Exploring matrix effects on photochemistry of organic aerosols

This work explores the effect of the environment on the rate of photolysis of 2,4-dinitrophenol (24-DNP), an important environmental toxin. In stark contrast to the slow photolysis of 24-DNP in an aqueous solution, the photolysis rate is increased by more than an order of magnitude for 24-DNP dissolved in 1-octanol or embedded in secondary organic material (SOM) produced by ozonolysis of α-pinene. Lowering the temperature decreased the photolysis rate of 24-DNP in SOM much more significantly than that of 24-DNP in octanol, with effective activation energies of 53 kJ/mol and 12 kJ/mol, respectively. We discuss the possibility that the increasing viscosity of the SOM matrix constrains the molecular motion, thereby suppressing the hydrogen atom transfer reaction to the photo-excited 24-DNP. This is, to our knowledge, the first report of a significant effect of the matrix, and possibly viscosity, on the rate of an atmospheric photochemical reaction within SOM. It suggests that rates of photochemical processes in organic aerosols will depend on both relative humidity and temperature and thus altitude. The results further suggest that photochemistry in SOM may play a key role in transformations of atmospheric organics. For example, 24-DNP and other nitro-aromatic compounds should readily photodegrade in organic particulate matter, which has important consequences for predicting their environmental fates and impacts

Laboratory Determination of the Infrared Band Strengths of Pyrene Frozen in Water Ice: Implications for the Composition of Interstellar Ices

Broad infrared emission features (e.g., at 3.3, 6.2, 7.7, 8.6, and 11.3 microns) from the gas phase interstellar medium have long been attributed to polycyclic aromatic hydrocarbons (PAHs). A significant portion (10%-20%) of the Milky Way's carbon reservoir is locked in PAH molecules, which makes their characterization integral to our understanding of astrochemistry. In molecular clouds and the dense envelopes and disks of young stellar objects (YSOs), PAHs are expected to be frozen in the icy mantles of dust grains where they should reveal themselves through infrared absorption. To facilitate the search for frozen interstellar PAHs, laboratory experiments were conducted to determine the positions and strengths of the bands of pyrene mixed with H2O and D2O ices. The D2O mixtures are used to measure pyrene bands that are masked by the strong bands of H2O, leading to the first laboratory determination of the band strength for the CH stretching mode of pyrene in water ice near 3.25 microns. Our infrared band strengths were normalized to experimentally determined ultraviolet band strengths, and we find that they are generally ~50% larger than those reported by Bouwman et al. based on theoretical strengths. These improved band strengths were used to reexamine YSO spectra published by Boogert et al. to estimate the contribution of frozen PAHs to absorption in the 5-8 micron spectral region, taking into account the strength of the 3.25 micron CH stretching mode. It is found that frozen neutral PAHs contain 5%-9% of the cosmic carbon budget, and account for 2%-9% of the unidentified absorption in the 5-8 micron region.Comment: Accepted for publication in ApJ on 14 Feb 201

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis

The Caltech Photooxidation Flow Tube reactor: design, fluid dynamics and characterization

Flow tube reactors are widely employed to study gas-phase atmospheric chemistry and secondary organic aerosol (SOA) formation. The development of a new laminar-flow tube reactor, the Caltech Photooxidation Flow Tube (CPOT), intended for the study of gas-phase atmospheric chemistry and SOA formation, is reported here. The present work addresses the reactor design based on fluid dynamical characterization and the fundamental behavior of vapor molecules and particles in the reactor. The design of the inlet to the reactor, based on computational fluid dynamics (CFD) simulations, comprises a static mixer and a conical diffuser to facilitate development of a characteristic laminar flow profile. To assess the extent to which the actual performance adheres to the theoretical CFD model, residence time distribution (RTD) experiments are reported with vapor molecules (O_3) and submicrometer ammonium sulfate particles. As confirmed by the CFD prediction, the presence of a slight deviation from strictly isothermal conditions leads to secondary flows in the reactor that produce deviations from the ideal parabolic laminar flow. The characterization experiments, in conjunction with theory, provide a basis for interpretation of atmospheric chemistry and SOA studies to follow. A 1-D photochemical model within an axially dispersed plug flow reactor (AD-PFR) framework is formulated to evaluate the oxidation level in the reactor. The simulation indicates that the OH concentration is uniform along the reactor, and an OH exposure (OH_(exp)) ranging from ∼ 10^9 to ∼ 10^(12) molecules cm^(−3) s can be achieved from photolysis of H_2O_2. A method to calculate OH_(exp) with a consideration for the axial dispersion in the present photochemical system is developed

Vapor wall deposition in Teflon chambers

Teflon chambers are ubiquitous in studies of atmospheric chemistry. Secondary organic aerosol (SOA) formation can be underestimated, owing to deposition of SOA-forming vapors to the chamber wall. We present here an experimental protocol and a model framework to constrain the vapor–wall interactions in Teflon chambers. We measured the wall deposition rates of 25 oxidized organic compounds generated from the photooxidation of isoprene, toluene, α-pinene, and dodecane in two chambers that had been extensively used and in two new unused chambers. We found that the extent of prior use of the chamber did not significantly affect the sorption behavior of the Teflon films. Among the 25 compounds studied, the maximum wall deposition rate is exhibited by the most highly oxygenated and least volatile compounds. By optimizing the model output to the observed vapor decay profiles, we identified that the dominant parameter governing the extent of wall deposition of a compound is its wall accommodation coefficient (α_(wi)), which can be correlated through its volatility with the number of carbons and oxygens in the molecule. By doing so, the wall-induced deposition rate of intermediate/semi-volatile organic vapors can be reasonably predicted based on their molecular constituency. The extent to which vapor wall deposition impacts measured SOA yields depends on the competition between uptake of organic vapors by suspended particles and the chamber wall. The timescale associated with vapor wall deposition can vary from minutes to hours depending on the value of α_(w,i). For volatile and intermediate volatility organic compounds (small α_(w,i)), gas-particle partitioning will dominate wall deposition for typical particle number concentrations in chamber experiments. For compounds characterized by relatively large α_(w,i), vapor transport to particles is suppressed by competition with the chamber wall even with perfect particle accommodation

Prenatal exposure to polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) may influence birth weight among infants in a Swedish cohort with background exposure: a cross-sectional study

BACKGROUND: Prenatal exposure to persistent organic pollutants, e.g. polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) has been suggested to negatively affect birth weight although epidemiological evidence is still inconclusive. We investigated if prenatal exposure to PCBs and PBDEs is related to birth weight in a Swedish population with background exposure. METHODS: Breast milk was sampled during the third week after delivery from first-time mothers in Uppsala county, Sweden 1996–2010 (POPUP cohort) (N = 413). Samples were analysed for di-ortho PCBs (CB-138, 153, 180) and tetra- to hexa- brominated PBDEs (BDE-47, 99, 100, 153). Simple and multiple linear regression models were used to investigate associations between lipid-adjusted, ln-transformed PCB and PBDE concentrations, and birth weight. Covariates included in the multivariate regression model were PCB and PBDE exposure, maternal age, pre-pregnancy BMI, weight gain during pregnancy, education, smoking, gender of the infant and gestational length. The effect of including fish consumption was also investigated. RESULTS: In the multivariate model, prenatal exposure to di-ortho PCBs was significantly associated with increased birth weight (β = 137; p = 0.02). The result did not change when gestational length was added to the model. An inverse association between PBDE(4) (sum of BDE-47, -99, -100 and −153) and birth weight was observed in the multivariate model including gestational length (β = −106; p = 0.04). Maternal pre-pregnancy BMI and weight gain during pregnancy were important confounders of the association between di-ortho PCBs and birth weight. The associations were not alleviated after adjustment for fish consumption, a major source of PCB and PBDE exposure. The observed associations were stronger for boys than for girls. CONCLUSIONS: Our results indicate that prenatal exposure to di-ortho PCBs and PBDE(4) may influence birth weight in different directions, i.e. PCB exposure was associated with higher birth weight and PBDE exposure with lower birth weight. Maternal pre-pregnancy BMI and weight gain during pregnancy were important confounders that may hide positive association between di-ortho PCB exposure and birth weight if they are not included in the statistical model. We speculate that even small PCB- and PBDE-induced shifts in the distribution of birth weight may influence future public health in populations with background exposure

Formation of highly oxygenated low-volatility products from cresol oxidation

Hydroxyl radical (OH) oxidation of toluene produces ring-retaining products: cresol and benzaldehyde, and ring-opening products: bicyclic intermediate compounds and epoxides. Here, first- and later-generation OH oxidation products from cresol and benzaldehyde are identified in laboratory chamber experiments. For benzaldehyde, first-generation ring-retaining products are identified, but later-generation products are not detected. For cresol, low-volatility (saturation mass concentration, C* ∼ 3.5  ×  10^4 − 7.7  ×  10^(−3) µg m^(−3)), first- and later-generation ring-retaining products are identified. Subsequent OH addition to the aromatic ring of o-cresol leads to compounds such as hydroxy, dihydroxy, and trihydroxy methyl benzoquinones and dihydroxy, trihydroxy, tetrahydroxy, and pentahydroxy toluenes. These products are detected in the gas phase by chemical ionization mass spectrometry (CIMS) and in the particle phase using offline direct analysis in real-time mass spectrometry (DART-MS). Our data suggest that the yield of trihydroxy toluene from dihydroxy toluene is substantial. While an exact yield cannot be reported as authentic standards are unavailable, we find that a yield for trihydroxy toluene from dihydroxy toluene of ∼ 0.7 (equal to the reported yield of dihydroxy toluene from o-cresol; Olariu et al., 2002) is consistent with experimental results for o-cresol oxidation under low-NO conditions. These results suggest that even though the cresol pathway accounts for only ∼ 20 % of the oxidation products of toluene, it is the source of a significant fraction (∼ 20–40 %) of toluene secondary organic aerosol (SOA) due to the formation of low-volatility products

Reengineering Java Game Variants into a Compositional Product Line: An empirical case study identifying activities and effort involved in a reengineering process

Compositional Software Product Line Engineering is known to be tidious but powerful approach to migrate existing systems into SPL. This paper analyses the pros and cons of compositional SPLE strategies and also attempts to migrate five related Java games into an SPL while outlining the necessary activities to perform such migration. This paper also presents how to measure migration efforts of each activity. Lastly, the results of the migration process is compared to the result of another Master thesis that also conducts an SPL migration but using the annotative approach

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns in single cells within their native environment. Preserving spatial relationships while accessing the transcriptome of selected cells is a crucial feature for advancing many biological areas, from developmental biology to neuroscience. However, because of the high autofluorescence background of many tissue samples, it is difficult to detect single-molecule fluorescence in situ hybridization (smFISH) signals robustly in opaque thick samples. Here, we draw on principles from the emerging discipline of dynamic nucleic acid nanotechnology to develop a robust method for multi-color, multi-RNA, imaging in deep tissues using single-molecule hybridization chain reaction (smHCR). Using this approach, single transcripts can be imaged using epifluorescence, confocal or selective plane illumination microscopy (SPIM) depending on the imaging depth required. We show that smHCR has high sensitivity in detecting mRNAs in cell culture and whole-mount zebrafish embryos, and that combined with SPIM and PACT (PAssive CLARITY Technique) tissue hydrogel embedding and clearing, smHCR can detect single mRNAs deep within thick (0.5 mm) brain slices. By simultaneously achieving ∼20-fold signal amplification and diffraction-limited spatial resolution, smHCR offers a robust and versatile approach for detecting single mRNAs in situ, including in thick tissues where high background undermines the performance of unamplified smFISH