on GLI1 induced transcription but the long form can enhance GLI2 activity. Apparently FU did not have any effect on SUFU induced inhibition of GLI. CONCLUSIONS: The FU gene and its genomic structure was identified. FU is a candidate gene for SD1, but we have not identified a pathogenic mutation in the FU coding region in a family with SD1. The sequence information and expression analyses show that transcripts of different sizes are expressed and subjected to alternative splicing. Thus, mRNAs may contain different 5'UTRs and encode different protein isoforms. Furthermore, FU is able to enhance the activity of GLI2 but not of GLI1, implicating FU in some aspects of Hedgehog signaling

Reduction of the ATPase inhibitory factor 1 (IF1) leads to visual impairment in vertebrates

In vertebrates, mitochondria are tightly preserved energy producing organelles, which sustain nervous system development and function. The understanding of proteins that regulate their homoeostasis in complex animals is therefore critical and doing so via means of systemic analysis pivotal to inform pathophysiological conditions associated with mitochondrial deficiency. With the goal to decipher the role of the ATPase inhibitory factor 1 (IF1) in brain development, we employed the zebrafish as elected model reporting that the Atpif1a−/− zebrafish mutant, pinotage (pnttq209), which lacks one of the two IF1 paralogous, exhibits visual impairment alongside increased apoptotic bodies and neuroinflammation in both brain and retina. This associates with increased processing of the dynamin-like GTPase optic atrophy 1 (OPA1), whose ablation is a direct cause of inherited optic atrophy. Defects in vision associated with the processing of OPA1 are specular in Atpif1−/− mice thus confirming a regulatory axis, which interlinks IF1 and OPA1 in the definition of mitochondrial fitness and specialised brain functions. This study unveils a functional relay between IF1 and OPA1 in central nervous system besides representing an example of how the zebrafish model could be harnessed to infer the activity of mitochondrial proteins during development

Functional divergence in the role of N-linked glycosylation in smoothened signaling

The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice