An Airborne A-Band Spectrometer for Remote Sensing Of Aerosol and Cloud Optical Properties

NASA Technical Reports Server (NTRS)

Pitts, Michael; Hostetler, Chris; Poole, Lamont; Holden, Carl; Rault, Didier

2000-01-01

Atmospheric remote sensing with the O2 A-band has a relatively long history, but most of these studies were attempting to estimate surface pressure or cloud-top pressure. Recent conceptual studies have demonstrated the potential of spaceborne high spectral resolution O2 A-band spectrometers for retrieval of aerosol and cloud optical properties. The physical rationale of this new approach is that information on the scattering properties of the atmosphere is embedded in the detailed line structure of the O2 A-band reflected radiance spectrum. The key to extracting this information is to measure the radiance spectrum at very high spectral resolution. Instrument performance requirement studies indicate that, in addition to high spectral resolution, the successful retrieval of aerosol and cloud properties from A-band radiance spectra will also require high radiometric accuracy, instrument stability, and high signal-to-noise measurements. To experimentally assess the capabilities of this promising new remote sensing application, the NASA Langley Research Center is developing an airborne high spectral resolution A-band spectrometer. The spectrometer uses a plane holographic grating with a folded Littrow geometry to achieve high spectral resolution (0.5 cm-1) and low stray light in a compact package. This instrument will be flown in a series of field campaigns beginning in 2001 to evaluate the overall feasibility of this new technique. Results from these campaigns should be particularly valuable for future spaceborne applications of A-band spectrometers for aerosol and cloud retrievals.

Observations of Aerosol-Cloud Interactions with Varying Vertical Separation between Biomass-Burning Aerosols and Stratocumulus Clouds over the South East Atlantic

NASA Astrophysics Data System (ADS)

Gupta, S.; McFarquhar, G. M.; Poellot, M.; O'Brien, J.; Delene, D. J.; Thornhill, K. L., II

2017-12-01

The ObseRvations of Aerosols above Clouds and their intEractionS (ORACLES) 2016 project provided in-situ measurements and remotely sensed retrievals of aerosol and cloud properties over the South East Atlantic during September, 2016 with a second deployment scheduled for August, 2017. Biomass burning aerosol from Southern Africa is advected toward the South East Atlantic at elevated altitudes and overlies the ubiquitous stratocumulus cloud deck over the ocean. The aerosols subside farther from the coast so that the vertical displacement between the clouds and aerosols varies, and whose effect on aerosol-cloud interaction is poorly known. A NASA P-3 aircraft was equipped with a Cloud Droplet Probe CDP sizing particles between 2 and 50μm, a Cloud and Aerosol Spectrometer CAS sizing between 0.51 and 50 μm and a 2D-stereo probe 2DS, nominally sizing between 10 and 1280 μm a Cloud Imaging Probe CIP, from 25 to 1600μm, and a High Volume Precipitation Sampler HVPS-3, from 150μm to 1.92cm for measuring number distribution functions (n(D)) along with a King probe for measuring liquid water content, LWC. A Passive Cavity Aerosol Spectrometer Probe PCASP measured aerosol particles between 0.1 to 3μm. Cloud legs from three research flights are classified into different regimes based on the aerosol concentration measured in the accumulation mode by the PCASP (Na) and its location above clouds. These legs include vertical transects through clouds and sawtooths (ramped legs starting above or below the cloud layer, completing a vertical transect through the cloud and repeating this pattern for several legs). The regimes; clean, mixing and separated, correspond to conditions with Na less than 100 cm-3 above cloud top, Na greater than 100 cm-3 within 100 m above cloud top and Na greater than 100 cm-3 separated from the cloud top by more than 100 m. During the mixing regime, measurements from CAS and 2DS show that droplet concentrations and cloud optical depths increased and

Effect of Vaporizer Temperature on Ambient Non-Refractory Submicron Aerosol Composition and Mass Spectra Measured by the Aerosol Mass Spectrometer

EPA Science Inventory

Aerodyne Aerosol Mass Spectrometers (AMS) are routinely operated with a constant vaporizer temperature (Tvap) of 600^oC in order to facilitate quantitative detection of non-refractory submicron (NR-PM1) species. By analogy with other thermal desorption instrument...

Measurements of fluorescent aerosols using a mutil-channel lidar spectrometer system during DUBI 2016 Campaign

NASA Astrophysics Data System (ADS)

Huang, Z.; Huang, J.; Zhou, T.; Shi, J.; Sugimoto, N.; Tang, K.

2016-12-01

Atmospheric bioaerosols are relevant for public health and may play an important role in the climate system. Previous studies have shown that abundant bioaerosols (such as microorganisms) injected into the atmosphere along with dust events, could affect leeward ecosystem and human health, even induce globe climate change. However, the challenge in quantifying bioaerosol climate effects (e.g., radiative forcing and aerosol-cloud interactions) arises from large spatial and temporal heterogeneity of their concentrations, compositions, sizes, shape and optical properties. Lidar, as one of most advanced active remote sensing, is used to offer some remarkable advantages for determining the vertical structure of atmospheric aerosols and their related optical properties. In order to investigate the characterization of atmospheric bioaerosols along transported pathways of dust aerosols, we carried out DUBI (DUst BIoaerosol) 2016 Campaign over Northern China in spring of 2016. Lots of instruments, including bioaerosol sampling, lidar as well as others, were installed at three sites­ (Erenhot, Zhangbei and Jinan) simultaneously. A multi-channel lidar spectrometer system was developed to observe Mie, Raman scattering and laser-induced fluorescence excitation at 355 nm from the atmosphere. The lidar system operated polarization measurements at 355nm, aiming to identify dust particles from other aerosols. It employs a high power pulsed laser with energy of 80mJ at 355nm and a received telescope with 350mm diameter. The receiver could simultaneously detect a wide fluorescent spectrum between 360nm and 720nm with spectral resolution 5.7 nm using two spectrometers simultaneously. The spectrometer mainly includes an F/3.7 Crossed Czerny-Turner spectrographs, a grating (1200 gr/mm) and a PMT array with 32 photocathode elements. Vertical structure of fluorescent aerosols in the atmosphere was observed by the developed lidar system at Zhangbei during DUBI 2016 Campaign. It has been

A New Optical Aerosol Spectrometer

NASA Technical Reports Server (NTRS)

Fonda, Mark; Malcolmson, Andrew; Bonin, Mike; Stratton, David; Rogers, C. Fred; Chang, Sherwood (Technical Monitor)

1998-01-01

An optical particle spectrometer capable of measuring aerosol particle size distributions from 0.02 to 100 micrometers has been developed. This instrument combines several optical methods in one, in-situ configuration; it can provide continuous data collection to encompass the wide dynamic size ranges and concentrations found in studies of modeled planetary atmospheres as well as terrestrial air quality research. Currently, the system is incorporated into an eight liter capacity spherical pressure vessel that is appropriate both for flowthrough and for in-situ particle generation. The optical sizing methods include polarization ratio, The scattering, and forward scattering detectors, with illumination from a fiber-coupled, Argon-ion laser. As particle sizes increase above 0.1 micrometer, a customized electronics and software system automatically shifts from polarization to diffraction-based measurements as the angular scattering detectors attain acceptable signal-to-noise ratios. The number concentration detection limits are estimated to be in the part-per-trillion (ppT by volume) range, or roughly 1000 submicron particles per cubic centimeter. Results from static experiments using HFC134A (approved light scattering gas standard), flow-through experiments using sodium chloride (NaCl) and carbon particles, and dynamic 'Tholin' (photochemical produced particles from ultraviolet (UV)-irradiated acetylene and nitrogen) experiments have been obtained. The optical spectrometer data obtained with particles have compared well with particle sizes determined by electron microscopy. The 'Tholin' tests provided real-time size and concentration data as the particles grew from about 30 nanometers to about 0.8 micrometers, with concentrations ranging from ppT to ppB, by volume. Tests are still underway, to better define sizing accuracy and concentration limits, these results will be reported.

Dual-wavelength dual-cavity spectrometer for NO2 detection in the presence of aerosol interference

NASA Astrophysics Data System (ADS)

Chandran, Satheesh; Puthukkudy, Anin; Varma, Ravi

2017-07-01

Precise determination of concentration of gases, such as NO2, in urban atmosphere is crucial in studying chemical reactions leading to secondary pollutants. In this study, a novel and sensitive yet simple and cost effective spectrometer was developed where two laser wavelengths and two parallel identical optical cavities were used. Monitoring of NO2 even in the presence of aerosol spectral interference was demonstrated. The intensity transmitted through one cavity, evacuated to 0.1 mbar, was designated as the reference signal ( I 0) while that through the other cavity, sampling air at atmospheric pressure, was designated as sample signal ( I). Quasi-simultaneous measurements of these I 0 and I were done for both laser wavelengths sequentially: one at 406.4 nm near the peak of the largest electronic transition of NO2 and the other at 446.9 nm, away from the peak yet exhibiting significant absorption. The addition of the second wavelength where NO2 has absorption was to ascertain the presence of aerosol scattering and compensate for it. Aerosol extinctions at both operating wavelengths were assumed to be the same, their ratio taken as unity for simplicity, and aerosol light extinction was retrieved. The spectrometer with average sampling interval of 5 s exhibited detection sensitivity of low parts per billion concentrations.

Airborne Aerosol in Situ Measurements during TCAP: A Closure Study of Total Scattering

DOE PAGES

Kassianov, Evgueni I.; Berg, Larry K.; Pekour, Mikhail S.; ...

2015-07-31

We present here a framework for calculating the total scattering of both non-absorbing and absorbing aerosol at ambient conditions from aircraft data. The synergistically employed aircraft data involve aerosol microphysical, chemical, and optical components and ambient relative humidity measurements. Our framework is developed emphasizing the explicit use of the complementary chemical composition data for estimating the complex refractive index (RI) of particles, and thus obtaining improved ambient size spectra derived from Optical Particle Counter (OPC) measurements. The feasibility of our framework for improved calculations of total aerosol scattering is demonstrated for different ambient conditions with a wide range of relativemore » humidities (from 5 to 80%) using three types of data collected by the U.S. Department of Energy (DOE) G-1 aircraft during the recent Two-Column Aerosol Project (TCAP). Namely, these three types of data employed are: (1) size distributions measured by an Ultra High Sensitivity Aerosol Spectrometer (UHSAS; 0.06-1 µm), a Passive Cavity Aerosol Spectrometer (PCASP; 0.1-3 µm) and a Cloud and Aerosol Spectrometer (CAS; 0.6- >10 µm), (2) chemical composition data measured by an Aerosol Mass Spectrometer (AMS; 0.06-0.6 µm) and a Single Particle Soot Photometer (SP2; 0.06-0.6 µm), and (3) the dry total scattering coefficient measured by a TSI integrating nephelometer at three wavelengths (0.45, 0.55, 0.7 µm) and scattering enhancement factor measured with a humidification system at three RHs (near 45%, 65% and 90%) at a single wavelength (0.525 µm). We demonstrate that good agreement (~10% on average) between the observed and calculated scattering at these three wavelengths can be obtained using the best available chemical composition data for the RI-based correction of the OPC-derived size spectra. We also demonstrate that ignoring the RI-based correction and using non-representative RI values can cause a substantial

Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

PubMed

Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

2017-10-03

Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

A Design of a Novel Airborne Aerosol Spectrometer for Remote Sensing Validation

NASA Astrophysics Data System (ADS)

Adler, G. A.; Brock, C. A.; Dube, W. P.; Erdesz, F.; Gordon, T.; Law, D. C.; Manfred, K.; Mason, B. J.; McLaughlin, R. J.; Richardson, M.; Wagner, N. L.; Washenfelder, R. A.; Murphy, D. M.

2016-12-01

Aerosols and their effect on the radiative properties of clouds contribute one of the largest sources of uncertainty to the Earth's energy budget. Many current global assessments, of atmospheric aerosol radiative forcing rely heavily on remote sensing observation; therefore, in situ aircraft and ground-based measurements are essential for validation of remote sensing measurements. Cavity ringdown spectrometers (CRD) measure aerosol extinction and are commonly used to validate remote sensing observations. These instruments have been deployed on aircraft based platforms over the years thus providing the opportunity to measure these properties over large areas in various conditions. However, deployment of the CRD on an aircraft platform has drawbacks. Typically, aircraft based CRDs draw sampled aerosol into a cabin based instrument through long lengths of tubing. This limits the ability of the instrument to measure: 1) Course mode aerosols (e.g. dust) 2) Aerosols at high relative humidity (above 90%) Here we describe the design of a novel aircraft based open path CRD. The open path CRD is intended to be mounted external to the cabin and has no sample tubing for aerosol delivery, thus measuring optical properties of all aerosol at the ambient conditions. However, the design of an open path CRD for operation on a wing-mounted aircraft platform has certain design complexities. The instrument's special design features include 2 CRD channels, 2 airfoils around the open Path CRD and a configuration which could be easily aligned and rigid at the same time. This novel implementation of cavity ringdown spectroscopy will provide a better assessment of the accuracy of remote sensing satellite measurements

Ambient Aerosol in Southeast Asia: High Resolution Aerosol Mass Spectrometer Measurements Over Oil Palm (Elaeis guineensis)

NASA Astrophysics Data System (ADS)

Phillips, G.; Dimarco, C.; Misztal, P.; Nemitz, E.; Farmer, D.; Kimmel, J.; Jimenez, J.

2008-12-01

The emission of organic compounds in the troposphere is important factor in the formation of secondary organic aerosol (SOA). A very large proportion of organic material emitted globally is estimated to arise from biogenic sources, with almost half coming from tropical and sub-tropical forests. Preliminary analyses of leave cuvette emission studies suggest that oil palm (Elaeis guineensis) is a significantly larger source of isoprene than tropical forest. Much larger sources of isoprene over oil palm allied with a larger anthropogenic component of local emissions contrast greatly with the remote tropical forest environment and therefore the character of SOA formed may differ significantly. These issues, allied with the high price of palm oil on international markets leading to increased use of land for oil palm production, could give rise to rapidly changing chemical and aerosol regimes in the tropics. It is therefore important to understand the current emissions and composition of organic aerosol over all important land-uses in the tropical environment. This in turn will lead to a greater understanding of the present, and to an improvement in predictive capacity for the future system. To help address these issues, a high resolution time of flight aerosol mass spectrometer (HR-ToF-AMS) was deployed in the Sabahmas (PPB OIL) oil palm plantation near Lahad Datu, in Eastern Sabah, as part of the field component of the Aerosol Coupling in the Earth System (ACES) project, part of the UK NERC APPRAISE program. This project was allied closely with measurements made of similar chemical species and aerosol components at a forest site in the Danum Valley as part of the UK Oxidant and Particle Photochemical Processes above a Southeast Asian tropical rainforest (OP3) project. Measurements of submicron non- refractory aerosol composition are presented along with some preliminary analysis of chemically resolved aerosol fluxes made with a new eddy covariance system, based on the

Response of an aerosol mass spectrometer to organonitrates and organosulfates and implications for atmospheric chemistry

PubMed Central

Farmer, D. K.; Matsunaga, A.; Docherty, K. S.; Surratt, J. D.; Seinfeld, J. H.; Ziemann, P. J.; Jimenez, J. L.

2010-01-01

Organonitrates (ON) are important products of gas-phase oxidation of volatile organic compounds in the troposphere; some models predict, and laboratory studies show, the formation of large, multifunctional ON with vapor pressures low enough to partition to the particle phase. Organosulfates (OS) have also been recently detected in secondary organic aerosol. Despite their potential importance, ON and OS remain a nearly unexplored aspect of atmospheric chemistry because few studies have quantified particulate ON or OS in ambient air. We report the response of a high-resolution time-of-flight aerosol mass spectrometer (AMS) to aerosol ON and OS standards and mixtures. We quantify the potentially substantial underestimation of organic aerosol O/C, commonly used as a metric for aging, and N/C. Most of the ON-nitrogen appears as ions in the AMS, which are typically dominated by inorganic nitrate. Minor organonitrogen ions are observed although their identity and intensity vary between standards. We evaluate the potential for using fragment ratios, organonitrogen ions, ions, the ammonium balance of the nominally inorganic ions, and comparison to ion-chromatography instruments to constrain the concentrations of ON for ambient datasets, and apply these techniques to a field study in Riverside, CA. OS manifests as separate organic and sulfate components in the AMS with minimal organosulfur fragments and little difference in fragmentation from inorganic sulfate. The low thermal stability of ON and OS likely causes similar detection difficulties for other aerosol mass spectrometers using vaporization and/or ionization techniques with similar or larger energy, which has likely led to an underappreciation of these species. PMID:20194777

Response of an aerosol mass spectrometer to organonitrates and organosulfates and implications for atmospheric chemistry.

PubMed

Farmer, D K; Matsunaga, A; Docherty, K S; Surratt, J D; Seinfeld, J H; Ziemann, P J; Jimenez, J L

2010-04-13

Organonitrates (ON) are important products of gas-phase oxidation of volatile organic compounds in the troposphere; some models predict, and laboratory studies show, the formation of large, multifunctional ON with vapor pressures low enough to partition to the particle phase. Organosulfates (OS) have also been recently detected in secondary organic aerosol. Despite their potential importance, ON and OS remain a nearly unexplored aspect of atmospheric chemistry because few studies have quantified particulate ON or OS in ambient air. We report the response of a high-resolution time-of-flight aerosol mass spectrometer (AMS) to aerosol ON and OS standards and mixtures. We quantify the potentially substantial underestimation of organic aerosol O/C, commonly used as a metric for aging, and N/C. Most of the ON-nitrogen appears as NO(x)+ ions in the AMS, which are typically dominated by inorganic nitrate. Minor organonitrogen ions are observed although their identity and intensity vary between standards. We evaluate the potential for using NO(x)+ fragment ratios, organonitrogen ions, HNO(3)+ ions, the ammonium balance of the nominally inorganic ions, and comparison to ion-chromatography instruments to constrain the concentrations of ON for ambient datasets, and apply these techniques to a field study in Riverside, CA. OS manifests as separate organic and sulfate components in the AMS with minimal organosulfur fragments and little difference in fragmentation from inorganic sulfate. The low thermal stability of ON and OS likely causes similar detection difficulties for other aerosol mass spectrometers using vaporization and/or ionization techniques with similar or larger energy, which has likely led to an underappreciation of these species.

Rapid measurement of sub-micrometer aerosol size distribution using a fast integrated mobility spectrometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yang; Pinterich, Tamara; Wang, Jian

We present rapid measurement of submicron particle size distributions enables the characterization of aerosols with fast changing properties, and is often necessary for measurements onboard mobile platforms (e.g., research aircraft). Aerosol mobility size distribution is commonly measured by a scanning mobility particle sizer (SMPS), which relies on voltage scanning or stepping to classify particles of different sizes, and may take up to several minutes to obtain a complete size spectrum of aerosol particles. The recently developed fast integrated mobility spectrometer (FIMS) with enhanced dynamic size range classifies and detects particles from 10 to ~600 nm simultaneously, allowing submicron aerosol mobilitymore » size distributions to be captured at a time resolution of 1 second. In this study, we present a detailed data inversion routine for deriving aerosol size distribution from FIMS measurements. The inversion routine takes into consideration the FIMS transfer function, particle penetration efficiency in the FIMS, and multiple charging of aerosols. The accuracy of the FIMS measurement is demonstrated by comparing parallel FIMS and SMPS measurements of stable aerosols with a wide range of size spectrum shapes, including ambient aerosols and aerosols classified by a differential mobility analyzer (DMA). The FIMS and SMPS-derived size distributions show excellent agreements for all aerosols tested. In addition, total number concentrations of ambient aerosols were integrated from 1 Hz FIMS size distributions, and compared with those directly measured by a condensation particle counter (CPC) operated in parallel. Finally, the integrated and measured total particle concentrations agree well within 5%.« less

Rapid measurement of sub-micrometer aerosol size distribution using a fast integrated mobility spectrometer

DOE PAGES

Wang, Yang; Pinterich, Tamara; Wang, Jian

2018-03-30

We present rapid measurement of submicron particle size distributions enables the characterization of aerosols with fast changing properties, and is often necessary for measurements onboard mobile platforms (e.g., research aircraft). Aerosol mobility size distribution is commonly measured by a scanning mobility particle sizer (SMPS), which relies on voltage scanning or stepping to classify particles of different sizes, and may take up to several minutes to obtain a complete size spectrum of aerosol particles. The recently developed fast integrated mobility spectrometer (FIMS) with enhanced dynamic size range classifies and detects particles from 10 to ~600 nm simultaneously, allowing submicron aerosol mobilitymore » size distributions to be captured at a time resolution of 1 second. In this study, we present a detailed data inversion routine for deriving aerosol size distribution from FIMS measurements. The inversion routine takes into consideration the FIMS transfer function, particle penetration efficiency in the FIMS, and multiple charging of aerosols. The accuracy of the FIMS measurement is demonstrated by comparing parallel FIMS and SMPS measurements of stable aerosols with a wide range of size spectrum shapes, including ambient aerosols and aerosols classified by a differential mobility analyzer (DMA). The FIMS and SMPS-derived size distributions show excellent agreements for all aerosols tested. In addition, total number concentrations of ambient aerosols were integrated from 1 Hz FIMS size distributions, and compared with those directly measured by a condensation particle counter (CPC) operated in parallel. Finally, the integrated and measured total particle concentrations agree well within 5%.« less

Characterization of aerosol composition, concentrations, and sources at Baengnyeong Island, Korea using an aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Lee, Taehyoung; Choi, Jinsoo; Lee, Gangwoong; Ahn, Junyoung; Park, Jin Soo; Atwood, Samuel A.; Schurman, Misha; Choi, Yongjoo; Chung, Yoomi; Collett, Jeffrey L.

2015-11-01

To improve understanding of the sources and chemical properties of particulate pollutants on the western side of the Korean Peninsula, an Aerodyne High Resolution Time of Flight Aerosol Mass Spectrometer (HR-ToF-AMS) measured non-refractory fine (PM1) particles from May to November, 2011 at Baengnyeong Island, South Korea. Organic matter and sulfate were generally the most abundant species and exhibited maximum concentrations of 36 μg/m3 and 39 μg/m3, respectively. Nitrate concentrations peaked at 32 μg/m3 but were typically much lower than sulfate and organic matter concentrations. May, September, October, and November featured the highest monthly average concentrations, with lower concentrations typically observed from June through August. Potential source contribution function (PSCF) analysis and individual case studies revealed that transport from eastern China, an area with high SO2 emissions, was associated with high particulate sulfate concentrations at the measurement site. Observed sulfate aerosol sometimes was fully neutralized by ammonium but often was acidic; the average ammonium to sulfate molar ratio was 1.49. Measured species size distributions revealed a range of sulfate particle size distributions with modes between 100 and 600 nm. Organic aerosol source regions were widespread, including contributions from eastern China and South Korea. Positive matrix factorization (PMF) analysis indicated three "factors," or types of organic aerosol, comprising one primary, hydrocarbon-like organic aerosol (HOA) and two oxidized organic aerosol (OOA) components, including a more oxidized (MO-OOA) and a less oxidized (LO-OOA) oxidized organic aerosol. On average, HOA and OOA contributed 21% and 79% of the organic mass (OM), respectively, with the MO-OOA fraction nearly three times as abundant as the LO-OOA fraction. Biomass burning contributions to observed OM were low during the late spring/early summer agricultural burning season in eastern China, since

Deriving aerosol parameters from in-situ spectrometer measurements for validation of remote sensing products

NASA Astrophysics Data System (ADS)

Riedel, Sebastian; Janas, Joanna; Gege, Peter; Oppelt, Natascha

2017-10-01

Uncertainties of aerosol parameters are the limiting factor for atmospheric correction over inland and coastal waters. For validating remote sensing products from these optically complex and spatially inhomogeneous waters the spatial resolution of automated sun photometer networks like AERONET is too coarse and additional measurements on the test site are required. We have developed a method which allows the derivation of aerosol parameters from measurements with any spectrometer with suitable spectral range and resolution. This method uses a pair of downwelling irradiance and sky radiance measurements for the extraction of the turbidity coefficient and aerosol Ångström exponent. The data can be acquired fast and reliable at almost any place during a wide range of weather conditions. A comparison to aerosol parameters measured with a Cimel sun photometer provided by AERONET shows a reasonable agreement for the Ångström exponent. The turbidity coefficient did not agree well with AERONET values due to fit ambiguities, indicating that future research should focus on methods to handle parameter correlations within the underlying model.

Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer

NASA Astrophysics Data System (ADS)

Ruske, S. T.; Topping, D. O.; Foot, V. E.; Kaye, P. H.; Stanley, W. R.; Morse, A. P.; Crawford, I.; Gallagher, M. W.

2016-12-01

Characterisation of bio-aerosols has important implications within Environment and Public Health sectors. Recent developments in Ultra-Violet Light Induced Fluorescence (UV-LIF) detectors such as the Wideband Integrated bio-aerosol Spectrometer (WIBS) and the newly introduced Multiparameter bio-aerosol Spectrometer (MBS) has allowed for the real time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal Spores and pollen. This new generation of instruments has enabled ever-larger data sets to be compiled with the aim of studying more complex environments, yet the algorithms used for specie classification remain largely invalidated. It is therefore imperative that we validate the performance of different algorithms that can be used for the task of classification, which is the focus of this study. For unsupervised learning we test Hierarchical Agglomerative Clustering with various different linkages. For supervised learning, ten methods were tested; including decision trees, ensemble methods: Random Forests, Gradient Boosting and AdaBoost; two implementations for support vector machines: libsvm and liblinear; Gaussian methods: Gaussian naïve Bayesian, quadratic and linear discriminant analysis and finally the k-nearest neighbours algorithm. The methods were applied to two different data sets measured using a new Multiparameter bio-aerosol Spectrometer. We find that clustering, in general, performs slightly worse than the supervised learning methods correctly classifying, at best, only 72.7 and 91.1 percent for the two data sets. For supervised learning the gradient boosting algorithm was found to be the most effective, on average correctly classifying 88.1 and 97.8 percent of the testing data respectively across the two data sets. We discuss the wider relevance of these results with regards to challenging existing classification in real-world environments.

Laboratory and field measurements of organic aerosols with the photoionization aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Dreyfus, Matthew A.

Analytical methods developed to sample and characterize ambient organic aerosols often face the trade-off between long sampling times and the loss of detailed information regarding specific chemical species present. The soft, universal ionization scheme of the Photoionization Aerosol Mass Spectrometer (PIAMS) allows for identification of various chemical compounds by a signature ion, often the molecular ion. The goal of this thesis work is to apply PIAMS to both laboratory and field experiments to answer questions regarding the formation, composition, and behavior of organic aerosols. To achieve this goal, a variety of hardware and software upgrades were administered to PIAMS to optimize the instrument. Data collection and processing software were either refined or built from the ground up to simplify difficult or monotonous tasks. Additional components were added to PIAMS with the intent to automate the instrument, enhance the results, and make the instrument more rugged and user-friendly. These changes, combined with the application of an external particle concentration system (mini-Versatile Aerosol Concentration Enrichment System, m-VACES), allowed PIAMS to be suitable for field measurements of organic aerosols. Two such field campaigns were completed, both at the State of Delaware Air Quality Monitoring Site in Wilmington, Delaware: a one week period in June, 2006, and an 18 day period in October and November of 2007. A sampling method developed was capable of collecting sufficient ambient organic aerosol and analyzing it with a time resolution of 3.5 minutes. Because of this method, short term concentration changes of individual species can be tracked. Combined with meteorological data, the behavior of these species can be analyzed as a function of time or wind direction. Many compounds are found at enhanced levels during the evening/night-time hours; potentially due to the combined effects of temperature inversion, and fresh emissions in a cooler environment

Development and characterization of an aircraft aerosol time-of-flight mass spectrometer.

PubMed

Pratt, Kerri A; Mayer, Joseph E; Holecek, John C; Moffet, Ryan C; Sanchez, Rene O; Rebotier, Thomas P; Furutani, Hiroshi; Gonin, Marc; Fuhrer, Katrin; Su, Yongxuan; Guazzotti, Sergio; Prather, Kimberly A

2009-03-01

Vertical and horizontal profiles of atmospheric aerosols are necessary for understanding the impact of air pollution on regional and global climate. To gain further insight into the size-resolved chemistry of individual atmospheric particles, a smaller aerosol time-of-flight mass spectrometer (ATOFMS) with increased data acquisition capabilities was developed for aircraft-based studies. Compared to previous ATOFMS systems, the new instrument has a faster data acquisition rate with improved ion transmission and mass resolution, as well as reduced physical size and power consumption, all required advances for use in aircraft studies. In addition, real-time source apportionment software allows the immediate identification and classification of individual particles to guide sampling decisions while in the field. The aircraft (A)-ATOFMS was field-tested on the ground during the Study of Organic Aerosols in Riverside, CA (SOAR) and aboard an aircraft during the Ice in Clouds Experiment-Layer Clouds (ICE-L). Initial results from ICE-L represent the first reported aircraft-based single-particle dual-polarity mass spectrometry measurements and provide an increased understanding of particle mixing state as a function of altitude. Improved ion transmission allows for the first single-particle detection of species out to approximately m/z 2000, an important mass range for the detection of biological aerosols and oligomeric species. In addition, high time resolution measurements of single-particle mixing state are demonstrated and shown to be important for airborne studies where particle concentrations and chemistry vary rapidly.

Aerosol Optical Depth Measurements by Airborne Sun Photometer in SOLVE II: Comparisons to SAGE III, POAM III and Airborne Spectrometer Measurements

NASA Technical Reports Server (NTRS)

Russell, P.; Livingston, J.; Schmid, B.; Eilers, J.; Kolyer, R.; Redemann, J.; Ramirez, S.; Yee, J-H.; Swartz, W.; Shetter, R.

2004-01-01

The 14-channel NASA Ames Airborne Tracking Sunphotometer (AATS-14) measured solar-beam transmission on the NASA DC-8 during the Second SAGE III Ozone Loss and Validation Experiment (SOLVE II). This paper presents AATS-14 results for multiwavelength aerosol optical depth (AOD), including its spatial structure and comparisons to results from two satellite sensors and another DC-8 instrument. These are the Stratospheric Aerosol and Gas Experiment III (SAGE III), the Polar Ozone and Aerosol Measurement III (POAM III) and the Direct beam Irradiance Airborne Spectrometer (DIAS).

Structural analysis of aerosol particles by microscopic observation using a time-of-flight secondary ion mass spectrometer

NASA Astrophysics Data System (ADS)

Takami, Akinori; Mayama, Norihito; Sakamoto, Tetsuo; Ohishi, Kenji; Irei, Satoshi; Yoshino, Ayako; Hatakeyama, Shiro; Murano, Kentaro; Sadanaga, Yasuhiro; Bandow, Hiroshi; Misawa, Kentaro; Fujii, Masaaki

2013-06-01

The chemical composition and structure of fine aerosol particles with diameters of less than 1 µm were analyzed in the spring of 2011 at Fukue Island, Japan, using an aerosol quadrupole mass spectrometer (Q-AMS, Aerodyne Research, Inc.) and a time-of-flight secondary ion mass spectrometer (TOF-SIMS). The Q-AMS results were similar to those of previous studies conducted at the same location, suggesting that the composition we observed is typical of this site. Based on the TOF-SIMS results, we classified the fine aerosol particles into three types: Type A, in which sulfate was covered with organic matter (OM); Type B, in which soil-containing particles with a diameter of 0.5 µm were associated with sulfate and OM; and Type C, in which black carbon (BC) and sulfate aggregates were associated with OM. During the observation period, the relative abundances of Type A, B, and C particles were 55%, 20%, and 25%, respectively. The structure, chemical composition, and the proportion of each type of particles provide information for a more representative particle model in radiative models. The relative abundance of Type C, i.e., BC-containing particles, is quite different to that in Tokyo, suggesting that Type C could be an indicator of transboundary air pollution, in this case from mainland China.

Thermal Emission Spectrometer Results: Mars Atmospheric Thermal Structure and Aerosol Distribution

NASA Technical Reports Server (NTRS)

Smith, Michael D.; Pearl, John C.; Conrath, Barney J.; Christensen, Philip R.; Vondrak, Richard R. (Technical Monitor)

2001-01-01

Infrared spectra returned by the Thermal Emission Spectrometer (TES) are well suited for retrieval of the thermal structure and the distribution of aerosols in the Martian atmosphere. Combined nadir- and limb-viewing spectra allow global monitoring of the atmosphere up to 0.01 mbar (65 km). We report here on the atmospheric thermal structure and the distribution of aerosols as observed thus far during the mapping phase of the Mars Global Surveyor mission. Zonal and temporal mean cross sections are used to examine the seasonal evolution of atmospheric temperatures and zonal winds during a period extending from northern hemisphere mid-summer through vernal equinox (L(sub s) = 104-360 deg). Temperature maps at selected pressure levels provide a characterization of planetary-scale waves. Retrieved atmospheric infrared dust opacity maps show the formation and evolution of regional dust storms during southern hemisphere summer. Response of the atmospheric thermal structure to the changing dust loading is observed. Maps of water-ice clouds as viewed in the thermal infrared are presented along with seasonal trends of infrared water-ice opacity. Uses of these observations for diagnostic studies of the dynamics of the atmosphere are discussed.

Characterization of urban aerosol in Cork city (Ireland) using aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Dall'Osto, M.; Ovadnevaite, J.; Ceburnis, D.; Martin, D.; Healy, R. M.; O'Connor, I. P.; Kourtchev, I.; Sodeau, J. R.; Wenger, J. C.; O'Dowd, C.

2013-05-01

Ambient wintertime background urban aerosol in Cork city, Ireland, was characterized using aerosol mass spectrometry. During the three-week measurement study in 2009, 93% of the ca. 1 350 000 single particles characterized by an Aerosol Time-of-Flight Mass Spectrometer (TSI ATOFMS) were classified into five organic-rich particle types, internally mixed to different proportions with elemental carbon (EC), sulphate and nitrate, while the remaining 7% was predominantly inorganic in nature. Non-refractory PM1 aerosol was characterized using a High Resolution Time-of-Flight Aerosol Mass Spectrometer (Aerodyne HR-ToF-AMS) and was also found to comprise organic aerosol as the most abundant species (62%), followed by nitrate (15%), sulphate (9%) and ammonium (9%), and chloride (5%). Positive matrix factorization (PMF) was applied to the HR-ToF-AMS organic matrix, and a five-factor solution was found to describe the variance in the data well. Specifically, "hydrocarbon-like" organic aerosol (HOA) comprised 20% of the mass, "low-volatility" oxygenated organic aerosol (LV-OOA) comprised 18%, "biomass burning" organic aerosol (BBOA) comprised 23%, non-wood solid-fuel combustion "peat and coal" organic aerosol (PCOA) comprised 21%, and finally a species type characterized by primary {m/z} peaks at 41 and 55, similar to previously reported "cooking" organic aerosol (COA), but possessing different diurnal variations to what would be expected for cooking activities, contributed 18%. Correlations between the different particle types obtained by the two aerosol mass spectrometers are also discussed. Despite wood, coal and peat being minor fuel types used for domestic space heating in urban areas, their relatively low combustion efficiencies result in a significant contribution to PM1 aerosol mass (44% and 28% of the total organic aerosol mass and non-refractory total PM1, respectively).

Aircraft-based Aerosol Size and Composition Measurements during ACE-Asia and CRYSTAL-FACE using an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Bahreini, R.; Jimenez, J.; Delia, A.; Flagan, R. C.; Seinfeld, J. H.; Jayne, J. T.; Worsnop, D. R.

2002-12-01

An Aerodyne Aerosol Mass Spectrometer (AMS) was deployed in an aircraft for the first time during the ACE-Asia field campaign. The AMS was operated on board the CIRPAS Twin Otter aircraft to measure the size-resolved chemical composition of the submicron aerosols in the outflow from Eastern Asia. Research flights were carried out from March 31 to May 1, 2001 in an area that covered 127 E-135 E and 32 N-38 N on longitude and latitude, respectively. The submicron aerosol was typically distributed in distinct layers (from the boundary layer to ~ 3700 m). This is consistent with other on-board measurements. The aerosol in the pollution layers was mainly composed of sulfate, ammonium, and organics separated by cleaner layers. Sub-micron nitrate aerosols were also detected in some layers. Since the molar ratio of positive to negative ions did not exceed one on most of the constant altitude legs of the flights, the particles were not completely neutralized. Sulfate and organics concentrations of up to 10 and 5 ug m-3 (STP), respectively, were measured on some pollution layers. AMS measurements of sulfate concentration and NH4/SO4 mass ratio (~0.16 on average) are consistent with previously reported measurements at Cheju Island, South Korea [Charmichael et al., 1997; Chen et al., 1997] and Sapporo, Japan [Kaneyasu et al., 1995]. The mass-weighed size distribution of the sub-micron sulfate was relatively constant from day to day and layer to layer, with an aerodynamic mode at 350-500 nm (vacuum aerodynamic diameter) and FWHM ~ 400 nm on most of the layers. Furthermore, the ratios between SO4/ NH4/ NO3/ Organics were approximately independent of size in the sub-micron size range. Comparisons of AMS data to other on-board aerosol measurements will be presented. In particular, the AMS mass concentration correlates well with the aerosol volume determined by the on-board Differential Automated Classifying Aerosol Detector (DCAD). In addition, preliminary results of airborne size

Airborne imaging spectrometers developed in China

NASA Astrophysics Data System (ADS)

Wang, Jianyu; Xue, Yongqi

1998-08-01

Airborne imaging spectral technology, principle means in airborne remote sensing, has been developed rapidly both in the world and in China recently. This paper describes Modular Airborne Imaging Spectrometer (MAIS), Operational Modular Airborne Imaging Spectrometer (OMAIS) and Pushbroom Hyperspectral Imagery (PHI) that have been developed or are being developed in Airborne Remote Sensing Lab of Shanghai Institute of Technical Physics, CAS.

Fast Airborne Aerosol Size and Chemistry Measurements with the High Resolution Aerosol Mass Spectrometer during the MILAGRO Campaign

NASA Technical Reports Server (NTRS)

DeCarlo, P. F.; Dunlea, E. J.; Kimmel, J. R.; Aiken, A. C.; Sueper, D.; Crounse, J.; Wennberg, P. O.; Emmons, L.; Shinozuka, Y.; Clarke, A.;

Chemical Characterization of Particulate Matter at the La Porte site Using an Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Silva, P. J.; Worsnop, D.; Canagaratna, M.; Jimenez, J. L.; Delia, A.; Purvis, K.; Davidovits, P.

2001-12-01

During the summer of 2000, a large atmospheric chemistry field campaign took place in the Greater Houston area in conjunction with an EPA supersite. As part of the campaign, we operated an aerosol mass spectrometer from 20 August, 2000 until 15 September, 2000. The aerosol mass spectrometer (AMS) obtained chemical composition data and particle size distributions continuously with 10 minute averaging times. The measured aerosol mass concentration ranged from approximately 2 μ g m-3 to a high of 30 μ g m-3. Ammonium and sulfate were the two dominant chemical species present during most of the study. The mass concentration of particulate nitrate was typically less than a few μ g m-3, with one major nitrate event on 23 August, 2000. Very small amounts of non-sea salt chloride were detected in the particles, typically less than one μ g m-3, again with the largest value detected on 23 August 2000. In addition to the inorganic species, several different organic aerosol types were identified based on simple evaluation of mass spectral and size distribution data. Three organic particle types appear to be from discrete primary sources of organic aerosol. A combustion particle type displays mass spectra similar to those observed from diesel exhaust emissions. The temporal variation of this type shows sharp spikes, consistent with primary sources and sharp plumes that drift pass. A second organic particle type is responsible for the largest particle mass concentrations observed during the entire study, occurring during a fire episode on 5-6 September, 2000. The mass spectra exhibit characteristic peaks representative of markers for compounds from biomass burning, including levoglucosan and dehydroabietic acid. A third organic particle type observed during the study exhibits peaks in the mass spectra that are characteristic of fluorinated hydrocarbons and are similar to mass spectra of pump oil. This particle type contributes several μ g m-3 to the ambient particle mass

Calibrations and Comparisons of Aerosol Spectrometers linking Ground and Airborne Measurements

NASA Astrophysics Data System (ADS)

Williamson, C.; Brock, C. A.; Erdesz, F.

2015-12-01

The nucleation-mode aerosol size spectrometer (NMASS), a fast-time response instrument measuring aerosol size distributions between 5 and 60nm, is to sample in the boundary layer and free troposphere on NASA's Atmospheric Tomography mission (ATom), providing contiguous data with global coverage in all four seasons. In preparation for this the NMASS is calibrated for the expected flight conditions and compatibility studies are made with ground-based instrumentation. The NMASS is comprised of 5 parallel condensation particle counters (CPCs) using perfluoro-tributylamine as a working fluid. Understanding the variation of CPC counting efficiencies with respect to the chemical composition of the sample is important for accurate data analysis and can be used to give indirect information about sample chemical composition. This variation is strongly dependent on the working fluid. The absolute responses and associated variations of the NMASS to ammonium sulfate and limonene ozonolysis products, compounds pertinent to the composition of particles nucleated in the free troposphere and boundary later, are compared to those of butanol, diethylene-glycol and water based CPCs, which are more commonly used in ground-based measurements. While fast time-response is key to measuring aerosol size distributions on flights, high size-resolution is often prioritized for ground-based measurements, and so a scanning mobility particle sizer (SMPS) is commonly used. Inter-comparison between NMASS and SMPS data is non-trivial because of the different working principles and resolutions of the instruments and yet it is vital, for example, for understanding the sources of particles observed during flights and the global relevance of phenomena observed from field stations and in chambers. We report compatibility studies on inversions of data from the SMPS and NMASS, evaluating temporal and spatial resolution and sources of uncertainty.

Rapid Measurements of Aerosol Size Distribution and Hygroscopic Growth via Image Processing with a Fast Integrated Mobility Spectrometer (FIMS)

NASA Astrophysics Data System (ADS)

Wang, Y.; Pinterich, T.; Spielman, S. R.; Hering, S. V.; Wang, J.

2017-12-01

Aerosol size distribution and hygroscopicity are among key parameters in determining the impact of atmospheric aerosols on global radiation and climate change. In situ submicron aerosol size distribution measurements commonly involve a scanning mobility particle sizer (SMPS). The SMPS scanning time is in the scale of minutes, which is often too slow to capture the variation of aerosol size distribution, such as for aerosols formed via nucleation processes or measurements onboard research aircraft. To solve this problem, a Fast Integrated Mobility Spectrometer (FIMS) based on image processing was developed for rapid measurements of aerosol size distributions from 10 to 500 nm. The FIMS consists of a parallel plate classifier, a condenser, and a CCD detector array. Inside the classifier an electric field separates charged aerosols based on electrical mobilities. Upon exiting the classifier, the aerosols pass through a three stage growth channel (Pinterich et al. 2017; Spielman et al. 2017), where aerosols as small as 7 nm are enlarged to above 1 μm through water or heptanol condensation. Finally, the grown aerosols are illuminated by a laser sheet and imaged onto a CCD array. The images provide both aerosol concentration and position, which directly relate to the aerosol size distribution. By this simultaneous measurement of aerosols with different sizes, the FIMS provides aerosol size spectra nearly 100 times faster than the SMPS. Recent deployment onboard research aircraft demonstrated that the FIMS is capable of measuring aerosol size distributions in 1s (Figure), thereby offering a great advantage in applications requiring high time resolution (Wang et al. 2016). In addition, the coupling of the FIMS with other conventional aerosol instruments provides orders of magnitude more rapid characterization of aerosol optical and microphysical properties. For example, the combination of a differential mobility analyzer, a relative humidity control unit, and a FIMS was

Measuring Sodium Chloride Contents of Aerosols

NASA Technical Reports Server (NTRS)

Sinha, M. P.; Friedlander, S. K.

1986-01-01

Amount of sodium chloride in individual aerosol particles measured in real time by analyzer that includes mass spectrometer. Analyzer used to determine mass distributions of active agents in therapeutic or diagnostic aerosols derived from saline solutions and in analyzing ocean spray. Aerosol particles composed of sodium chloride introduced into oven, where individually vaporized on hot wall. Vapor molecules thermally dissociated, and some of resulting sodium atoms ionized on wall. Ions leave oven in burst and analyzed by spectrometer, which is set to monitor sodium-ion intensity.

Characterization of biomass burning aerosols produced in the laboratory with a light-scattering aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Middlebrook, A. M.; Adler, G. A.; Coggon, M.; De Gouw, J. A.; Franchin, A.; Gilman, J.; Koss, A.; Krechmer, J. E.; Lamb, K.; Manfred, K.; Roberts, J. M.; Schwarz, J. P.; Sekimoto, K.; Selimovic, V.; Stockwell, C.; Wagner, N.; Warneke, C.; Washenfelder, R. A.; Womack, C.; Yokelson, R. J.; Yuan, B.

2017-12-01

During the 2016 NOAA FIREX project at the Missoula Fire Sciences Laboratory, small fires of known fuel type and properties were ignited to characterize their direct emissions with a large variety of new sampling methods. Two types of experiments were employed: sampling smoke directly from the exhaust stack throughout the lifecycle of the fires (stack burns) or sampling when the exhaust vent was closed to fill the room with smoke (room burns). For both types of burns, photo-oxidation chambers were at times used to mimic aging in the atmosphere. During all these experiments, we measured the non-refractory components of the smoke particles using an Aerodyne compact time-of-flight aerosol mass spectrometer (AMS) with a light scattering module and diluted the sample line as little as possible (usually by a factor of 10) without overwhelming our instrument. For the stack burns, our AMS was placed near the top of the exhaust stack to capture the composition and size distribution during the rapidly changing stages of the fires. We found that the chemical composition of the aerosols varied with fuel type and combustion conditions on time scales of a few minutes as the fuels went through different stages of heating and combustion. For the room burns, we obtained additional measurements with the light-scattering module aimed at understanding how well smoke particles are measured with the AMS, along with characterization of their physical properties. We will present a summary of our results, with connections to their relevance for constraining model treatments of fire emissions on the atmosphere.

The complex refractive index of atmospheric and model humic-like substances (HULIS) retrieved by a cavity ring down aerosol spectrometer (CRD-AS).

PubMed

Dinar, E; Riziq, A Abo; Spindler, C; Erlick, C; Kiss, G; Rudich, Y

2008-01-01

Atmospheric aerosols absorb and reflect solar radiation causing surface cooling and heating of the atmosphere. The interaction between aerosols and radiation depends on their complex index of refraction, which is related to the particles' chemical composition. The contribution of light absorbing organic compounds, such as HUmic-LIke Substances (HULIS) to aerosol scattering and absorption is among the largest uncertainties in assessing the direct effect of aerosols on climate. Using a Cavity Ring Down Aerosol Spectrometer (CRD-AS), the complex index of refraction of aerosols containing HULIS extracted from pollution, smoke, and rural continental aerosols, and molecular weight-fractionated fulvic acid was measured at 390 nm and 532 nm. The imaginary part of the refractive index (absorption) substantially increases towards the UV range with increasing molecular weight and aromaticity. At both wavelengths, HULIS extracted from pollution and smoke particles absorb more than HULIS from the rural aerosol. Sensitivity calculations for a pollution-type aerosol containing ammonium sulfate, organic carbon (HULIS), and soot suggests that accounting for absorption by HULIS leads in most cases to a significant decrease in the single scattering albedo and to a significant increase in aerosol radiative forcing efficiency, towards more atmospheric absorption and heating. This indicates that HULIS in biomass smoke and pollution aerosols, in addition to black carbon, can contribute significantly to light absorption in the ultraviolet and visible spectral regions.

Measurements of Size Resolved Organic Particulate Mass Using An On-line Aerosol Mass Spectrometer (ams) Laboratory Validation; Analysis Tool Development; and Interpretation of Field Data

NASA Astrophysics Data System (ADS)

Alfarra, M. R.; Coe, H.; Allan, J. D.; Bower, K. N.; Garforth, A. A.; Canagaratna, M.; Worsnop, D.

The aerosol mass spectrometer (AMS) is a quantitative instrument designed to deliver real-time size resolved chemical composition of the volatile and semi volatile aerosol fractions. The AMS response to a wide range of organic compounds has been exper- imentally characterized, and has been shown to compare well with standard libraries of 70 eV electron impact ionization mass spectra. These results will be presented. Due to the scanning nature of the quadrupole mass spectrometer, the AMS provides averaged composition of ensemble of particles rather than single particle composi- tion. However, the mass spectra measured by AMS are reproducible and similar to those of standard libraries so analysis tools can be developed on large mass spectral libraries that can provide chemical composition information about the type of organic compounds in the aerosol. One such tool is presented and compared with laboratory measurements of single species and mixed component organic particles by the AMS. We will then discuss the applicability of these tools to interpreting field AMS data ob- tained in a range of experiments at different sites in the UK and Canada. The data will be combined with other measurements to show the behaviour of the organic aerosol fraction in urban and sub-urban environments.

Chemical Composition of African Biomass Burning Aerosols Over the Southeast Atlantic: Aerosol Mass Spectrometer Results from the 2016 and 2017 ORACLES Field Campaigns.

NASA Astrophysics Data System (ADS)

Dobracki, A. N.; Howell, S. G.; Freitag, S.; Smirnow, N.; Podolske, J. R.

2017-12-01

Biomass burning (BB) is one of the largest contributors of anthropogenic aerosols in the atmosphere. During BB events, organic and inorganic gases and particles are emitted into the atmosphere. Because of their abundance, particle size, and radiative properties, BB aerosols play an important role in global climate. Southern Africa produces 30% of the Earth's BB aerosol particles. Organics, Nitrates, sulfates, and refractory black carbon, along with other chemical species are lofted into the free troposphere and transported over the Southeast Atlantic Ocean. However, considerate uncertainty remains in the chemical composition of these plumes with its large variety of organic and inorganic species. As part of the NASA ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) 2016 and 2017 airborne field campaigns, an Aerosol Mass Spectrometer (AMS) was used to sample the chemical composition and chemical structure of the aerosol in this region. Results show constant vertical stratification within the plume over the course of the campaign (August 2017 / September 2016). Using nitrate (NO3) and organic carbon (OC) as two tracers, the structure of the September 2016 plume had a ratio of 1:8 (NO3:OC) in the upper plume (3km-5km), while the lower plume (1km-2.5km) had a ratio of 1:12 (NO3:OC). AMS measurements were supported by carbon monoxide (CO) and carbon dioxide (CO2) measurements. This data revealed a modified combustion efficiency (MCE= ΔCO2/ΔCO2 + ΔCO) of <0.97 in the upper plume, and a higher MCE > 0.97 in the lower plume. An MCE above 0.9 represents efficient burning processes. Additionally, concentrations of C2(H2O)2 (m/z60), a common chemical fragment from breaking up carbohydrates (primarily levoglucosan) emitted by burning biomass only represented <1% of total organics throughout the campaign. These low concentrations are due to efficient combustion rather than oxidation during transport. These results are consistent with earlier studies of

Characterizing particulate matter emissions from vehicles: chassis-dynamometer tests using a High-Resolution Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Collier, S.; Zhang, Q.; Forestieri, S.; Kleeman, M.; Cappa, C. D.; Kuwayama, T.

2012-12-01

During September of 2011 a suite of real-time instruments was used to sample vehicle emissions at the California Air Resources Board Haagen-Schmidt facility in El Monte, CA. A representative fleet of 8 spark ignition gasoline vehicles, a diesel passenger vehicle, a gasoline direct-injection vehicle and an ultra-low emissions vehicle were tested on a chassis dynamometer. The emissions were sampled into the facility's standard CVS tunnel and diluted to atmospherically relevant levels (5-30 μg/m3) while controlling other factors such as relative humidity or background black carbon particulate loading concentrations. An Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-MS) was among the real-time instruments used and sampled vehicle emissions at 10 second time resolution in order to characterize the non-refractory organic and inorganic particulate matter (PM). PM composition and concentration were tracked throughout the cold start driving cycle which included periods of fast acceleration and high velocity cruise control, meant to recreate typical commuter driving behavior. Variations in inorganic and organic PM composition for a given vehicle throughout the driving cycle as well as for various vehicles with differing emissions loading were characterized. Differences in PM composition for a given vehicle whose emissions are being exposed to differing experimental conditions such as varying relative humidity will also be reported. In conjunction with measurements from a Multi Wavelength Photoacoustic Black Carbon Spectrometer (MWPA-BC) and real-time gas measurements from the CARB facility, we determine the real-time emission ratios of primary organic aerosols (POA) with respect to BC and common combustion gas phase pollutants and compared to different vehicle driving conditions. The results of these tests offer the vehicle emissions community a first time glimpse at the real-time behavior of vehicle PM emissions for a variety of conditions and

Expected trace gas and aerosol retrieval accuracy of the Geostationary Environment Monitoring Spectrometer

NASA Astrophysics Data System (ADS)

Jeong, U.; Kim, J.; Liu, X.; Lee, K. H.; Chance, K.; Song, C. H.

2015-12-01

The predicted accuracy of the trace gases and aerosol retrievals from the geostationary environment monitoring spectrometer (GEMS) was investigated. The GEMS is one of the first sensors to monitor NO2, SO2, HCHO, O3, and aerosols onboard geostationary earth orbit (GEO) over Asia. Since the GEMS is not launched yet, the simulated measurements and its precision were used in this study. The random and systematic component of the measurement error was estimated based on the instrument design. The atmospheric profiles were obtained from Model for Ozone And Related chemical Tracers (MOZART) simulations and surface reflectances were obtained from climatology of OMI Lambertian equivalent reflectance. The uncertainties of the GEMS trace gas and aerosol products were estimated based on the OE method using the atmospheric profile and surface reflectance. Most of the estimated uncertainties of NO2, HCHO, stratospheric and total O3 products satisfied the user's requirements with sufficient margin. However, about 26% of the estimated uncertainties of SO2 and about 30% of the estimated uncertainties of tropospheric O3 do not meet the required precision. Particularly the estimated uncertainty of SO2 is high in winter, when the emission is strong in East Asia. Further efforts are necessary in order to improve the retrieval accuracy of SO2 and tropospheric O3 in order to reach the scientific goal of GEMS. Random measurement error of GEMS was important for the NO2, SO2, and HCHO retrieval, while both the random and systematic measurement errors were important for the O3 retrievals. The degree of freedom for signal of tropospheric O3 was 0.8 ± 0.2 and that for stratospheric O3 was 2.9 ± 0.5. The estimated uncertainties of the aerosol retrieval from GEMS measurements were predicted to be lower than the required precision for the SZA range of the trace gas retrievals.

Design Of A Novel Open-Path Aerosol Extinction Cavity Ringdown Spectrometer And Initial Data From Deployment At NOAA's Atmospheric Observatory

NASA Astrophysics Data System (ADS)

Gordon, T. D.; Wagner, N. L.; Richardson, M.; Law, D. C.; Wolfe, D. E.; Brock, C. A.; Erdesz, F.; Murphy, D. M.

2014-12-01

The ability to frame effective climate change policy depends strongly on reducing the uncertainty in aerosol radiative forcing, which is currently nearly as great as best estimates of its magnitude. Achieving this goal will require significant progress in measuring aerosol properties, including aerosol optical depth, single scattering albedo and the effect of relative humidity on these properties for both fine and coarse particles. However both ground- and space-based instruments fail or are highly biased in the presence of clouds, severely limiting quantitative estimates of the radiative effects of aerosols where they are advected over low-level clouds. Moreover, many in situ aerosol measurements exclude the coarse fraction, which can be very important in and downwind of desert regions. By measuring the decay rate of a pulsed laser in an optically resonant cavity, cavity ringdown spectrometers (CRDSs) have been employed successfully in measuring aerosol extinction for particles in relative humidities below 90%. At very high humidities (as found in and near clouds), however, existing CRDSs perform poorly, diverging significantly from theoretical extinction values as humidities approach 100%. The new open-path aerosol extinction CRDS described in this poster measures extinction as aerosol is drawn through the sample cavity directly without inlets or tubing for channeling the flow, which cause particle losses, condensation at high RH and other artifacts. This poster presents the key elements of the new open-path CRDS design as well as comparisons with an earlier generation closed-path CRDS and preliminary data obtained during a field study at the 300 meter tower at NOAA's Boulder Atmospheric Observatory (BAO) in Colorado.

Characterization of urban aerosol in Cork City (Ireland) using aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Dall'Osto, M.; Ovadnevaite, J.; Ceburnis, D.; Martin, D.; Healy, R. M.; O'Connor, I. P.; Sodeau, J. R.; Wenger, J. C.; O'Dowd, C.

2012-11-01

Ambient wintertime background urban aerosol in Cork City, Ireland, was characterized using aerosol mass spectrometry. During the three-week measurement study in 2009, 93% of the 1 200 000 single particles characterized by an Aerosol Time-Of-Flight Mass Spectrometer (TSI ATOFMS) were classified into five organic-rich particle types, internally-mixed to different proportions with Elemental Carbon (EC), sulphate and nitrate while the remaining 7% was predominantly inorganic in nature. Non-refractory PM1 aerosol was also characterized using a High Resolution Time-Of-Flight Aerodyne Aerosol Mass Spectrometer (HR-ToF-AMS) and was also found to comprise organic matter as the most abundant species (62%), followed by nitrate (15%), sulphate (9%) and ammonium (9%), and then chloride (5%). Positive matrix factorization (PMF) was applied to the HR-ToF-AMS organic matrix and a five-factor solution was found to describe the variance in the data well. Specifically, "Hydrocarbon-like" Organic Aerosol (HOA) comprised 19% of the mass, "Oxygenated low volatility" Organic Aerosols (LV-OOA) comprised 19%, "Biomass wood Burning" Organic Aerosol (BBOA) comprised 23%, non-wood solid-fuel combustion "Peat and Coal" Organic Aerosol (PCOA) comprised 21%, and finally, a species type characterized by primary m/z peaks at 41 and 55, similar to previously-reported "Cooking" Organic Aerosol (COA) but possessing different diurnal variations to what would be expected for cooking activities, contributed 18%. Despite wood, cool and peat being minor fuel types used for domestic space heating in urban areas, their relatively low combustion efficiencies result in a significant contribution to PM1 aerosol mass (44% and 28% of the total organic aerosols mass and non refractory PM1, respectively).

Receptor modeling of near-roadway aerosol mass spectrometer data in Las Vegas, Nevada, with EPA PMF

NASA Astrophysics Data System (ADS)

Brown, S. G.; Lee, T.; Norris, G. A.; Roberts, P. T.; Collett, J. L., Jr.; Paatero, P.; Worsnop, D. R.

2012-01-01

Ambient non-refractory PM1 aerosol particles were measured with an Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-AMS) at an elementary school 18 m from the US 95 freeway soundwall in Las Vegas, Nevada, during January 2008. Additional collocated continuous measurements of black carbon (BC), carbon monoxide (CO), nitrogen oxides (NOx), and meteorological data were collected. The US~Environmental Protection Agency's~(EPA) positive matrix factorization (PMF) data analysis tool was used to apportion organic matter (OM) as measured by HR-AMS, and rotational tools in EPA PMF were used to better characterize the solution space and pull resolved factors toward known source profiles. Three- to six-factor solutions were resolved. The four-factor solution was the most interpretable, with the typical AMS PMF factors of hydrocarbon-like organic aerosol (HOA), low-volatility oxygenated organic aerosol (LV-OOA), biomass burning organic aerosol (BBOA), and semi-volatile oxygenated organic aerosol (SV-OOA). When the measurement site was downwind of the freeway, HOA composed about half the OM, with SV-OOA and LV-OOA accounting for the rest. Attempts to pull the PMF factor profiles toward source profiles were successful but did not qualitatively change the results, indicating that these factors are very stable. Oblique edges were present in G-space plots, suggesting that the obtained rotation may not be the most plausible one. Since solutions found by pulling the profiles or using Fpeak retained these oblique edges, there appears to be little rotational freedom in the base solution. On average, HOA made up 26% of the OM, while LV-OOA was highest in the afternoon and accounted for 26% of the OM. BBOA occurred in the evening hours, was predominantly from the residential area to the north, and on average constituted 12% of the OM; SV-OOA accounted for the remaining third of the OM. Use of the pulling techniques available in EPA PMF and ME-2 suggested that the four

Long-range transport biomass burning emissions to the Himalayas: insights from high-resolution aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Xu, J.; Zhang, X.; Liu, Y.; Shichang, K.; Ma, Y.

2017-12-01

An intensive measurement was conducted at a remote, background, and high-altitude site (Qomolangma station, QOMS, 4276 m a.s.l.) in the northern Himalayas, using an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) along with other collocated instruments. The field measurement was performed from April 12 to May 12, 2016 to chemically characterize high time-resolved submicron particulate matter (PM1) and obtain the influence of biomass burning emissions to the Himalayas, frequently transported from south Asia during pre-monsoon season. Two high aerosol loading periods were observed during the study. Overall, the average (± 1σ) PM1 mass concentration was 4.44 (± 4.54) µg m-3 for the entire study, comparable with those observed at other remote sites worldwide. Organic aerosols (OA) was the dominant PM1 species (accounting for 54.3% of total PM1 mass on average) and its contribution increased with the increase of total PM1 mass loading. The average size distributions of PM1 species all peaked at an overlapping accumulation mode ( 500 nm), suggesting that aerosol particles were internally well-mixed and aged during long-range transportations. Positive matrix factorization (PMF) analysis on the high-resolution organic mass spectra identified three distinct OA factors, including a biomass burning related OA (BBOA, 43.7%) and two oxygenated OA (Local-OOA and LRT-OOA; 13.9% and 42.4%) represented sources from local emissions and long-range transportations, respectively. Two polluted air mass origins (generally from the west and southwest of QOMS) and two polluted episodes with enhanced PM1 mass loadings and elevated BBOA contributions were observed, respectively, suggesting the important sources of wildfires from south Asia. One of polluted aerosol plumes was investigated in detail to illustrate the evolution of aerosol characteristics at QOMS driving by different impacts of wildfires, air mass origins, meteorological conditions and

Aerosol Climate Time Series Evaluation In ESA Aerosol_cci

NASA Astrophysics Data System (ADS)

Popp, T.; de Leeuw, G.; Pinnock, S.

2015-12-01

Within the ESA Climate Change Initiative (CCI) Aerosol_cci (2010 - 2017) conducts intensive work to improve algorithms for the retrieval of aerosol information from European sensors. By the end of 2015 full mission time series of 2 GCOS-required aerosol parameters are completely validated and released: Aerosol Optical Depth (AOD) from dual view ATSR-2 / AATSR radiometers (3 algorithms, 1995 - 2012), and stratospheric extinction profiles from star occultation GOMOS spectrometer (2002 - 2012). Additionally, a 35-year multi-sensor time series of the qualitative Absorbing Aerosol Index (AAI) together with sensitivity information and an AAI model simulator is available. Complementary aerosol properties requested by GCOS are in a "round robin" phase, where various algorithms are inter-compared: fine mode AOD, mineral dust AOD (from the thermal IASI spectrometer), absorption information and aerosol layer height. As a quasi-reference for validation in few selected regions with sparse ground-based observations the multi-pixel GRASP algorithm for the POLDER instrument is used. Validation of first dataset versions (vs. AERONET, MAN) and inter-comparison to other satellite datasets (MODIS, MISR, SeaWIFS) proved the high quality of the available datasets comparable to other satellite retrievals and revealed needs for algorithm improvement (for example for higher AOD values) which were taken into account for a reprocessing. The datasets contain pixel level uncertainty estimates which are also validated. The paper will summarize and discuss the results of major reprocessing and validation conducted in 2015. The focus will be on the ATSR, GOMOS and IASI datasets. Pixel level uncertainties validation will be summarized and discussed including unknown components and their potential usefulness and limitations. Opportunities for time series extension with successor instruments of the Sentinel family will be described and the complementarity of the different satellite aerosol products

Aerosol Climate Time Series in ESA Aerosol_cci

NASA Astrophysics Data System (ADS)

Popp, Thomas; de Leeuw, Gerrit; Pinnock, Simon

2016-04-01

Within the ESA Climate Change Initiative (CCI) Aerosol_cci (2010 - 2017) conducts intensive work to improve algorithms for the retrieval of aerosol information from European sensors. Meanwhile, full mission time series of 2 GCOS-required aerosol parameters are completely validated and released: Aerosol Optical Depth (AOD) from dual view ATSR-2 / AATSR radiometers (3 algorithms, 1995 - 2012), and stratospheric extinction profiles from star occultation GOMOS spectrometer (2002 - 2012). Additionally, a 35-year multi-sensor time series of the qualitative Absorbing Aerosol Index (AAI) together with sensitivity information and an AAI model simulator is available. Complementary aerosol properties requested by GCOS are in a "round robin" phase, where various algorithms are inter-compared: fine mode AOD, mineral dust AOD (from the thermal IASI spectrometer, but also from ATSR instruments and the POLDER sensor), absorption information and aerosol layer height. As a quasi-reference for validation in few selected regions with sparse ground-based observations the multi-pixel GRASP algorithm for the POLDER instrument is used. Validation of first dataset versions (vs. AERONET, MAN) and inter-comparison to other satellite datasets (MODIS, MISR, SeaWIFS) proved the high quality of the available datasets comparable to other satellite retrievals and revealed needs for algorithm improvement (for example for higher AOD values) which were taken into account for a reprocessing. The datasets contain pixel level uncertainty estimates which were also validated and improved in the reprocessing. For the three ATSR algorithms the use of an ensemble method was tested. The paper will summarize and discuss the status of dataset reprocessing and validation. The focus will be on the ATSR, GOMOS and IASI datasets. Pixel level uncertainties validation will be summarized and discussed including unknown components and their potential usefulness and limitations. Opportunities for time series extension

Laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF): performance, reference spectra and classification of atmospheric samples

NASA Astrophysics Data System (ADS)

Shen, Xiaoli; Ramisetty, Ramakrishna; Mohr, Claudia; Huang, Wei; Leisner, Thomas; Saathoff, Harald

2018-04-01

The laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF, AeroMegt GmbH) is able to identify the chemical composition and mixing state of individual aerosol particles, and thus is a tool for elucidating their impacts on human health, visibility, ecosystem, and climate. The overall detection efficiency (ODE) of the instrument we use was determined to range from ˜ (0.01 ± 0.01) to ˜ (4.23 ± 2.36) % for polystyrene latex (PSL) in the size range of 200 to 2000 nm, ˜ (0.44 ± 0.19) to ˜ (6.57 ± 2.38) % for ammonium nitrate (NH4NO3), and ˜ (0.14 ± 0.02) to ˜ (1.46 ± 0.08) % for sodium chloride (NaCl) particles in the size range of 300 to 1000 nm. Reference mass spectra of 32 different particle types relevant for atmospheric aerosol (e.g. pure compounds NH4NO3, K2SO4, NaCl, oxalic acid, pinic acid, and pinonic acid; internal mixtures of e.g. salts, secondary organic aerosol, and metallic core-organic shell particles; more complex particles such as soot and dust particles) were determined. Our results show that internally mixed aerosol particles can result in spectra with new clusters of ions, rather than simply a combination of the spectra from the single components. An exemplary 1-day ambient data set was analysed by both classical fuzzy clustering and a reference-spectra-based classification method. Resulting identified particle types were generally well correlated. We show how a combination of both methods can greatly improve the interpretation of single-particle data in field measurements.

Receptor modeling of near-roadway aerosol mass spectrometer data in Las Vegas, Nevada, with EPA PMF

NASA Astrophysics Data System (ADS)

Brown, S. G.; Lee, T.; Norris, G. A.; Roberts, P. T.; Collett, J. L., Jr.; Paatero, P.; Worsnop, D. R.

2011-08-01

Ambient non-refractory PM1 aerosol particles were measured with an Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-AMS) at an elementary school 20 m from the US 95 freeway in Las Vegas, Nevada, during January 2008. Additional collocated continuous measurements of black carbon (BC), carbon monoxide (CO), nitrogen oxides (NOx), and meteorological data were collected. The US Environmental Protection Agency's (EPA) positive matrix factorization (PMF) data analysis tool was used to apportion organic matter (OM) as measured by HR-AMS, and rotational tools in EPA PMF were used to better characterize the solution space and pull resolved factors toward known source profiles. Three- to six-factor solutions were resolved. The four-factor solution was the most interpretable, with the typical AMS PMF factors of hydrocarbon-like organic aerosol (HOA), low-volatility oxygenated organic aerosol (LV-OOA), biomass burning organic aerosol (BBOA), and semi-volatile oxygenated organic aerosol (SV-OOA). When the measurement site was downwind of the freeway, HOA composed about half the OM, with SV-OOA and LV-OOA accounting for the rest. Attempts to pull the PMF factor profiles toward source profiles were successful but did not qualitatively change the results, indicating that these factors are very stable. Oblique edges were present in G-space plots, suggesting that the obtained rotation may not be the most plausible one. Since solutions found by pulling the profiles or using Fpeak retained these oblique edges, there appears to be little rotational freedom in the base solution. On average, HOA made up 26 % of the OM, and it made up nearly half of the OM when the monitoring site was downwind of US 95 during morning rush hour. LV-OOA was highest in the afternoon and accounted for 26 % of the OM. BBOA occurred in the evening hours, was predominantly from the residential area to the north, and on average constituted 12 % of the OM; SV-OOA accounted for the remaining

Mass Spectrometer for Airborne Micro-Organisms

NASA Technical Reports Server (NTRS)

Sinha, M. P.; Friedlander, S. K.

1986-01-01

Bacteria and other micro-organisms identified continously with aid of new technique for producing samples for mass spectrometer. Technique generates aerosol of organisms and feeds to spectrometer. Given species of organism produces characteristic set of peaks in mass spectrum and thereby identified. Technique useful for monitoring bacterial makeup in environmental studies and in places where cleanliness is essential, such as hospital operating rooms, breweries, and pharmaceutical plants.

Aerosol Chemical Composition and its Effects on Cloud-Aerosol Interactions during the 2007 CHAPS Experiment

NASA Astrophysics Data System (ADS)

Lee, Y.; Alexander, L.; Newburn, M.; Jayne, J.; Hubbe, J.; Springston, S.; Senum, G.; Andrews, B.; Ogren, J.; Kleinman, L.; Daum, P.; Berg, L.; Berkowitz, C.

2007-12-01

Chemical composition of submicron aerosol particles was determined using an Aerodyne Time-of-Flight Aerosol Mass Spectrometer (AMS) outfitted on the DOE G-1 aircraft during the Cumulus Humilis Aerosol Processing Study (CHAPS) conducted in Oklahoma City area in June 2007. The primary objective of CHAPS was to investigate the effects of urban emissions on cloud aerosol interactions as a function of processing of the emissions. Aerosol composition was typically determined at three different altitudes: below, in, and above cloud, in both upwind and downwind regions of the urban area. Aerosols were sampled from an isokinetic inlet with an upper size cut-off of ~1.5 micrometer. During cloud passages, the AMS also sampled particles that were dried from cloud droplets collected using a counter-flow virtual impactor (CVI) sampler. The aerosol mass concentrations were typically below 10 microgram per cubic meter, and were dominated by organics and sulfate. Ammonium was often less than required for complete neutralization of sulfate. Aerosol nitrate levels were very low. We noted that nitrate levels were significantly enhanced in cloud droplets compared to aerosols, most likely resulting from dissolution of gaseous nitric acid. Organic to sulfate ratios appeared to be lower in cloud droplets than in aerosols, suggesting cloud condensation nuclei properties of aerosol particles might be affected by loading and nature of the organic components in aerosols. In-cloud formation of sulfate was considered unimportant because of the very low SO2 concentration in the region. A detailed examination of the sources of the aerosol organic components (based on hydrocarbons determined using a proton transfer reaction mass spectrometer) and their effects on cloud formation as a function of atmospheric processing (based on the degree of oxidation of the organic components) will be presented.

Evaluating aerosol influence on cloud models using in-situ measurements during the INUPIAQ campaign

NASA Astrophysics Data System (ADS)

Farrington, R.; Connolly, P.; Choularton, T.; Bower, K.; Lloyd, G.; Flynn, M.; Crosier, J.; Field, P.

2014-12-01

At temperatures between -35°C and 0°C, the presence of insoluble aerosols acting as ice nuclei (IN) initiate the nucleation of ice under atmospheric conditions. Previous field and laboratory campaigns have suggested that mineral dust present in the atmosphere act as IN at temperatures around -20°C (e.g. Sassen et al. 2003), however the cause of ice nucleation at temperatures of around -5°C is less certain. Coupled with the limited representation of aerosol and cloud processes in large-scale weather and climate models, the need for improved in-situ measurements of aerosol properties and cloud micro-physical processes to drive the improvement of aerosol-clouds processes in models is evident. As part of the Ice NUcleation Process Investigation and Quantification (INUPIAQ) project, two field campaigns were conducted in early 2013 and early 2014. Both campaigns included measurements of cloud micro-physical properties at the summit of Jungfraujoch in Switzerland (3580m asl). Using data from the 2013 campaign and modelling simulations from the Weather Research and Forecasting model (WRF), an upwind site, located at Schilthorn (2970m asl), was determined for measuring aerosol properties out of cloud during the 2014 campaign. Further measurements of the cloud and aerosols properties were taken remotely using a doppler LiDAR located at Kleine Scheidegg (2061m asl). The aim of this project is to determine whether detailed aerosol information is important to determining cloud and precipitation properties downwind. To this end WRF was run using the aerosol number concentrations and size distributions measured at the Schilthorn site to compare modelled ice number concentrations with measurements taken at Jungfraujoch using state of the science cloud ice probes, including the Three-View Cloud Particle Imager (3V-CPI) and the Cloud Aerosol Spectrometer with Depolarization (CAS-DPOL), with the results of the comparison presented and discussed at this meeting. References

Fullerene Soot in Eastern China Air: Results from Soot Particle-Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Wang, J.; Ge, X.; Chen, M.; Zhang, Q.; Yu, H.; Sun, Y.; Worsnop, D. R.; Collier, S.

2015-12-01

In this work, we present for the first time, the observation and quantification of fullerenes in ambient airborne particulate using an Aerodyne Soot Particle - Aerosol Mass Spectrometer (SP-AMS) deployed during 2015 winter in suburban Nanjing, a megacity in eastern China. The laser desorption and electron impact ionization techniques employed by the SP-AMS allow us to differentiate various fullerenes from other aerosol components. Mass spectrum of the identified fullerene soot is consisted by a series of high molecular weight carbon clusters (up to m/z of 2000 in this study), almost identical to the spectral features of commercially available fullerene soot, both with C70 and C60 clusters as the first and second most abundant species. This type of soot was observed throughout the entire study period, with an average mass loading of 0.18 μg/m3, accounting for 6.4% of the black carbon mass, 1.2% of the total organic mass. Temporal variation and diurnal pattern of fullerene soot are overall similar to those of black carbon, but are clearly different in some periods. Combining the positive matrix factorization, back-trajectory and analyses of the meteorological parameters, we identified the petrochemical industrial plants situating upwind from the sampling site, as the major source of fullerene soot. In this regard, our findings imply the ubiquitous presence of fullerene soot in ambient air of industry-influenced area, especially the oil and gas production regions. This study also offers new insights into the characterization of fullerenes from other environmental samples via the advanced SP-AMS technique.

Sources and atmospheric processing of winter aerosols in Seoul, Korea: insights from real-time measurements using a high-resolution aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Kim, Hwajin; Zhang, Qi; Bae, Gwi-Nam; Kim, Jin Young; Bok Lee, Seung

2017-02-01

Highly time-resolved chemical characterization of nonrefractory submicrometer particulate matter (NR-PM1) was conducted in Seoul, the capital and largest metropolis of Korea, using an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). The measurements were performed during winter, when elevated particulate matter (PM) pollution events are often observed. This is the first time that detailed real-time aerosol measurement results have been reported from Seoul, Korea, and they reveal valuable insights into the sources and atmospheric processes that contribute to PM pollution in this region. The average concentration of submicron aerosol (PM1 = NR-PM1+ black carbon (BC)) was 27.5 µg m-3, and the total mass was dominated by organics (44 %), followed by nitrate (24 %) and sulfate (10 %). The average atomic ratios of oxygen to carbon (O / C), hydrogen to carbon (H / C), and nitrogen to carbon (N / C) of organic aerosols (OA) were 0.37, 1.79, and 0.018, respectively, which result in an average organic mass-to-carbon (OM / OC) ratio of 1.67. The concentrations (2.6-90.7 µg m-3) and composition of PM1 varied dynamically during the measurement period due to the influences of different meteorological conditions, emission sources, and air mass origins. Five distinct sources of OA were identified via positive matrix factorization (PMF) analysis of the HR-ToF-AMS data: vehicle emissions represented by a hydrocarbon-like OA factor (HOA, O / C = 0.06), cooking activities represented by a cooking OA factor (COA, O / C = 0.14), wood combustion represented by a biomass burning OA factor (BBOA, O / C = 0.34), and secondary organic aerosol (SOA) represented by a semivolatile oxygenated OA factor (SV-OOA, O / C = 0.56) and a low-volatility oxygenated OA factor (LV-OOA, O / C = 0.68). On average, primary OA (POA = HOA + COA + BBOA) accounted for 59 % the OA mass, whereas SV-OOA and LV-OOA contributed 15 and 26 %, respectively. Our results indicate that air

Dust transport over the eastern Mediterranean derived from Total Ozone Mapping Spectrometer, Aerosol Robotic Network, and surface measurements

NASA Astrophysics Data System (ADS)

Kalivitis, N.; Gerasopoulos, E.; Vrekoussis, M.; Kouvarakis, G.; Kubilay, N.; Hatzianastassiou, N.; Vardavas, I.; Mihalopoulos, N.

2007-02-01

Multiyear surface PM10 measurements performed on Crete Island, Greece, have been used in conjunction with satellite (Total Ozone Mapping Spectrometer (TOMS)) and ground-based remote sensing measurements (Aerosol Robotic Network (AERONET)) to enhance our understanding of the evolution of mineral dust events over the eastern Mediterranean. An analysis of southerly air masses at altitudes of 1000 and 3000 m over a 5 year period (2000-2005), showed that dust can potentially arrive over Crete, either simultaneously in the lower free troposphere and inside the boundary layer (vertical extended transport (VET)) or initially into the free troposphere with the heavier particles gradually being scavenged inside the boundary layer (free troposphere transport (FTT)). Both pathways present significant seasonal variations but on an annual basis contribute almost equally to the dust transport in the area. During VET the aerosol index (AI) derived from TOMS was significantly correlated with surface PM10, and in general AI was found to be adequate for the characterization of dust loadings over the eastern Mediterranean on a climatological basis. A significant covariance between PM10 and AOT was observed during VET as well, indicating that AOT levels from AERONET may be estimated by PM10 levels at the surface. Surface measurements are thus crucial for the validation of remote sensing measurements and hence are a powerful tool for the investigation of the impact of aerosols on climate.

Characterization of submicron aerosols at a rural site in Pearl River Delta of China using an Aerodyne High-Resolution Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Huang, X.-F.; He, L.-Y.; Hu, M.; Canagaratna, M. R.; Kroll, J. H.; Ng, N. L.; Zhang, Y.-H.; Lin, Y.; Xue, L.; Sun, T.-L.; Liu, X.-G.; Shao, M.; Jayne, J. T.; Worsnop, D. R.

2010-11-01

The Pearl River Delta (PRD) region in South China is one of the most economically developed regions in China, but it is also noted for its severe air pollution due to industrial/metropolitan emissions. In order to continuously improve the understanding and quantification of air pollution in this region, an intensive campaign was executed in PRD during October-November 2008. Here, we report and analyze Aerodyne High-Resolution Aerosol Mass Spectrometer measurements at Kaiping, a rural site downwind of the highly-polluted central PRD area, to characterize the general features of submicron particulate pollution in the regional air. The mean measured PM1 mass concentration was 33.1 ± 18.1 μg m-3 during the campaign and composed of organic matter (33.8%), sulfate (33.7%), ammonium (14.0%), nitrate (10.7%), black carbon (6.7%), and chloride (1.1%), which is characterized by high fractions of inorganic ions due to huge emissions of SO2 and NOx in PRD. The average size distributions of the species (except BC) were all dominated by an accumulation mode peaking at ~450 nm in vacuum aerodynamic diameter. Calculations based on high-resolution organic mass spectra indicate that C, H, O, and N on average contributed 56.6, 7.0, 35.1, and 1.3% to the total organic mass, respectively, corresponding to an organic matter mass to organic carbon mass ratio (OM/OC) of 1.77 ± 0.08. Based on the high-resolution organic mass spectral dataset observed, Positive Matrix Factorization (PMF) analysis differentiated the organic aerosol into three components, i.e., biomass burning (BBOA) and two oxygenated (LV-OOA and SV-OOA) organic aerosols, which on average accounted for 24.5, 39.6 and 35.8% of the total organic mass, respectively. The BBOA showed strong features of biomass burning emissions and has been mainly attributed to field rice straw burning after harvest. The LV-OOA and SV-OOA were found to correspond to more aged (and thus less-volatile) and fresher (and semi-volatile) secondary

Synergetic use of Aerosol Robotic Network (AERONET) and Moderate Image Spectrometer (MODIS)

NASA Technical Reports Server (NTRS)

Kaufman, Y.

2004-01-01

I shall describe several distinct modes in which AERONET data are used in conjunction with MODIS data to evaluate the global aerosol system and its impact on climate. These includes: 1) Evaluation of the aerosol diurnal cycle not available from MODIS, and the relationship between the aerosol properties derived from MODIS and the daily average of these properties; 2) Climatology of the aerosol size distribution and single scattering albedo. The climatology is used to formulate the assumptions used in the MODIS look up tables used in the inversion of MODIS data; 3) Measurement of the aerosol effect on irradiation of the surface, this is used in conjunction with the MODIS evaluation of the aerosol effect at the TOA; and 4) Assessment of the aerosol baseline on top off which the satellite data are used to find the amount of dust or anthropogenic aerosol.

Characterization of urban aerosol using aerosol mass spectrometry and proton nuclear magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Cleveland, M. J.; Ziemba, L. D.; Griffin, R. J.; Dibb, J. E.; Anderson, C. H.; Lefer, B.; Rappenglück, B.

2012-07-01

Particulate matter was measured during August and September of 2006 in Houston as part of the Texas Air Quality Study II Radical and Aerosol Measurement Project. Aerosol size and composition were determined using an Aerodyne quadrupole aerosol mass spectrometer. Aerosol was dominated by sulfate (4.1 ± 2.6 μg m-3) and organic material (5.5 ± 4.0 μg m-3), with contributions of organic material from both primary (˜32%) and secondary (˜68%) sources. Secondary organic aerosol appears to be formed locally. In addition, 29 aerosol filter samples were analyzed using proton nuclear magnetic resonance (1H NMR) spectroscopy to determine relative concentrations of organic functional groups. Houston aerosols are less oxidized than those observed elsewhere, with smaller relative contributions of carbon-oxygen double bonds. These particles do not fit 1H NMR source apportionment fingerprints for identification of secondary, marine, and biomass burning organic aerosol, suggesting that a new fingerprint for highly urbanized and industrially influenced locations be established.

Aerosol Inlet Characterization Experiment Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullard, Robert L.; Kuang, Chongai; Uin, Janek

2017-05-01

The U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility Aerosol Observation System inlet stack was characterized for particle penetration efficiency from 10 nm to 20 μm in diameter using duplicate scanning mobility particle sizers (10 nm-450 nm), ultra-high-sensitivity aerosol spectrometers (60 nm-μm), and aerodynamic particle sizers (0.5 μm-20 μm). Results show good model-measurement agreement and unit transmission efficiency of aerosols from 10 nm to 4 μm in diameter. Large uncertainties in the measured transmission efficiency exist above 4 μm due to low ambient aerosol signal in that size range.

Characterizing the Hygroscopicity of Nascent Sea Spray Aerosol from Synthetic Blooms

NASA Astrophysics Data System (ADS)

Forestieri, S.; Cappa, C. D.; Sultana, C. M.; Lee, C.; Wang, X.; Helgestad, T.; Moore, K.; Prather, K. A.; Cornwell, G.; Novak, G.; Bertram, T. H.

2015-12-01

Marine sea spray aerosol (SSA) particles make up a significant portion of natural aerosols and are therefore important in establishing the baseline for anthropogenic aerosol climate impacts. Scattering of solar radiation by aerosols affects Earth's radiative budget and the degree of scattering is size-dependent. Thus, aerosols scatter more light at elevated relative humidities when they grow larger via water uptake. This growth depends critically on chemical composition. SSA can become enriched in organics during phytoplankton blooms, becoming less salty and therefore less hygroscopic. Subsaturated hygroscopic growth factors at 85% relative humidity (GF(85%)) of SSA particles were quantified during two mesocosm experiments in enclosed marine aerosol reference tanks (MARTs). The two experiments were conducted with filtered seawater collected at separate times from the Scripps Institute of Oceanography Pier in La Jolla, CA. Phytoplankton blooms in each tank were induced via the addition of nutrients and photosynthetically active radiation. The "indoor" MART was illuminated with fluorescent light and the other "outdoor" MART was illuminated with sunlight. The peak chlorophyll-a concentrations were 59 micrograms/L and 341 micrograms /L for the indoor and outdoor MARTs, respectively. GF(85%) values for SSA particles were quantified using a humidified cavity ringdown spectrometer and particle size distributions. Particle composition was monitored with a single particle aerosol mass spectrometer (ATOFMS) and an Aerodyne aerosol mass spectrometer (AMS). Relationships between the observed particle GFs and the particle composition markers will be discussed.

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

NASA Astrophysics Data System (ADS)

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.; Day, D. A.; Ortega, A. M.; Hayes, P. L.; Krechmer, J. E.; Chen, Q.; Kuwata, M.; Liu, Y. J.; de Sá, S. S.; McKinney, K.; Martin, S. T.; Hu, M.; Budisulistiorini, S. H.; Riva, M.; Surratt, J. D.; St. Clair, J. M.; Isaacman-Van Wertz, G.; Yee, L. D.; Goldstein, A. H.; Carbone, S.; Brito, J.; Artaxo, P.; de Gouw, J. A.; Koss, A.; Wisthaler, A.; Mikoviny, T.; Karl, T.; Kaser, L.; Jud, W.; Hansel, A.; Docherty, K. S.; Alexander, M. L.; Robinson, N. H.; Coe, H.; Allan, J. D.; Canagaratna, M. R.; Paulot, F.; Jimenez, J. L.

2015-10-01

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accounted by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C5H6O+ (m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine fC5H6O (fC5H6O= C5H6O+/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher fC5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. fC5H6O in IEPOX-SOA is always elevated (12-40 ‰) but varies substantially between locations, which is shown to reflect

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accountedmore » by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C 5H 6O + ( m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine f C5H6O ( f C5H6O= C 5H 6O +/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher f C5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. f C5H6O in IEPOX-SOA is always elevated (12–40 ‰) but varies substantially between locations

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

DOE PAGES

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.; ...

2015-10-23

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accountedmore » by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C 5H 6O + ( m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine f C5H6O ( f C5H6O= C 5H 6O +/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher f C5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. f C5H6O in IEPOX-SOA is always elevated (12–40 ‰) but varies substantially between locations

How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.

PubMed

Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun; Ke, Ailong

2017-10-05

CRISPR (clustered regularly interspaced short palindromic repeats) and the nearby Cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes. Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer. Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical. The conserved Cas1 and Cas2 proteins form an integrase complex consisting of two distal Cas1 dimers bridged by a Cas2 dimer. The prespacer is bound by Cas1-Cas2 as a dual-forked DNA, and the terminal 3'-OH of each 3' overhang serves as an attacking nucleophile during integration. The prespacer is preferentially integrated into the leader-proximal region of the CRISPR array, guided by the leader sequence and a pair of inverted repeats inside the CRISPR repeat. Spacer integration in the well-studied Escherichia coli type I-E CRISPR system also relies on the bacterial integration host factor. In type II-A CRISPR, however, Cas1-Cas2 alone integrates spacers efficiently in vitro; other Cas proteins (such as Cas9 and Csn2) have accessory roles in the biogenesis phase of prespacers. Here we present four structural snapshots from the type II-A system of Enterococcus faecalis Cas1 and Cas2 during spacer integration. Enterococcus faecalis Cas1-Cas2 selectively binds to a splayed 30-base-pair prespacer bearing 4-nucleotide 3' overhangs. Three molecular events take place upon encountering a target: first, the Cas1-Cas2-prespacer complex searches for half-sites stochastically, then it preferentially interacts with the leader-side CRISPR repeat, and finally, it catalyses a nucleophilic attack that connects one strand of the leader-proximal repeat to the prespacer 3' overhang. Recognition of the spacer half-site requires DNA bending and leads to full integration. We derive a mechanistic framework to explain the stepwise spacer

Global Survey of Submicron Aerosol Acidity (pH)

NASA Astrophysics Data System (ADS)

Nault, B.; Day, D. A.; Campuzano Jost, P.; Hu, W.; Schroder, J. C.; Bian, H.; Chin, M.; Clegg, S. L.; Colarco, P. R.; Dibb, J. E.; Kim, M. J.; Kodros, J.; Marais, E. A.; Pierce, J. R.; Scheuer, E. M.; Wennberg, P. O.; Jimenez, J. L.

2017-12-01

Aerosol acidity (H+, often expressed as "pH" defined in various ways) is an important property that influences uptake and partitioning of gases, and homogeneous and surface aqueous reactions of key inorganic and organic compounds. As there is currently no rapid method to measure ambient aerosol acidity, a thermodynamic model, constrained by both inorganic aerosol species (e.g., NH4, NO3, SO4, Cl) and at least one inorganic gas (HNO3, NH3, or HCl), are currently understood to lead to the most reliable estimates of aerosol acidity. In this study, we calculated submicron (less than PM1) aerosol pH from the NASA ATom, "pole-to-pole," flights that covers both the Pacific and Atlantic ocean basins. The E-AIM thermodynamic model was used with measurements by an Aerodyne high-resolution time-of-flight aerosol-mass-spectrometer (HR-ToF-AMS) of inorganic aerosol species, along with inorganic gas measurements from other mass spectrometers and ion chromatography. We compare the results with those for the NASA KORUS-AQ, SEAC4RS, DC3, and ARCTAS campaigns, as well as several ground-based campaigns and recently-published studies. This provides an opportunity to compare the aerosol acidity in urban, rural, and remote regions, by season, and between the boundary layer and free troposphere. In addition, we compare the submicron aerosol acidity from these various localities with results from global models, such as GEOS-Chem, in order to investigate the ability of the global models to simulate aerosol acidity, and the processes it affects, such as nitrate, ammonium, and MSA partitioning.

How Type II CRISPR-Cas establish immunity through Cas1-Cas2 mediated spacer integration

PubMed Central

Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun; Ke, Ailong

2017-01-01

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the nearby cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes1–5. Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer6–9. Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical7–9. The conserved Cas1 and Cas2 proteins form an integrase complex consisting two distal Cas1 dimers bridged by a Cas2 dimer in the middle6,10. The prespacer is bound by Cas1-Cas2 as a dual forked DNA, and the terminal 3′-OH of each 3′-overhang serves as an attacking nucleophile during integration11–14. Importantly, the prespacer is preferentially integrated into the leader-proximal region of the CRISPR array1,7,10,15, guided by the leader sequence and a pair of inverted repeats (IRs) inside the CRISPR repeat7,15–20. Spacer integration in the most well-studied Escherichia coli Type I-E CRISPR system further relies on the bacterial Integration Host Factor (IHF)21,22. In Type II-A CRISPR, however, Cas1-Cas2 alone integrates spacer efficiently in vitro18; other Cas proteins (Cas9 and Csn2) play accessory roles in prespacer biogenesis17,23. Focusing on the Enterococcus faecalis Type II-A system24, here we report four structure snapshots of Cas1-Cas2 during spacer integration. EfaCas1-Cas2 selectively binds to a splayed 30-bp prespacer bearing 4-nt 3′-overhangs. Three molecular events take place upon encountering a target: Cas1-Cas2/prespacer first searches for half-sites stochastically, then preferentially interacts with the leader-side CRISPR repeat and catalyzes a nucleophilic attack that connects one strand of the leader-proximal repeat to the prespacer 3′-overhang. Recognition of the spacer half-site requires DNA bending and leads to full integration. We derive a mechanistic framework explaining

Optical and physical properties of stratospheric aerosols from balloon measurements in the visible and near-infrared domains. I. Analysis of aerosol extinction spectra from the AMON and SALOMON balloonborne spectrometers

NASA Astrophysics Data System (ADS)

Berthet, Gwenaël; Renard, Jean-Baptiste; Brogniez, Colette; Robert, Claude; Chartier, Michel; Pirre, Michel

2002-12-01

Aerosol extinction coefficients have been derived in the 375-700-nm spectral domain from measurements in the stratosphere since 1992, at night, at mid- and high latitudes from 15 to 40 km, by two balloonborne spectrometers, Absorption par les Minoritaires Ozone et NOx (AMON) and Spectroscopie d'Absorption Lunaire pour l'Observation des Minoritaires Ozone et NOx (SALOMON). Log-normal size distributions associated with the Mie-computed extinction spectra that best fit the measurements permit calculation of integrated properties of the distributions. Although measured extinction spectra that correspond to background aerosols can be reproduced by the Mie scattering model by use of monomodal log-normal size distributions, each flight reveals some large discrepancies between measurement and theory at several altitudes. The agreement between measured and Mie-calculated extinction spectra is significantly improved by use of bimodal log-normal distributions. Nevertheless, neither monomodal nor bimodal distributions permit correct reproduction of some of the measured extinction shapes, especially for the 26 February 1997 AMON flight, which exhibited spectral behavior attributed to particles from a polar stratospheric cloud event.

Characterization of aerosol particles from grass mowing by joint deployment of ToF-AMS and ATOFMS instruments

NASA Astrophysics Data System (ADS)

Drewnick, Frank; Dall'Osto, Manuel; Harrison, Roy

During a measurement campaign at a semi-urban/industrial site a grass-cutting event was observed, when the lawn in the immediate surrounding of the measurement site was mowed. Using a wide variety of state-of-the-art aerosol measurement technology allowed a broad characterization of the aerosol generated by the lawn mowing. The instrumentation included two on-line aerosol mass spectrometers: an Aerodyne Time-of-Flight Aerosol Mass Spectrometer (ToF-AMS) and a TSI Aerosol Time-of-Flight Mass Spectrometer (ATOFMS); in addition, a selection of on-line aerosol concentration and size distribution instruments (OPC, APS, SMPS, CPC, FDMS-TEOM, MAAP) was deployed. From comparison of background aerosol measurements during most of the day with the aerosol measured during the lawn mowing, the grass cutting was found to generate mainly two different types of aerosol particles: an intense ultrafine particle mode (1 h average: 4 μg m -3) of almost pure hydrocarbon-like organics and a distinct particle mode in the upper sub-micrometer size range containing particles with potassium and nitrogen-organic compounds. The ultrafine particles are probably lubricating oil particles from the lawn mower exhaust; the larger particles are swirled-up plant debris particles from the mowing process. While these particle types were identified in the data from the two mass spectrometers, the on-line aerosol concentration and size distribution data support these findings. The results presented here show that the combination of quantitative aerosol particle ensemble mass spectrometry (ToF-AMS) and single particle mass spectrometry (ATOFMS) provides much deeper insights into the nature of the aerosol properties than each of the instruments could do alone. Therefore a combined deployment of both types of instruments is strongly recommended.

Single particles measured by a light scattering module coupled to a time-of-flight aerosol mass spectrometer onboard the NOAA P-3 aircraft during SENEX

NASA Astrophysics Data System (ADS)

Liao, J.; Middlebrook, A. M.; Welti, A.; Sueper, D.; Murphy, D. M.

2014-12-01

Single particles in the eastern US were characterized by a light scattering module coupled to a time-of-flight aerosol mass spectrometer (LS-ToF-AMS) onboard the NOAA P-3 aircraft during the Southeastern Nexus (SENEX) campaign. Single particle data were collected for 30 seconds every 5 minutes. Aerosols larger than 200-300 nm in vacuum aerodynamic diameter can be optically detected by the 405 nm crystal laser and trigger the saving of single particle mass spectra. The measured single particles are internally-mixed as expected. The single particles were classified as prompt, delayed, and null based on the chemical ion signal arrival time difference between prediction from the light scattering signal and measurement by mass spectrometer and the presence or absence of a mass spectrum. On average the number fraction of particles detected as prompt, delayed, and null (no spectrum) is about 30%, 10%, and 60%. The number fraction of these three particle types varied with aerosol size, chemical composition and the investigation region and will be discussed in detail. For example, the number fraction of prompt particles was significantly higher for the flight to the Pennsylvania natural gas shale region on July 6, 2013, which is probably related to the chemical composition (more acidic) and phase of the ambient particles. These particle types and detection efficiency are related to the bouncing effect on the vaporizer and may provide insight into the non-unit AMS collection efficiency. Moreover, most of the particles larger than 800 nm in vacuum aerodynamic diameter sized with the traditional AMS PToF mode are delayed particles and their mass spectral signals appear to be affected by this process.

Transforming plant biology and breeding with CRISPR/Cas9, Cas12 and Cas13.

PubMed

Schindele, Patrick; Wolter, Felix; Puchta, Holger

2018-04-30

Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed. Cas9- and Cas12- mediated DNA binding is used to develop tools for many useful applications, such as transcriptional regulation or fluorescence-based imaging of specific chromosomal loci in plant genomes. Cas13 has recently been applied to degrade mRNAs and combat viral RNA replication. By the possibility to address multiple sequences with different guide RNAs and by the simultaneous use of different Cas proteins in a single cell, we should soon be able to achieve complex changes of plant metabolism in a controlled way. © 2018 Federation of European Biochemical Societies.

A fast integrated mobility spectrometer for rapid measurement of sub-micrometer aerosol size distribution, Part II: Experimental characterization

DOE PAGES

Wang, Jian; Pikridas, Michael; Pinterich, Tamara; ...

2017-06-08

A Fast Integrated Mobility Spectrometer (FIMS) with a wide dynamic size range has been developed for rapid aerosol size distribution measurements. The design and model evaluation of the FIMS are presented in the preceding paper (Paper I), and this paper focuses on the experimental characterization of the FIMS. Monodisperse aerosol with diameter ranging from 8 to 600 nm was generated using Differential Mobility Analyzer (DMA), and was measured by the FIMS in parallel with a Condensation Particle Counter (CPC). The mean particle diameter measured by the FIMS is in good agreement with the DMA centroid diameter. Comparison of the particlemore » concentrations measured by the FIMS and CPC indicates the FIMS detection efficiency is essentially 100% for particles with diameters of 8 nm or larger. For particles smaller than 20 nm or larger than 200 nm, FIMS transfer function and resolution can be well represented by the calculated ones based on simulated particle trajectories in the FIMS. For particles between 20 and 200 nm, the FIMS transfer function is boarder than the calculated, likely due to non-ideality of the electric field, including edge effects near the end of the electrode, which are not represented by the 2-D electric field used to simulate particle trajectories.« less

A fast integrated mobility spectrometer for rapid measurement of sub-micrometer aerosol size distribution, Part II: Experimental characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jian; Pikridas, Michael; Pinterich, Tamara

A Fast Integrated Mobility Spectrometer (FIMS) with a wide dynamic size range has been developed for rapid aerosol size distribution measurements. The design and model evaluation of the FIMS are presented in the preceding paper (Paper I), and this paper focuses on the experimental characterization of the FIMS. Monodisperse aerosol with diameter ranging from 8 to 600 nm was generated using Differential Mobility Analyzer (DMA), and was measured by the FIMS in parallel with a Condensation Particle Counter (CPC). The mean particle diameter measured by the FIMS is in good agreement with the DMA centroid diameter. Comparison of the particlemore » concentrations measured by the FIMS and CPC indicates the FIMS detection efficiency is essentially 100% for particles with diameters of 8 nm or larger. For particles smaller than 20 nm or larger than 200 nm, FIMS transfer function and resolution can be well represented by the calculated ones based on simulated particle trajectories in the FIMS. For particles between 20 and 200 nm, the FIMS transfer function is boarder than the calculated, likely due to non-ideality of the electric field, including edge effects near the end of the electrode, which are not represented by the 2-D electric field used to simulate particle trajectories.« less

Measurements of the aerosol chemical composition and mixing state in the Po Valley using multiple spectroscopic techniques

NASA Astrophysics Data System (ADS)

Decesari, S.; Allan, J.; Plass-Duelmer, C.; Williams, B. J.; Paglione, M.; Facchini, M. C.; O'Dowd, C.; Harrison, R. M.; Gietl, J. K.; Coe, H.; Giulianelli, L.; Gobbi, G. P.; Lanconelli, C.; Carbone, C.; Worsnop, D.; Lambe, A. T.; Ahern, A. T.; Moretti, F.; Tagliavini, E.; Elste, T.; Gilge, S.; Zhang, Y.; Dall'Osto, M.

2014-11-01

The use of co-located multiple spectroscopic techniques can provide detailed information on the atmospheric processes regulating aerosol chemical composition and mixing state. So far, field campaigns heavily equipped with aerosol mass spectrometers have been carried out mainly in large conurbations and in areas directly affected by their outflow, whereas lesser efforts have been dedicated to continental areas characterised by a less dense urbanisation. We present here the results obtained at a background site in the Po Valley, Italy, in summer 2009. For the first time in Europe, six state-of-the-art spectrometric techniques were used in parallel: aerosol time-of-flight mass spectrometer (ATOFMS), two aerosol mass spectrometers (high-resolution time-of-flight aerosol mass spectrometer - HR-ToF-AMS and soot particle aerosol mass spectrometer - SP-AMS), thermal desorption aerosol gas chromatography (TAG), chemical ionisation mass spectrometry (CIMS) and (offline) proton nuclear magnetic resonance (1H-NMR) spectroscopy. The results indicate that, under high-pressure conditions, atmospheric stratification at night and early morning hours led to the accumulation of aerosols produced by anthropogenic sources distributed over the Po Valley plain. Such aerosols include primary components such as black carbon (BC), secondary semivolatile compounds such as ammonium nitrate and amines and a class of monocarboxylic acids which correspond to the AMS cooking organic aerosol (COA) already identified in urban areas. In daytime, the entrainment of aged air masses in the mixing layer is responsible for the accumulation of low-volatility oxygenated organic aerosol (LV-OOA) and also for the recycling of non-volatile primary species such as black carbon. According to organic aerosol source apportionment, anthropogenic aerosols accumulating in the lower layers overnight accounted for 38% of organic aerosol mass on average, another 21% was accounted for by aerosols recirculated in

Influences of upwind emission sources and atmospheric processing on aerosol chemistry and properties at a rural location in the Northeastern U.S.: URBAN INFLUENCE ON RURAL AEROSOL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Shan; Collier, Sonya; Xu, Jianzhong

2016-05-19

Continuous real-time measurements of atmospheric aerosol with an Aerodyne High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-AMS) coupled with a fast temperature-stepping thermodenuder were carried out in summer 2011 at Brookhaven National Laboratory (BNL, 40.871°N, 72.89°W) during the DOE Aerosol Life Cycle Intensive Operational Period (ALC-IOP) campaign.

ACTRIS ACSM intercomparison - Part 2: Intercomparison of ME-2 organic source apportionment results from 15 individual, co-located aerosol mass spectrometers

NASA Astrophysics Data System (ADS)

Fröhlich, R.; Crenn, V.; Setyan, A.; Belis, C. A.; Canonaco, F.; Favez, O.; Riffault, V.; Slowik, J. G.; Aas, W.; Aijälä, M.; Alastuey, A.; Artiñano, B.; Bonnaire, N.; Bozzetti, C.; Bressi, M.; Carbone, C.; Coz, E.; Croteau, P. L.; Cubison, M. J.; Esser-Gietl, J. K.; Green, D. C.; Gros, V.; Heikkinen, L.; Herrmann, H.; Jayne, J. T.; Lunder, C. R.; Minguillón, M. C.; Močnik, G.; O'Dowd, C. D.; Ovadnevaite, J.; Petralia, E.; Poulain, L.; Priestman, M.; Ripoll, A.; Sarda-Estève, R.; Wiedensohler, A.; Baltensperger, U.; Sciare, J.; Prévôt, A. S. H.

2015-02-01

Chemically resolved atmospheric aerosol data sets from the largest intercomparison of the Aerodyne aerosol chemical speciation monitors (ACSM) performed to date were collected at the French atmospheric supersite SIRTA. In total 13 quadrupole ACSMs (Q-ACSM) from the European ACTRIS ACSM network, one time-of-flight ACSM (ToF-ACSM), and one high-resolution ToF aerosol mass spectrometer (AMS) were operated in parallel for about three weeks in November and December 2013. Part 1 of this study reports on the accuracy and precision of the instruments for all the measured species. In this work we report on the intercomparison of organic components and the results from factor analysis source apportionment by positive matrix factorisation (PMF) utilising the multilinear engine 2 (ME-2). Except for the organic contribution of m/z 44 to the total organics (f44), which varied by factors between 0.6 and 1.3 compared to the mean, the peaks in the organic mass spectra were similar among instruments. The m/z 44 differences in the spectra resulted in a variable f44 in the source profiles extracted by ME-2, but had only a minor influence on the extracted mass contributions of the sources. The presented source apportionment yielded four factors for all 15 instruments: hydrocarbon-like organic aerosol (HOA), cooking-related organic aerosol (COA), biomass burning-related organic aerosol (BBOA) and secondary oxygenated organic aerosol (OOA). Individual application and optimisation of the ME-2 boundary conditions (profile constraints) are discussed together with the investigation of the influence of alternative anchors (reference profiles). A comparison of the ME-2 source apportionment output of all 15 instruments resulted in relative SD from the mean between 13.7 and 22.7% of the source's average mass contribution depending on the factors (HOA: 14.3 ± 2.2%, COA: 15.0 ± 3.4%, OOA: 41.5 ± 5.7%, BBOA: 29.3 ± 5.0%). Factors which tend to be subject to minor factor mixing (in this case COA

Exploration of Venus with the Venera-15 IR Fourier spectrometer and the Venus Express planetary Fourier spectrometer

NASA Astrophysics Data System (ADS)

Zasova, L. V.; Moroz, V. I.; Formisano, V.; Ignatiev, N. I.; Khatuntsev, I. V.

2006-07-01

The infrared spectrometry of Venus in the range 6-45 μm allows one to sound the middle atmosphere of Venus in the altitude range 55-100 km and its cloud layer. This experiment was carried out onboard the Soviet automatic interplanetary Venera-15 station, where the Fourier spectrometer for this spectral range was installed. The measurements have shown that the main component of the cloud layer at all measured latitudes in the northern hemisphere is concentrated sulfuric acid (75-85%). The vertical profiles of temperature and aerosol were reconstructed in a self-consistent manner: the three-dimensional fields of temperature and zonal wind in the altitude range 55-100 km and aerosol at altitudes 55-70 km have been obtained, as well as vertical SO2 profiles and H2O concentration in the upper cloud layer. The solar-related waves at isobaric levels in the fields of temperature, zonal wind, and aerosol were investigated. This experiment has shown the efficiency of the method for investigation of the Venusian atmosphere. The Planetary Fourier Spectrometer has the spectral interval 0.9-45 μm and a spectral resolution of 1.8 cm-1. It will allow one to sound the middle atmosphere (55-100 km) of Venus and its cloud layer on the dayside, as well as the lower atmosphere and the planetary surface on the night side.

Direct Observations of Isoprene Secondary Organic Aerosol Formation in Ambient Cloud Droplets

NASA Astrophysics Data System (ADS)

Zelenyuk, A.; Bell, D.; Thornton, J. A.; Fast, J. D.; Shrivastava, M. B.; Berg, L. K.; Imre, D. G.; Mei, F.; Shilling, J.; Suski, K. J.; Liu, J.; Tomlinson, J. M.; Wang, J.

2017-12-01

Multiphase chemistry of isoprene photooxidation products has been shown to be one of the major sources of secondary organic aerosol (SOA) in the atmosphere. A number of recent studies indicate that aqueous aerosol phase provides a medium for reactive uptake of isoprene photooxidation products, and in particular, isomeric isoprene epoxydiols (IEPOX), with reaction rates and yields being dependent on aerosol acidity, water content, sulfate concentration, and organic coatings. However, very few studies focused on chemistry occurring within actual cloud droplets. We will present data acquired during recent Holistic Interactions of Shallow Clouds, Aerosols, and Land Ecosystems (HI-SCALE) Campaign, which provide direct evidence for IEPOX-SOA formation in cloud droplets. Single particle mass spectrometer, miniSPLAT, and a high-resolution, time-of-flight aerosol mass spectrometer were used to characterize the composition of aerosol particles and cloud droplet residuals, while a high-resolution, time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS) was used to characterize gas-phase compounds. We find that the composition of cloud droplet residuals was markedly different than that of aerosol particles sampled outside the cloud. Cloud droplet residuals were comprised of individual particles with high relative fractions of sulfate and nitrate and significant fraction of particles with mass spectra that are nearly identical to those of laboratory-generated IEPOX-SOA particles. The observed cloud-induced formation of IEPOX-SOA was accompanied by simultaneous decrease in measured concentrations of IEPOX and other gas-phase isoprene photooxidation products. Ultimately, the combined cloud, aerosol, and gas-phase measurements conducted during HI-SCALE will be used to develop and evaluate model treatments of aqueous-phase isoprene SOA formation.

Validation of TOMS Aerosol Products using AERONET Observations

NASA Technical Reports Server (NTRS)

Bhartia, P. K.; Torres, O.; Sinyuk, A.; Holben, B.

2002-01-01

The Total Ozone Mapping Spectrometer (TOMS) aerosol algorithm uses measurements of radiances at two near UV channels in the range 331-380 nm to derive aerosol optical depth and single scattering albedo. Because of the low near UV surface albedo of all terrestrial surfaces (between 0.02 and 0.08), the TOMS algorithm has the capability of retrieving aerosol properties over the oceans and the continents. The Aerosol Robotic Network (AERONET) routinely derives spectral aerosol optical depth and single scattering albedo at a large number of sites around the globe. We have performed comparisons of both aerosol optical depth and single scattering albedo derived from TOMS and AERONET. In general, the TOMS aerosol products agree well with the ground-based observations, Results of this validation will be discussed.

Aerosol in the Pacific troposphere

NASA Technical Reports Server (NTRS)

Clarke, Antony D.

1989-01-01

The use of near real-time optical techniques is emphasized for the measurement of mid-tropospheric aerosol over the Central Pacific. The primary focus is on measurement of the aerosol size distribution over the range of particle diameters from 0.15 to 5.0 microns that are essential for modeling CO2 backscatter values in support of the laser atmospheric wind sounder (LAWS) program. The measurement system employs a LAS-X (Laser Aerosol Spectrometer-PMS, Boulder, CO) with a custom 256 channel pulse height analyzer and software for detailed measurement and analysis of aerosol size distributions. A thermal preheater system (Thermo Optic Aerosol Descriminator (TOAD) conditions the aerosol in a manner that allows the discrimination of the size distribution of individual aerosol components such as sulfuric acid, sulfates and refractory species. This allows assessment of the relative contribution of each component to the BCO2 signal. This is necessary since the different components have different sources, exhibit independent variability and provide different BCO2 signals for a given mass and particle size. Field activities involve experiments designed to examine both temporal and spatial variability of these aerosol components from ground based and aircraft platforms.

Characterization of a real-time tracer for Isoprene Epoxydiols-derived Secondary Organic Aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

NASA Astrophysics Data System (ADS)

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.; Day, D. A.; Ortega, A. M.; Hayes, P. L.; Krechmer, J. E.; Chen, Q.; Kuwata, M.; Liu, Y. J.; de Sá, S. S.; Martin, S. T.; Hu, M.; Budisulistiorini, S. H.; Riva, M.; Surratt, J. D.; St. Clair, J. M.; Isaacman-Van Wertz, G.; Yee, L. D.; Goldstein, A. H.; Carbone, S.; Artaxo, P.; de Gouw, J. A.; Koss, A.; Wisthaler, A.; Mikoviny, T.; Karl, T.; Kaser, L.; Jud, W.; Hansel, A.; Docherty, K. S.; Robinson, N. H.; Coe, H.; Allan, J. D.; Canagaratna, M. R.; Paulot, F.; Jimenez, J. L.

2015-04-01

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene low-NO oxidation pathways, was quantified by applying Positive Matrix Factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of OA in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the SOAS study, 78% of IEPOX-SOA is accounted for the measured molecular tracers, making it the highest level of molecular identification of an ambient SOA component to our knowledge. Enhanced signal at C5H6O+ (m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine fC5H6O ( fC5H6O = C5H6O+/OA) across multiple field, chamber and source datasets. A background of ~ 1.7 ± 0.1‰ is observed in studies strongly influenced by urban, biomass-burning and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.8‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7‰). Locations strongly influenced by isoprene emissions under low-NO levels had higher fC5H6O (~ 6.5 ± 2.2‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. fC5H6O in IEPOX-SOA is always elevated (12-40‰) but varies substantially between locations, which is shown to reflect large variations in its detailed molecular composition. The low fC5H6O (< 3‰) observed in non IEPOX-derived isoprene-SOA indicates that this tracer ion is specifically enhanced from IEPOX-SOA, and is not a tracer for all SOA from

Martian atmospheric O3 retrieval development for the NOMAD-UVIS spectrometer

NASA Astrophysics Data System (ADS)

Hewson, W.; Mason, J. P.; Leese, M.; Hathi, B.; Holmes, J.; Lewis, S. R.; Iriwin, P. G. J.; Patel, M. R.

2017-09-01

The composition of atmospheric trace gases and aerosols is a highly variable and poorly constrained component of the martian atmosphere, and by affecting martian climate and UV surface dose, represents a key parameter in the assessment of suitability for martian habitability. The ExoMars Trace Gas Orbiter (TGO) carries the Open University (OU) designed Ultraviolet and VIsible Spectrometer (UVIS) instrument as part of the Belgian-led Nadir and Occultation for MArs Discovery (NOMAD) spectrometer suite. NOMAD will begin transmitting science observations of martian surface and atmosphere back-scattered UltraViolet (UV) and visible radiation in Spring 2018, which will be processed to derive spatially and temporally averaged atmospheric trace gas and aerosol concentrations, intended to provide a better understanding of martian atmospheric photo-chemistry and dynamics, and will also improve models of martian atmospheric chemistry, climate and habitability. Work presented here illustrates initial development and testing of the OU's new retrieval algorithm for determining O3 and aerosol concentrations from the UVIS instrument.

Development of a new corona discharge based ion source for high resolution time-of-flight chemical ionization mass spectrometer to measure gaseous H2SO4 and aerosol sulfate

NASA Astrophysics Data System (ADS)

Zheng, Jun; Yang, Dongsen; Ma, Yan; Chen, Mindong; Cheng, Jin; Li, Shizheng; Wang, Ming

2015-10-01

A new corona discharge (CD) based ion source was developed for a commercial high-resolution time-of-flight chemical ionization mass spectrometer (HRToF-CIMS) (Aerodyne Research Inc.) to measure both gaseous sulfuric acid (H2SO4) and aerosol sulfate after thermal desorption. Nitrate core ions (NO3-) were used as reagent ions and were generated by a negative discharge in zero air followed by addition of excess nitrogen dioxide (NO2) to convert primary ions and hydroxyl radicals (OH) into NO3- ions and nitric acid (HNO3). The CD-HRToF-CIMS showed no detectable interference from hundreds parts per billion by volume (ppbv) of sulfur dioxide (SO2). Unlike the atmospheric pressure ionization (API) ToF-CIMS, the CD ion source was integrated onto the ion-molecule reaction (IMR) chamber and which made it possible to measure aerosol sulfate by coupling to a filter inlet for gases and aerosols (FIGAERO). Moreover, compared with a quadrupole-based mass spectrometer, the desired HSO4- signal was detected by its exact mass of m/z 96.960, which was well resolved from the potential interferences of HCO3-ṡ(H2O)2 (m/z 97.014) and O-ṡH2OṡHNO3 (m/z 97.002). In this work, using laboratory-generated standards the CD-HRToF-CIMS was demonstrated to be able to detect as low as 3.1 × 105 molecules cm-3 gaseous H2SO4 and 0.5 μg m-3 ammonium sulfate based on 10-s integration time and two times of the baseline noise. The CD ion source had the advantages of low cost and a simple but robust structure. Since the system was non-radioactive and did not require corrosive HNO3 gas, it can be readily field deployed. The CD-HRToF-CIMS can be a powerful tool for both field and laboratory studies of aerosol formation mechanism and the chemical processes that were critical to understand the evolution of aerosols in the atmosphere.

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, Vincent J.; Johnson, Stanley A.

1999-01-01

A vapor sample detection method where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample.

Remote sensing of cloud, aerosol and water vapor properties from the Moderate Resolution Imaging Spectrometer (MODIS)

NASA Technical Reports Server (NTRS)

King, M. D.

1992-01-01

The Moderate Resolution Imaging Spectrometer (MODIS) is an Earth-viewing sensor being developed as a facility instrument for the Earth Observing System (EOS) to be launched in the late 1990s. MODIS consists of two separate instruments that scan a swath width sufficient to provide nearly complete global coverage every two days from a polar-orbiting, Sun-synchronous, platform at an altitude of 705 km. Of primary interest for studies of atmospheric physics is the MODIS-N (nadir) instrument which will provide images in 36 spectral bands between 0.415 and 14.235 micrometers with spatial resoulutions of 250 m (2 bands), 500 m (5 bands) and 1000 m (29 bands). These bands have been carefully selected to enable advanced studies of land, ocean and atmosperhic processes. The intent of this lecture is to describe the current status of MODIS-N and its companion instrument MODIS-T (tilt), a tiltable cross-track scanning radiometer with 32 uniformly spaced channels between 0.410 and 0.875 micrometers, and to describe the physical principles behind the development of MODIS for the remote sensing of atmospheric properties. Primary emphasis will be placed on the main atmospheric applications of determining the optical, microphysical and physical properties of clouds and aerosol particles form spectral-reflection and thermal-emission measurements. In addition to cloud and aerosol properties, MODIS-N will be utilized for the determination of the total precipitable water vapor over land and atmospheric stability. The physical principles behind the determination of each of these atmospheric products will be described herein.

Highly time-resolved chemical characterization of atmospheric submicron particles during 2008 Beijing Olympic Games using an Aerodyne High-Resolution Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Huang, X.-F.; He, L.-Y.; Hu, M.; Canagaratna, M. R.; Sun, Y.; Zhang, Q.; Zhu, T.; Xue, L.; Zeng, L.-W.; Liu, X.-G.; Zhang, Y.-H.; Jayne, J. T.; Ng, N. L.; Worsnop, D. R.

2010-09-01

As part of Campaigns of Air Quality Research in Beijing and Surrounding Region-2008 (CAREBeijing-2008), an Aerodyne High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) was deployed in urban Beijing to characterize submicron aerosol particles during the time of 2008 Beijing Olympic Games and Paralympic Games (24 July to 20 September 2008). The campaign mean PM1 mass concentration was 63.1 ± 39.8 μg m-3; the mean composition consisted of organics (37.9%), sulfate (26.7%), ammonium (15.9%), nitrate (15.8%), black carbon (3.1%), and chloride (0.87%). The average size distributions of the species (except BC) were all dominated by an accumulation mode peaking at about 600 nm in vacuum aerodynamic diameter, and organics was characterized by an additional smaller mode extending below 100 nm. Positive Matrix Factorization (PMF) analysis of the high resolution organic mass spectral dataset differentiated the organic aerosol into four components, i.e., hydrocarbon-like (HOA), cooking-related (COA), and two oxygenated organic aerosols (OOA-1 and OOA-2), which on average accounted for 18.1, 24.4, 33.7 and 23.7% of the total organic mass, respectively. The HOA was identified to be closely associated with primary combustion sources, while the COA mass spectrum and diurnal pattern showed similar characteristics to that measured for cooking emissions. The OOA components correspond to aged secondary organic aerosol. Although the two OOA components have similar elemental (O/C, H/C) compositions, they display differences in mass spectra and time series which appear to correlate with the different source regions sampled during the campaign. Back trajectory clustering analysis indicated that the southerly air flows were associated with the highest PM1 pollution during the campaign. Aerosol particles in southern airmasses were especially rich in inorganic and oxidized organic species. Aerosol particles in northern airmasses contained a large fraction of primary HOA

Cas9 specifies functional viral targets during CRISPR-Cas adaptation.

PubMed

Heler, Robert; Samai, Poulami; Modell, Joshua W; Weiner, Catherine; Goldberg, Gregory W; Bikard, David; Marraffini, Luciano A

2015-03-12

Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins provide adaptive immunity against viral infection in prokaryotes. Upon infection, short phage sequences known as spacers integrate between CRISPR repeats and are transcribed into small RNA molecules that guide the Cas9 nuclease to the viral targets (protospacers). Streptococcus pyogenes Cas9 cleavage of the viral genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately downstream of the viral target. It is not known whether and how viral sequences flanked by the correct PAM are chosen as new spacers. Here we show that Cas9 selects functional spacers by recognizing their PAM during spacer acquisition. The replacement of cas9 with alleles that lack the PAM recognition motif or recognize an NGGNG PAM eliminated or changed PAM specificity during spacer acquisition, respectively. Cas9 associates with other proteins of the acquisition machinery (Cas1, Cas2 and Csn2), presumably to provide PAM-specificity to this process. These results establish a new function for Cas9 in the genesis of prokaryotic immunological memory.

ACTRIS ACSM intercomparison - Part 2: Intercomparison of ME-2 organic source apportionment results from 15 individual, co-located aerosol mass spectrometers

NASA Astrophysics Data System (ADS)

Fröhlich, R.; Crenn, V.; Setyan, A.; Belis, C. A.; Canonaco, F.; Favez, O.; Riffault, V.; Slowik, J. G.; Aas, W.; Aijälä, M.; Alastuey, A.; Artiñano, B.; Bonnaire, N.; Bozzetti, C.; Bressi, M.; Carbone, C.; Coz, E.; Croteau, P. L.; Cubison, M. J.; Esser-Gietl, J. K.; Green, D. C.; Gros, V.; Heikkinen, L.; Herrmann, H.; Jayne, J. T.; Lunder, C. R.; Minguillón, M. C.; Močnik, G.; O'Dowd, C. D.; Ovadnevaite, J.; Petralia, E.; Poulain, L.; Priestman, M.; Ripoll, A.; Sarda-Estève, R.; Wiedensohler, A.; Baltensperger, U.; Sciare, J.; Prévôt, A. S. H.

2015-06-01

Chemically resolved atmospheric aerosol data sets from the largest intercomparison of the Aerodyne aerosol chemical speciation monitors (ACSMs) performed to date were collected at the French atmospheric supersite SIRTA. In total 13 quadrupole ACSMs (Q-ACSM) from the European ACTRIS ACSM network, one time-of-flight ACSM (ToF-ACSM), and one high-resolution ToF aerosol mass spectrometer (AMS) were operated in parallel for about 3 weeks in November and December~2013. Part 1 of this study reports on the accuracy and precision of the instruments for all the measured species. In this work we report on the intercomparison of organic components and the results from factor analysis source apportionment by positive matrix factorisation (PMF) utilising the multilinear engine 2 (ME-2). Except for the organic contribution of mass-to-charge ratio m/z 44 to the total organics (f44), which varied by factors between 0.6 and 1.3 compared to the mean, the peaks in the organic mass spectra were similar among instruments. The m/z 44 differences in the spectra resulted in a variable f44 in the source profiles extracted by ME-2, but had only a minor influence on the extracted mass contributions of the sources. The presented source apportionment yielded four factors for all 15 instruments: hydrocarbon-like organic aerosol (HOA), cooking-related organic aerosol (COA), biomass burning-related organic aerosol (BBOA) and secondary oxygenated organic aerosol (OOA). ME-2 boundary conditions (profile constraints) were optimised individually by means of correlation to external data in order to achieve equivalent / comparable solutions for all ACSM instruments and the results are discussed together with the investigation of the influence of alternative anchors (reference profiles). A comparison of the ME-2 source apportionment output of all 15 instruments resulted in relative standard deviations (SD) from the mean between 13.7 and 22.7 % of the source's average mass contribution depending on the

A scattering methodology for droplet sizing of e-cigarette aerosols.

PubMed

Pratte, Pascal; Cosandey, Stéphane; Goujon-Ginglinger, Catherine

2016-10-01

Knowledge of the droplet size distribution of inhalable aerosols is important to predict aerosol deposition yield at various respiratory tract locations in human. Optical methodologies are usually preferred over the multi-stage cascade impactor for high-throughput measurements of aerosol particle/droplet size distributions. Evaluate the Laser Aerosol Spectrometer technology based on Polystyrene Sphere Latex (PSL) calibration curve applied for the experimental determination of droplet size distributions in the diameter range typical of commercial e-cigarette aerosols (147-1361 nm). This calibration procedure was tested for a TSI Laser Aerosol Spectrometer (LAS) operating at a wavelength of 633 nm and assessed against model di-ethyl-hexyl-sebacat (DEHS) droplets and e-cigarette aerosols. The PSL size response was measured, and intra- and between-day standard deviations calculated. DEHS droplet sizes were underestimated by 15-20% by the LAS when the PSL calibration curve was used; however, the intra- and between-day relative standard deviations were < 3%. This bias is attributed to the fact that the index of refraction of PSL calibrated particles is different in comparison to test aerosols. This 15-20% does not include the droplet evaporation component, which may reduce droplet size prior a measurement is performed. Aerosol concentration was measured accurately with a maximum uncertainty of 20%. Count median diameters and mass median aerodynamic diameters of selected e-cigarette aerosols ranged from 130-191 nm to 225-293 nm, respectively, similar to published values. The LAS instrument can be used to measure e-cigarette aerosol droplet size distributions with a bias underestimating the expected value by 15-20% when using a precise PSL calibration curve. Controlled variability of DEHS size measurements can be achieved with the LAS system; however, this method can only be applied to test aerosols having a refractive index close to that of PSL particles used

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, V.J.; Johnson, S.A.

1999-08-03

A vapor sample detection method is described where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample. 13 figs.

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

PubMed Central

Fonfara, Ines; Le Rhun, Anaïs; Chylinski, Krzysztof; Makarova, Kira S.; Lécrivain, Anne-Laure; Bzdrenga, Janek; Koonin, Eugene V.; Charpentier, Emmanuelle

2014-01-01

The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool. PMID:24270795

Sugars in Antarctic aerosol

NASA Astrophysics Data System (ADS)

Barbaro, Elena; Kirchgeorg, Torben; Zangrando, Roberta; Vecchiato, Marco; Piazza, Rossano; Barbante, Carlo; Gambaro, Andrea

2015-10-01

The processes and transformations occurring in the Antarctic aerosol during atmospheric transport were described using selected sugars as source tracers. Monosaccharides (arabinose, fructose, galactose, glucose, mannose, ribose, xylose), disaccharides (sucrose, lactose, maltose, lactulose), alcohol-sugars (erythritol, mannitol, ribitol, sorbitol, xylitol, maltitol, galactitol) and anhydrosugars (levoglucosan, mannosan and galactosan) were measured in the Antarctic aerosol collected during four different sampling campaigns. For quantification, a sensitive high-pressure anion exchange chromatography was coupled with a single quadrupole mass spectrometer. The method was validated, showing good accuracy and low method quantification limits. This study describes the first determination of sugars in the Antarctic aerosol. The total mean concentration of sugars in the aerosol collected at the ;Mario Zucchelli; coastal station was 140 pg m-3; as for the aerosol collected over the Antarctic plateau during two consecutive sampling campaigns, the concentration amounted to 440 and 438 pg m-3. The study of particle-size distribution allowed us to identify the natural emission from spores or from sea-spray as the main sources of sugars in the coastal area. The enrichment of sugars in the fine fraction of the aerosol collected on the Antarctic plateau is due to the degradation of particles during long-range atmospheric transport. The composition of sugars in the coarse fraction was also investigated in the aerosol collected during the oceanographic cruise.

Ubiquitous influence of wildfire emissions and secondary organic aerosol on summertime atmospheric aerosol in the forested Great Lakes region

NASA Astrophysics Data System (ADS)

Gunsch, Matthew J.; May, Nathaniel W.; Wen, Miao; Bottenus, Courtney L. H.; Gardner, Daniel J.; VanReken, Timothy M.; Bertman, Steven B.; Hopke, Philip K.; Ault, Andrew P.; Pratt, Kerri A.

2018-03-01

Long-range aerosol transport affects locations hundreds of kilometers from the point of emission, leading to distant particle sources influencing rural environments that have few major local sources. Source apportionment was conducted using real-time aerosol chemistry measurements made in July 2014 at the forested University of Michigan Biological Station near Pellston, Michigan, a site representative of the remote forested Great Lakes region. Size-resolved chemical composition of individual 0.5-2.0 µm particles was measured using an aerosol time-of-flight mass spectrometer (ATOFMS), and non-refractory aerosol mass less than 1 µm (PM1) was measured with a high-resolution aerosol mass spectrometer (HR-AMS). The field site was influenced by air masses transporting Canadian wildfire emissions and urban pollution from Milwaukee and Chicago. During wildfire-influenced periods, 0.5-2.0 µm particles were primarily aged biomass burning particles (88 % by number). These particles were heavily coated with secondary organic aerosol (SOA) formed during transport, with organics (average O/C ratio of 0.8) contributing 89 % of the PM1 mass. During urban-influenced periods, organic carbon, elemental carbon-organic carbon, and aged biomass burning particles were identified, with inorganic secondary species (ammonium, sulfate, and nitrate) contributing 41 % of the PM1 mass, indicative of atmospheric processing. With current models underpredicting organic carbon in this region and biomass burning being the largest combustion contributor to SOA by mass, these results highlight the importance for regional chemical transport models to accurately predict the impact of long-range transported particles on air quality in the upper Midwest, United States, particularly considering increasing intensity and frequency of Canadian wildfires.

Measurements of the aerosol chemical composition and mixing state in the Po Valley using multiple spectroscopic techniques

NASA Astrophysics Data System (ADS)

Decesari, S.; Allan, J.; Plass-Duelmer, C.; Williams, B. J.; Paglione, M.; Facchini, M. C.; O'Dowd, C.; Harrison, R. M.; Gietl, J. K.; Coe, H.; Giulianelli, L.; Gobbi, G. P.; Lanconelli, C.; Carbone, C.; Worsnop, D.; Lambe, A. T.; Ahern, A. T.; Moretti, F.; Tagliavini, E.; Elste, T.; Gilde, S.; Zhang, Y.; Dall'Osto, M.

2014-04-01

The use of co-located multiple spectroscopic techniques can provide detailed information on the atmospheric processes regulating aerosol chemical composition and mixing state. So far, field campaigns heavily equipped with aerosol mass spectrometers have been carried out mainly in large conurbations and in areas directly affected by their outflow, whereas lesser efforts have been dedicated to continental areas characterized by a less dense urbanization. We present here the results obtained in San Pietro Capofiume, which is located in a sparsely inhabited sector of the Po Valley, Italy. The experiment was carried out in summer 2009 in the framework of the EUCAARI project ("European Integrated Project on Aerosol, Cloud Climate Aerosol Interaction"). For the first time in Europe, six state-of-the-art techniques were used in parallel: (1) on-line TSI aerosol time-of-flight mass spectrometer (ATOFMS), (2) on-line Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS), (3) soot particle aerosol mass spectrometer (SP-AMS), (4) on-line high resolution time-of-flight mass spectrometer-thermal desorption aerosol gas chromatograph (HR-ToFMS-TAG), (5) off-line twelve-hour resolution proton nuclear magnetic resonance (H-NMR) spectroscopy, and (6) chemical ionization mass spectrometry (CIMS) for the analysis of gas-phase precursors of secondary aerosol. Data from each aerosol spectroscopic method were analysed individually following ad-hoc tools (i.e. PMF for AMS, Art-2a for ATOFMS). The results obtained from each techniques are herein presented and compared. This allows us to clearly link the modifications in aerosol chemical composition to transitions in air mass origin and meteorological regimes. Under stagnant conditions, atmospheric stratification at night and early morning hours led to the accumulation of aerosols produced by anthropogenic sources distributed over the Po Valley plain. Such aerosols include primary components such as black carbon (BC

Black carbon aerosol mixing state, organic aerosols and aerosol optical properties over the UK

NASA Astrophysics Data System (ADS)

McMeeking, G. R.; Morgan, W. T.; Flynn, M.; Highwood, E. J.; Turnbull, K.; Haywood, J.; Coe, H.

2011-05-01

Black carbon (BC) aerosols absorb sunlight thereby leading to a positive radiative forcing and a warming of climate and can also impact human health through their impact on the respiratory system. The state of mixing of BC with other aerosol species, particularly the degree of internal/external mixing, has been highlighted as a major uncertainty in assessing its radiative forcing and hence its climate impact, but few in situ observations of mixing state exist. We present airborne single particle soot photometer (SP2) measurements of refractory BC (rBC) mass concentrations and mixing state coupled with aerosol composition and optical properties measured in urban plumes and regional pollution over the UK. All data were obtained using instrumentation flown on the UK's BAe-146-301 large Atmospheric Research Aircraft (ARA) operated by the Facility for Airborne Atmospheric Measurements (FAAM). We measured sub-micron aerosol composition using an aerosol mass spectrometer (AMS) and used positive matrix factorization to separate hydrocarbon-like (HOA) and oxygenated organic aerosols (OOA). We found a higher number fraction of thickly coated rBC particles in air masses with large OOA relative to HOA, higher ozone-to-nitrogen oxides (NOx) ratios and large concentrations of total sub-micron aerosol mass relative to rBC mass concentrations. The more ozone- and OOA-rich air masses were associated with transport from continental Europe, while plumes from UK cities had higher HOA and NOx and fewer thickly coated rBC particles. We did not observe any significant change in the rBC mass absorption efficiency calculated from rBC mass and light absorption coefficients measured by a particle soot absorption photometer despite observing significant changes in aerosol composition and rBC mixing state. The contributions of light scattering and absorption to total extinction (quantified by the single scattering albedo; SSA) did change for different air masses, with lower SSA observed in

A fast integrated mobility spectrometer for rapid measurement of sub-micrometer aerosol size distribution, Part I: Design and model evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jian; Pikridas, Michael; Spielman, Steven R.

This study discusses, a fast integrated mobility spectrometer (FIMS) was previously developed to characterize submicron aerosol size distributions at a frequency of 1 Hz and with high size resolution and counting statistics. However, the dynamic size range of the FIMS was limited to one decade in particle electrical mobility. It was proposed that the FIMS dynamic size range can be greatly increased by using a spatially varying electric field. This electric field creates regions with drastically different field strengths in the separator, such that particles of a wide diameter range can be simultaneously classified and subsequently measured. A FIMS incorporatingmore » this spatially varying electric field is developed. This paper describes the theoretical frame work and numerical simulations of the FIMS with extended dynamic size range, including the spatially varying electric field, particle trajectories, activation of separated particles in the condenser, and the transfer function, transmission efficiency, and mobility resolution. The influences of the particle Brownian motion on FIMS transfer function and mobility resolution are examined. The simulation results indicate that the FIMS incorporating the spatially varying electric field is capable of measuring aerosol size distribution from 8 to 600 nm with high time resolution. As a result, the experimental characterization of the FIMS is presented in an accompanying paper.« less

A fast integrated mobility spectrometer for rapid measurement of sub-micrometer aerosol size distribution, Part I: Design and model evaluation

DOE PAGES

Wang, Jian; Pikridas, Michael; Spielman, Steven R.; ...

2017-06-01

This study discusses, a fast integrated mobility spectrometer (FIMS) was previously developed to characterize submicron aerosol size distributions at a frequency of 1 Hz and with high size resolution and counting statistics. However, the dynamic size range of the FIMS was limited to one decade in particle electrical mobility. It was proposed that the FIMS dynamic size range can be greatly increased by using a spatially varying electric field. This electric field creates regions with drastically different field strengths in the separator, such that particles of a wide diameter range can be simultaneously classified and subsequently measured. A FIMS incorporatingmore » this spatially varying electric field is developed. This paper describes the theoretical frame work and numerical simulations of the FIMS with extended dynamic size range, including the spatially varying electric field, particle trajectories, activation of separated particles in the condenser, and the transfer function, transmission efficiency, and mobility resolution. The influences of the particle Brownian motion on FIMS transfer function and mobility resolution are examined. The simulation results indicate that the FIMS incorporating the spatially varying electric field is capable of measuring aerosol size distribution from 8 to 600 nm with high time resolution. As a result, the experimental characterization of the FIMS is presented in an accompanying paper.« less

In-situ droplet monitoring for self-tuning spectrometers

DOEpatents

Montaser, Akbar; Jorabchi, Kaveh; Kahen, Kaveh

2010-09-28

A laser scattering based imaging technique is utilized in order to visualize the aerosol droplets in an inductively coupled plasma (ICP) torch from an aerosol source to the site of analytical measurements. The resulting snapshots provide key information about the spatial distribution of the aerosol introduced by direct and indirect injection devices: 1) a direct injection high efficiency nebulizer (DIHEN); 2) a large-bore DIHEN (LB-DIHEN); and 3) a PFA microflow nebulizer with a PFA Scott-type spray chamber. Moreover, particle image velocimetry (PIV) is used to study the in-situ behavior of the aerosol before interaction with, for example, plasma, while the individual surviving droplets are explored by particle tracking velocimetry (PTV). Further, the velocity distribution of the surviving droplets demonstrates the importance of the initial droplet velocities in complete desolvation of the aerosol for optimum analytical performance in ICP spectrometries. These new observations are important in the design of the next-generation direct injection devices for lower sample consumption, higher sensitivity, lower noise levels, suppressed matrix effects, and for developing smart spectrometers. For example, a controller can be provided to control the output of the aerosol source by controlling the configuration of the source or the gas flow rate via feedback information concerning the aerosol.

Mixing state of particles with secondary species by single particle aerosol mass spectrometer in an atmospheric pollution event

NASA Astrophysics Data System (ADS)

Xu, Lingling; Chen, Jinsheng

2016-04-01

Single particle aerosol mass spectrometer (SPAMS) was used to characterize size distribution, chemical composition, and mixing state of particles in an atmospheric pollution event during 20 Oct. - 5 Nov., 2015 in Xiamen, Southeast China. A total of 533,012 particle mass spectra were obtained and clustered into six groups, comprising of industry metal (4.5%), dust particles (2.6%), carbonaceous species (70.7%), K-Rich particles (20.7%), seasalt (0.6%) and other particles (0.9%). Carbonaceous species were further divided into EC (70.6%), OC (28.5%), and mixed ECOC (0.9%). There were 61.7%, 58.3%, 4.0%, and 14.6% of particles internally mixed with sulfate, nitrate, ammonium and C2H3O, respectively, indicating that these particles had undergone significant aging processing. Sulfate was preferentially mixed with carbonaceous particles, while nitrate tended to mix with metal-containing and dust particles. Compared to clear days, the fractions of EC-, metal- and dust particles remarkably increased, while the fraction of OC-containing particles decreased in pollution days. The mixing state of particles, excepted for OC-containing particles with secondary species was much stronger in pollution days than that in clear days, which revealed the significant influence of secondary particles in atmospheric pollution. The different activity of OC-containing particles might be related to their much smaller aerodynamic diameter. These results could improve our understanding of aerosol characteristics and could be helpful to further investigate the atmospheric process of particles.

The CAS Classroom

ERIC Educational Resources Information Center

Garner, Sue

2004-01-01

The Victorian Curriculum and Assessment Authority (VCAA) Computer Algebra System (CAS)Pilot study (2001-2005) is monitoring the use of CAS in senior secondary mathematics. This article explores the author's experiences in the CAS classroom and delineates changes in teaching style, as a result of the introduction of CAS into the senior mathematics…

Airborne Aerosol Closure Studies During PRIDE

NASA Technical Reports Server (NTRS)

Redemann, Jens; Livingston, John M.; Russell, Philip B.; Schmid, Beat; Reid, Jeff

2000-01-01

The Puerto Rico Dust Experiment (PRIDE) was conducted during June/July of 2000 to study the properties of Saharan dust aerosols transported across the Atlantic Ocean to the Caribbean Islands. During PRIDE, the NASA Ames Research Center six-channel (380 - 1020 nm) airborne autotracking sunphotometer (AATS-6) was operated aboard a Piper Navajo airplane alongside a suite of in situ aerosol instruments. The in situ aerosol instrumentation relevant to this paper included a Forward Scattering Spectrometer Probe (FSSP-100) and a Passive Cavity Aerosol Spectrometer Probe (PCASP), covering the radius range of approx. 0.05 to 10 microns. The simultaneous and collocated measurement of multi-spectral aerosol optical depth and in situ particle size distribution data permits a variety of closure studies. For example, vertical profiles of aerosol optical depth obtained during local aircraft ascents and descents can be differentiated with respect to altitude and compared to extinction profiles calculated using the in situ particle size distribution data (and reasonable estimates of the aerosol index of refraction). Additionally, aerosol extinction (optical depth) spectra can be inverted to retrieve estimates of the particle size distributions, which can be compared directly to the in situ size distributions. In this paper we will report on such closure studies using data from a select number of vertical profiles at Cabras Island, Puerto Rico, including measurements in distinct Saharan Dust Layers. Preliminary results show good agreement to within 30% between mid-visible aerosol extinction derived from the AATS-6 optical depth profiles and extinction profiles forward calculated using 60s-average in situ particle size distributions and standard Saharan dust aerosol refractive indices published in the literature. In agreement with tendencies observed in previous studies, our initial results show an underestimate of aerosol extinction calculated based on the in situ size distributions

Formation of Oxidized Organic Aerosol (OOA) through Fog Processing in the Po Valley

NASA Astrophysics Data System (ADS)

Gilardoni, S.; Paglione, M.; Rinaldi, M.; Giulianelli, L.; Massoli, P.; Hillamo, R. E.; Carbone, S.; Lanconelli, C.; Laaksonen, A. J.; Russell, L. M.; Poluzzi, V.; Fuzzi, S.; Facchini, C.

2014-12-01

Aqueous phase chemistry might be responsible for the formation of a significant fraction of the organic aerosol (OA) observed in the atmosphere, and could explain some of the discrepancies between OA concentration and properties predicted by models and observed in the environment. Aerosol - fog interaction and its effect on submicron aerosol properties were investigated in the Po Valley (northern Italy) during fall 2011, in the framework of the Supersite project (ARPA Emilia Romagna). Composition and physical properties of submicron aerosol were measured online by a High Resolution- Time of Flight - Aerosol Mass Spectrometer (HR-TOF-AMS), a Soot Photometer - Aerosol Mass Spectrometer (SP-AMS), and a Tandem Differential Mobility Particle Sizer (TDMPS). Organic functional group analysis was performed off-line by Hydrogen - Nuclear Magnetic Resonance (H-NMR) spectrometry and by Fourier Transform Infrared (FTIR) spectrometry. Aerosol absorption, scattering, and total extinction were measured simultaneously with a Particle Soot Absorption Photometer (PSAP), a Nephelometer, and a Cavity Attenuated Phase Shift Spectrometer particle extinction monitor (CAPS PMex), respectively. Water-soluble organic carbon in fog-water was characterized off-line by HR-TOF-AMS. Fourteen distinct fog events were observed. Fog dissipation left behind an aerosol enriched in particles larger than 400 nm, typical of fog and cloud processing, and dominated by secondary species, including ammonium nitrate, ammonium sulfate and oxidized OA (OOA). Source apportionment of OA allowed us to identify OOA as the difference between total OA and primary OA (hydrocarbon like OA and biomass burning OA). The formation of OOA through fog processing is proved by the correlation of OOA concentration with hydroxyl methyl sulfonate signal and by the similarity of OOA spectra with organic mass spectra obtained by re-aerosolization of fog water samples. The oxygen to carbon ratio and the hydrogen to carbon ratio of

Black carbon aerosol mixing state, organic aerosols and aerosol optical properties over the United Kingdom

NASA Astrophysics Data System (ADS)

McMeeking, G. R.; Morgan, W. T.; Flynn, M.; Highwood, E. J.; Turnbull, K.; Haywood, J.; Coe, H.

2011-09-01

Black carbon (BC) aerosols absorb sunlight thereby leading to a positive radiative forcing and a warming of climate and can also impact human health through their impact on the respiratory system. The state of mixing of BC with other aerosol species, particularly the degree of internal/external mixing, has been highlighted as a major uncertainty in assessing its radiative forcing and hence its climate impact, but few in situ observations of mixing state exist. We present airborne single particle soot photometer (SP2) measurements of refractory BC (rBC) mass concentrations and mixing state coupled with aerosol composition and optical properties measured in urban plumes and regional pollution over the United Kingdom. All data were obtained using instrumentation flown on the UK's BAe-146-301 large Atmospheric Research Aircraft (ARA) operated by the Facility for Airborne Atmospheric Measurements (FAAM). We measured sub-micron aerosol composition using an aerosol mass spectrometer (AMS) and used positive matrix factorization to separate hydrocarbon-like (HOA) and oxygenated organic aerosols (OOA). We found a higher number fraction of thickly coated rBC particles in air masses with large OOA relative to HOA, higher ozone-to-nitrogen oxides (NOx) ratios and large concentrations of total sub-micron aerosol mass relative to rBC mass concentrations. The more ozone- and OOA-rich air masses were associated with transport from continental Europe, while plumes from UK cities had higher HOA and NOx and fewer thickly coated rBC particles. We did not observe any significant change in the rBC mass absorption efficiency calculated from rBC mass and light absorption coefficients measured by a particle soot absorption photometer despite observing significant changes in aerosol composition and rBC mixing state. The contributions of light scattering and absorption to total extinction (quantified by the single scattering albedo; SSA) did change for different air masses, with lower SSA

Organic Aerosols from SÃO Paulo and its Relationship with Aerosol Absorption and Scattering Properties

NASA Astrophysics Data System (ADS)

Artaxo, P.; Brito, J. F.; Rizzo, L. V.

2012-12-01

The megacity of São Paulo with its 19 million people and 7 million cars is a challenge from the point of view of air pollution. High levels of organic aerosols, PM10, black carbon and ozone and the peculiar situation of the large scale use of ethanol fuel makes it a special case. Little is known about the impact of ethanol on air quality and human health and the increase of ethanol as vehicle fuel is rising worldwide An experiment was designed to physico-chemical properties of aerosols in São Paulo, as well as their optical properties. Aerosol size distribution in the size range of 1nm to 10 micrometers is being measured with a Helsinki University SMPS (Scanning Mobility Particle Sizer), an NAIS (Neutral ion Spectrometer) and a GRIMM OPC (Optical Particle Counter). Optical properties are being measured with a TSI Nephelometer and a Thermo MAAP (Multi Angle Absorption Photometer). A CIMEL sunphotometer from the AERONET network measure the aerosol optical depth. Furthermore, a Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) and an Aerosol Chemical Speciation Monitor (ACSM) are used to real-time VOC analysis and aerosol composition, respectively. The ACSM was operated for 3 months continuosly during teh wintertime of 2012. The measured total particle concentration typically varies between 10,000 and 30,000 cm-3 being the lowest late in the night and highest around noon and frequently exceeding 50,000 cm-3. Clear diurnal patterns in aerosol optical properties were observed. Scattering and absorption coefficients typically range between 20 and 100 Mm-1 at 450 nm, and between 10 to 40 Mm-1 at 637 nm, respectively, both of them peaking at 7:00 local time, the morning rush hour. The corresponding single scattering albedo varies between 0.50 and 0.85, indicating a significant contribution of primary absorbing particles to the aerosol population. During the first month a total of seven new particle formation events were observed with growth rates ranging from 9 to 25

Environmental Temperature Effect on the Far-Infrared Absorption Features of Aromatic-Based Titan's Aerosol Analogs

NASA Technical Reports Server (NTRS)

Gautier, Thomas; Trainer, Melissa G.; Loeffler, Mark J.; Sebree, Joshua A.; Anderson, Carrie M.

2016-01-01

Benzene detection has been reported in Titans atmosphere both in the stratosphere at ppb levels by remote sensing and in the thermosphere at ppm levels by the Cassini's Ion and Neutral Mass Spectrometer. This detection supports the idea that aromatic and heteroaromatic reaction pathways may play an important role in Titans atmospheric chemistry, especially in the formation of aerosols. Indeed, aromatic molecules are easily dissociated by ultraviolet radiation and can therefore contribute significantly to aerosol formation. It has been shown recently that aerosol analogs produced from a gas mixture containing a low concentration of aromatic and/or heteroaromatic molecules (benzene, naphthalene, pyridine, quinoline and isoquinoline) have spectral signatures below 500/cm, a first step towards reproducing the aerosol spectral features observed by Cassini's Composite InfraRed Spectrometer (CIRS) in the far infrared. In this work we investigate the influence of environmental temperature on the absorption spectra of such aerosol samples, simulating the temperature range to which aerosols, once formed, are exposed during their transport through Titans stratosphere. Our results show that environmental temperature does not have any major effect on the spectral shape of these aerosol analogs in the far-infrared, which is consistent with the CIRS observations.

Laboratory Experiments and Instrument Intercomparison Studies of Carbonaceous Aerosol Particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davidovits, Paul

particles: (a) two well-characterized source of soot particles and (b) a flow reactor for controlled OH and/or O3 oxidation of relevant gas phase species to produce well-characterized SOA particles. After formation, the aerosol particles are subjected to physical and chemical processes that simulate aerosol growth and aging. A suite of instruments in our laboratory is used to characterize the physical and chemical properties of aerosol particles before and after processing. The Time of Flight Aerosol Mass Spectrometer (ToF-AMS) together with a Scanning Mobility Particle Sizer (SMPS) measures particle mass, volume, density, composition (including black carbon content), dynamic shape factor, and fractal dimension. The–ToF-AMS was developed at ARI with Boston College participation. About 120 AMS instruments are now in service (including 5 built for DOE laboratories) performing field and laboratory studies world-wide. Other major instruments include a thermal denuder, two Differential Mobility Analyzers (DMA), a Cloud Condensation Nuclei Counter (CCN), a Thermal desorption Aerosol GC/MS (TAG) and the new Soot Particle Aerosol Mass Spectrometer (SP-AMS). Optical instrumentation required for the studies have been brought to our laboratory as part of ongoing and planned collaborative projects with colleagues from DOE, NOAA and university laboratories. Optical instruments that will be utilized include a Photoacoustic Spectrometer (PAS), a Cavity Ring Down Aerosol Extinction Spectrometer (CRD-AES), a Photo Thermal Interferometer (PTI), a new 7-wavelength Aethalometer and a Cavity Attenuated Phase Shift Extinction Monitor (CAPS). These instruments are providing aerosol absorption, extinction and scattering coefficients at a range of atmospherically relevant wavelengths. During the past two years our work has continued along the lines of our original proposal. We report on 12 completed and/or continuing projects conducted during the period 08/14 to 0814/2015. These projects are

Variability of Biomass Burning Aerosols Layers and Near Ground

NASA Astrophysics Data System (ADS)

Vasilescu, Jeni; Belegante, Livio; Marmureanu, Luminita; Toanca, Flori

2016-06-01

The aim of this study is to characterize aerosols from both chemical and optical point of view and to explore the conditions to sense the same particles in elevated layers and at the ground. Three days of continuous measurements using a multi-wavelength depolarization lidar(RALI) and a C-ToF-AMS aerosol mass spectrometer are analyzed. The presence of smoke particles was assessed in low level layers from RALI measurements. Chemical composition of submicronic volatile/semi-volatile aerosols at ground level was monitored by the CTOF AMS Several episodes of biomass burning aerosols have been identified by both techniques due to the presence of specific markers (f60, linear particle depolarization ratio, Ängström exponent).

Synthesizing Scientific Progress: Outcomes from US EPA’s Carbonaceous Aerosols and Source Apportionment STAR Grants

EPA Science Inventory

ABSTRACTA number of studies in the past decade have transformed the way we think about atmospheric aerosols. The advances include, but are not limited to, source apportionment of organics using aerosol mass spectrometer data, the volatility basis set approach, quantifying isopre...

Evaluation of Organic Aerosol Formation and Apportionment in a polluted Megacity

NASA Astrophysics Data System (ADS)

Tsimpidi, A. P.; Karydis, V. A.; Zavala, M.; Lei, W.; Decarlo, P. F.; Ulbrich, I.; Jimenez, J. L.; Molina, L. T.; Pandis, S. N.

2009-04-01

Pollution from megacities and large urban areas is important not only for local effects on health, visibility, and ecosystems but also because of their collective influence on atmospheric chemistry and radiative forcing in regional and global scale. Organic species account for a large fraction of the submicron aerosol mass at most megacities. Urban areas are large sources of organic aerosols and their precursors. Nevertheless, the contributions of primary (POA) and secondary organic aerosol (SOA) have been difficult to quantify. In this study, new primary and secondary organic aerosol modules were added to PMCAMx, a three dimensional chemical transport model (Gaydos et al., 2007). The new modeling framework is based on the volatility basis-set approach (Lane et al., 2007): both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The emission inventory is modified and the POA emissions are distributed by volatility based on dilution experiments (Robinson et al., 2007). PMCAMx is applied in the Mexico City Metropolitan Area during April 2003 and March 2006. The model predictions are compared with Aerodyne's Aerosol Mass Spectrometer (AMS) observations from the MCMA and MILAGRO campaigns respectively. Furthermore, the predicted concentrations over Mexico City are compared against measurements from a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) which was onboard the NSF/NCAR C-130 aircraft as part of the MILAGRO field campaign (DeCarlo et al., 2008). The organic aerosol (OA) to CO ratio is used as an indicator in order to evaluate the photo-oxidation of the predicted OA after its horizontal and vertical advection. References Gaydos, T.M.; Pinder, R.W.; Koo, B.; Fahey, K.M.; Pandis, S.N., 2007. Development and application of a three-dimensional aerosol chemical transport model, PMCAMx. Atmospheric Environment 41, 2594-2611. Lane, T

Measuring Aerosol Size Distributions from the NASA DC-8 in SOLVE II

NASA Technical Reports Server (NTRS)

Reeves, Michael

2003-01-01

The University of Denver Focused Cavity Aerosol Spectrometer (FCAS 11) and Nucleation-Mode Aerosol Size Spectrometer (N-MASS) were successfully integrated and flown aboard NASA s DC-8 for the second SAGE I11 Ozone Loss and Validation Experiment (SOLVE 11). Both instruments performed well during SOLVE, with virtually complete data coverage for all mission and test flights. The few exceptions to this were the occasional simultaneous zero-check for the instruments, and some data loss for channel 4 of the N-MASS. The only consequence of the latter is reduced resolution in the 15 to 60 nm range for the affected size distributions.

Peak fitting and integration uncertainties for the Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Corbin, J. C.; Othman, A.; Haskins, J. D.; Allan, J. D.; Sierau, B.; Worsnop, D. R.; Lohmann, U.; Mensah, A. A.

2015-04-01

The errors inherent in the fitting and integration of the pseudo-Gaussian ion peaks in Aerodyne High-Resolution Aerosol Mass Spectrometers (HR-AMS's) have not been previously addressed as a source of imprecision for these instruments. This manuscript evaluates the significance of these uncertainties and proposes a method for their estimation in routine data analysis. Peak-fitting uncertainties, the most complex source of integration uncertainties, are found to be dominated by errors in m/z calibration. These calibration errors comprise significant amounts of both imprecision and bias, and vary in magnitude from ion to ion. The magnitude of these m/z calibration errors is estimated for an exemplary data set, and used to construct a Monte Carlo model which reproduced well the observed trends in fits to the real data. The empirically-constrained model is used to show that the imprecision in the fitted height of isolated peaks scales linearly with the peak height (i.e., as n1), thus contributing a constant-relative-imprecision term to the overall uncertainty. This constant relative imprecision term dominates the Poisson counting imprecision term (which scales as n0.5) at high signals. The previous HR-AMS uncertainty model therefore underestimates the overall fitting imprecision. The constant relative imprecision in fitted peak height for isolated peaks in the exemplary data set was estimated as ~4% and the overall peak-integration imprecision was approximately 5%. We illustrate the importance of this constant relative imprecision term by performing Positive Matrix Factorization (PMF) on a~synthetic HR-AMS data set with and without its inclusion. Finally, the ability of an empirically-constrained Monte Carlo approach to estimate the fitting imprecision for an arbitrary number of known overlapping peaks is demonstrated. Software is available upon request to estimate these error terms in new data sets.

Characterization of ambient aerosols at the San Francisco International Airport using BioAerosol Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steele, P T; McJimpsey, E L; Coffee, K R

2006-03-16

The BioAerosol Mass Spectrometry (BAMS) system is a rapidly fieldable, fully autonomous instrument that can perform correlated measurements of multiple orthogonal properties of individual aerosol particles. The BAMS front end uses optical techniques to nondestructively measure a particle's aerodynamic diameter and fluorescence properties. Fluorescence can be excited at 266nm or 355nm and is detected in two broad wavelength bands. Individual particles with appropriate size and fluorescence properties can then be analyzed more thoroughly in a dual-polarity time-of-flight mass spectrometer. Over the course of two deployments to the San Francisco International Airport, more than 6.5 million individual aerosol particles were fullymore » analyzed by the system. Analysis of the resulting data has provided a number of important insights relevant to rapid bioaerosol detection, which are described here.« less

Identification of secondary aerosol precursors emitted by an aircraft turbofan

NASA Astrophysics Data System (ADS)

Kılıç, Doğuşhan; El Haddad, Imad; Brem, Benjamin T.; Bruns, Emily; Bozetti, Carlo; Corbin, Joel; Durdina, Lukas; Huang, Ru-Jin; Jiang, Jianhui; Klein, Felix; Lavi, Avi; Pieber, Simone M.; Rindlisbacher, Theo; Rudich, Yinon; Slowik, Jay G.; Wang, Jing; Baltensperger, Urs; Prévôt, Andre S. H.

2018-05-01

Oxidative processing of aircraft turbine-engine exhausts was studied using a potential aerosol mass (PAM) chamber at different engine loads corresponding to typical flight operations. Measurements were conducted at an engine test cell. Organic gases (OGs) and particle emissions pre- and post-PAM were measured. A suite of instruments, including a proton-transfer-reaction mass spectrometer (PTR-MS) for OGs, a multigas analyzer for CO, CO2, NOx, and an aerosol mass spectrometer (AMS) for nonrefractory particulate matter (NR-PM1) were used. Total aerosol mass was dominated by secondary aerosol formation, which was approximately 2 orders of magnitude higher than the primary aerosol. The chemical composition of both gaseous and particle emissions were also monitored at different engine loads and were thrust-dependent. At idling load (thrust 2.5-7 %), more than 90 % of the secondary particle mass was organic and could mostly be explained by the oxidation of gaseous aromatic species, e.g., benzene; toluene; xylenes; tri-, tetra-, and pentamethyl-benzene; and naphthalene. The oxygenated-aromatics, e.g., phenol, furans, were also included in this aromatic fraction and their oxidation could alone explain up to 25 % of the secondary organic particle mass at idling loads. The organic fraction decreased with thrust level, while the inorganic fraction increased. At an approximated cruise load sulfates comprised 85 % of the total secondary particle mass.

Chemical Properties of Brown Carbon Aerosol Generated at the Missoula Fire Sciences Laboratory

NASA Astrophysics Data System (ADS)

Washenfelder, R. A.; Womack, C.; Franchin, A.; Middlebrook, A. M.; Wagner, N.; Manfred, K.

2017-12-01

Aerosol scattering and absorption are still among the largest uncertainties in quantifying radiative forcing. Biomass burning is a major source of light-absorbing carbonaceous aerosol in the United States. These aerosol are generally classified into two categories: black carbon (graphitic-like aerosol that absorbs broadly across the ultraviolet and visible spectral regions) and brown carbon (organic aerosol that absorbs strongly in the ultraviolet and near-visible spectral regions). The composition, volatility, and chemical aging of brown carbon are poorly known, but are important to understanding its radiative effects. We deployed three novel instruments to the Missoula Fire Sciences Laboratory in 2016 to measure brown carbon absorption: a photoacoustic spectrometer, broadband cavity enhanced spectrometer, and particle-into-liquid sampler coupled to a liquid waveguide capillary cell. The instruments sampled from a shared inlet with well-characterized dilution and thermal denuding. We sampled smoke from 32 controlled burns of fuels relevant to western U.S. wildfires. We use these measurements to determine the volatility of water-soluble brown carbon, and compare this to the volatility of water-soluble organic aerosol and total organic aerosol. We further examine the wavelength-dependence of the water-soluble brown carbon absorption as a function of denuder temperature. Together this gives new information about the solubility, volatility, and chemical composition of brown carbon.

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

PubMed

Hochstrasser, Megan L; Taylor, David W; Bhat, Prashant; Guegler, Chantal K; Sternberg, Samuel H; Nogales, Eva; Doudna, Jennifer A

2014-05-06

In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a sequence matching that of the crRNA. Cascade comprises the CasA-E proteins and one crRNA, forming a structure that binds and unwinds dsDNA to form an R loop in which the target strand of the DNA base pairs with the 32-nt RNA guide sequence. Single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of the DNA duplex at the CasA subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage.

Evaluation of the new capture vapourizer for aerosol mass spectrometers (AMS) through laboratory studies of inorganic species

NASA Astrophysics Data System (ADS)

Hu, Weiwei; Campuzano-Jost, Pedro; Day, Douglas A.; Croteau, Philip; Canagaratna, Manjula R.; Jayne, John T.; Worsnop, Douglas R.; Jimenez, Jose L.

2017-08-01

Aerosol mass spectrometers (AMSs) and Aerosol Chemical Speciation Monitors (ACSMs) commercialized by Aerodyne are widely used to measure the non-refractory species in submicron particles. With the standard vapourizer (SV) that is installed in all commercial instruments to date, the quantification of ambient aerosol mass concentration requires the use of the collection efficiency (CE) to correct for the loss of particles due to bounce. A new capture vapourizer (CV) has been designed to reduce the need for a bounce-related CE correction. Two high-resolution AMS instruments, one with a SV and one with a CV, were operated side by side in the laboratory. Four standard species, NH4NO3, NaNO3, (NH4)2SO4 and NH4Cl, which typically constitute the majority of the mass of ambient submicron inorganic species, are studied. The effect of vapourizer temperature (Tv ˜ 200-800 °C) on the detected fragments, CE and size distributions are investigated. A Tv of 500-550 °C for the CV is recommended. In the CV, CE was identical (around unity) for more volatile species (e.g. NH4NO3) and comparable to or higher than the SV for less-volatile species (e.g. (NH4)2SO4), demonstrating an improvement in CE for laboratory inorganic species in the CV. The detected relative intensities of fragments of NO3 and SO4 species observed with the CV are different from those observed with the SV, and are consistent with additional thermal decomposition arising from the increased residence time and multiple collisions. Increased residence times with the CV also lead to broader particle size distribution measurements than with the SV. A method for estimating whether pure species will be detected in AMS sizing mode is proposed. Production of CO2(g) from sampled nitrate on the vapourizer surface, which has been reported for the SV, is negligible for the CV for NH4NO3 and comparable to the SV for NaNO3. . We observe an extremely consistent fragmentation for ammonium compared to very large changes for the

Observational Study and Parameterization of Aerosol-fog Interactions

NASA Astrophysics Data System (ADS)

Duan, J.; Guo, X.; Liu, Y.; Fang, C.; Su, Z.; Chen, Y.

2014-12-01

Studies have shown that human activities such as increased aerosols affect fog occurrence and properties significantly, and accurate numerical fog forecasting depends on, to a large extent, parameterization of fog microphysics and aerosol-fog interactions. Furthermore, fogs can be considered as clouds near the ground, and enjoy an advantage of permitting comprehensive long-term in-situ measurements that clouds do not. Knowledge learned from studying aerosol-fog interactions will provide useful insights into aerosol-cloud interactions. To serve the twofold objectives of understanding and improving parameterizations of aerosol-fog interactions and aerosol-cloud interactions, this study examines the data collected from fogs, with a focus but not limited to the data collected in Beijing, China. Data examined include aerosol particle size distributions measured by a Passive Cavity Aerosol Spectrometer Probe (PCASP-100X), fog droplet size distributions measured by a Fog Monitor (FM-120), Cloud Condensation Nuclei (CCN), liquid water path measured by radiometers and visibility sensors, along with meteorological variables measured by a Tethered Balloon Sounding System (XLS-Ⅱ) and Automatic Weather Station (AWS). The results will be compared with low-level clouds for similarities and differences between fogs and clouds.

Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR) Instrument Improvements

NASA Technical Reports Server (NTRS)

Dunagan, Stephen E.; Redemann, Jens; Chang, Cecilia; Dahlgren, Robert; Fahey, Lauren; Flynn, Connor; Johnson, Roy; Kacenelenbogen, Meloe; Leblanc, Samuel; Liss, Jordan;

Aerosol volatility in a boreal forest environment

NASA Astrophysics Data System (ADS)

Häkkinen, S. A. K.; ńijälä, M.; Lehtipalo, K.; Junninen, H.; Virkkula, A.; Worsnop, D. R.; Kulmala, M.; Petäjä, T.; Riipinen, I.

2012-04-01

Climate and health effects of atmospheric aerosols are determined by their properties such as their chemical composition. Aerosol chemical composition can be studied indirectly by measuring volatility of aerosol particles. The volatility of submicron aerosol particles (20-500 nm) was studied in a boreal forest site at SMEAR II (Station for Measuring Ecosystem-Atmosphere Relations II) station (Vesala et al., 1998) in Hyytiälä, Finland, during 01/2008-05/2010. The instrument used for the measurements was VDMPS (Volatility Differential Mobility Particle Sizer), which consists of two separate instruments: DMPS (Differential Mobility Particle Sizer, Aalto et al., 2001) and TD (Thermodenuder, Wehner et al., 2002). Aerosol evaporation was examined by heating the aerosol and comparing the total aerosol mass before and after heating. In the VDMPS system ambient aerosol sample was heated up to temperatures ranging from 80 °C to 280 °C. The higher the heating temperature was the more aerosol material was evaporated. There was a non-volatile residual present in aerosol particles when heated up to 280 °C. This residual explained (20±8)% of the total aerosol mass. Aerosol non-volatile mass fraction was highest during winter and smallest during summer months. The role of black carbon in the observed non-volatile residual was determined. Black carbon explained 40 to 90% of the non-volatile mass. Especially during colder seasons noticeable amount of non-volatile material, something else than black carbon, was observed. According to Kalberer et al. (2004) some atmospheric organic species can form polymers that have high evaporation temperatures. Also low-volatile organic salts may contribute to the non-volatile aerosol (Smith et al., 2010). Aerosol mass composition measured directly with AMS (Aerosol Mass Spectrometer, Jayne et al., 2000) was analyzed in order to examine the properties of the non-volatile material (other than black carbon). The AMS measurements were performed

A COMPARISON OF PARTICLE MASS SPECTROMETERS DURING THE 1999 ATLANTA SUPERSITES EXPERIMENT

EPA Science Inventory

During the Atlanta SuperSite Experiment, four particle mass spectrometers were operated together for the first time: NOAA's PALMS (Particle Analysis by Laser Mass Spectrometry), U. C. Riverside's ATOFMS (Aerosol Time-of-Flight Mass Spectrometry), U. Delaware's RSMS-II (Rapid Si...

Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b.

PubMed

Richter, Hagen; Rompf, Judith; Wiegel, Julia; Rau, Kristina; Randau, Lennart

2017-11-01

CRISPR arrays are transcribed into long precursor RNA species, which are further processed into mature CRISPR RNAs (crRNAs). Cas proteins utilize these crRNAs, which contain spacer sequences that can be derived from mobile genetic elements, to mediate immunity during a reoccurring virus infection. Type I CRISPR-Cas systems are defined by the presence of different Cascade interference complexes containing large and small subunits that play major roles during target DNA selection. Here, we produce the protein and crRNA components of the Type I-B CRISPR-Cas complex of Clostridium thermocellum and Methanococcus maripaludis. The C. thermocellum Cascade complexes were reconstituted and analyzed via size-exclusion chromatography. Activity of the heterologous M. maripaludis CRISPR-Cas system was followed using phage lambda plaques assays. The reconstituted Type-I-B Cascade complex contains Cas7, Cas5, Cas6b and the large subunit Cas8b. Cas6b can be omitted from the reconstitution protocol. The large subunit Cas8b was found to be represented by two tightly associated protein fragments and a small C-terminal Cas8b segment was identified in recombinant complexes and C. thermocellum cell lysate. Production of Cas8b generates a small C-terminal fragment, which is suggested to fulfill the role of the missing small subunit. A heterologous, synthetic M. maripaludis Type I-B system is active in E. coli against phage lambda, highlighting a potential for genome editing using endogenous Type-I-B CRISPR-Cas machineries. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Satellite remote sensing of dust aerosol indirect effects on ice cloud formation.

PubMed

Ou, Steve Szu-Cheng; Liou, Kuo-Nan; Wang, Xingjuan; Hansell, Richard; Lefevre, Randy; Cocks, Stephen

2009-01-20

We undertook a new approach to investigate the aerosol indirect effect of the first kind on ice cloud formation by using available data products from the Moderate-Resolution Imaging Spectrometer (MODIS) and obtained physical understanding about the interaction between aerosols and ice clouds. Our analysis focused on the examination of the variability in the correlation between ice cloud parameters (optical depth, effective particle size, cloud water path, and cloud particle number concentration) and aerosol optical depth and number concentration that were inferred from available satellite cloud and aerosol data products. Correlation results for a number of selected scenes containing dust and ice clouds are presented, and dust aerosol indirect effects on ice clouds are directly demonstrated from satellite observations.

Toward Creating A Global Retrospective Climatology of Aerosol Properties

NASA Technical Reports Server (NTRS)

Curran, Robert J.; Mishchenko, Michael I.; Hansen, James E. (Technical Monitor)

2000-01-01

Tropospheric aerosols are thought to cause a significant direct and indirect climate forcing, but the magnitude of this forcing remains highly uncertain because of poor knowledge of global aerosol characteristics and their temporal changes. The standard long-term global product, the one-channel Advanced Very-High-Resolution Radiometer (AVHRR) aerosol optical thickness over the ocean, relies on a single predefined aerosol model and can be inaccurate in many cases. Furthermore, it provides no information on aerosol column number density, thus making it impossible to estimate the indirect aerosol effect on climate. Total Ozone Mapping Spectrometer (TOMS) data can be used to detect absorbing aerosols over land, but are insensitive to aerosols located below one kilometer. It is thus clear that innovative approaches must be employed in order to extract a more quantitative and accurate aerosol climatology from available satellite and other measurements, thus enabling more reliable estimates of the direct and indirect aerosol forcings. The Global Aerosol Climatology Project (GACP) was established in 1998 as part of the Global Energy and Water Cycle Experiment (GEWEX). Its main objective is to analyze satellite radiance measurements and field observations to infer the global distribution of aerosols, their properties, and their seasonal and interannual variations. The overall goal is to develop advanced global aerosol climatologies for the period of satellite data and to make the aerosol climatologies broadly available through the GACP web site.

[A review of atmospheric aerosol research by using polarization remote sensing].

PubMed

Guo, Hong; Gu, Xing-Fa; Xie, Dong-Hai; Yu, Tao; Meng, Qing-Yan

2014-07-01

In the present paper, aerosol research by using polarization remote sensing in last two decades (1993-2013) was reviewed, including aerosol researches based on POLDER/PARASOL, APS(Aerosol Polarimetry Sensor), Polarized Airborne camera and Ground-based measurements. We emphasize the following three aspects: (1) The retrieval algorithms developed for land and marine aerosol by using POLDER/PARASOL; The validation and application of POLDER/PARASOL AOD, and cross-comparison with AOD of other satellites, such as MODIS AOD. (2) The retrieval algorithms developed for land and marine aerosol by using MICROPOL and RSP/APS. We also introduce the new progress in aerosol research based on The Directional Polarimetric Camera (DPC), which was produced by Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences (CAS). (3) The aerosol retrieval algorithms by using measurements from ground-based instruments, such as CE318-2 and CE318-DP. The retrieval results from spaceborne sensors, airborne camera and ground-based measurements include total AOD, fine-mode AOD, coarse-mode AOD, size distribution, particle shape, complex refractive indices, single scattering albedo, scattering phase function, polarization phase function and AOD above cloud. Finally, based on the research, the authors present the problems and prospects of atmospheric aerosol research by using polarization remote sensing, and provide a valuable reference for the future studies of atmospheric aerosol.

Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex.

PubMed

Fagerlund, Robert D; Wilkinson, Max E; Klykov, Oleg; Barendregt, Arjan; Pearce, F Grant; Kieper, Sebastian N; Maxwell, Howard W R; Capolupo, Angela; Heck, Albert J R; Krause, Kurt L; Bostina, Mihnea; Scheltema, Richard A; Staals, Raymond H J; Fineran, Peter C

2017-06-27

CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas1 4 -Cas2-3 2 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.

Deriving the concentration of airborne ash with a CAS-DPOL instrument: assessing uncertainties introduced by the instrument design

NASA Astrophysics Data System (ADS)

Spanu, Antonio; Weinzierl, Bernadett; Freudenthaler, Volker; Sauer, Daniel; Gasteiger, Josef

2016-04-01

sensitive to the sample flow and on the mechanical instrument design. Using a fluid dynamics model coupled with an optical model we analyze the effects of instrument design on the measurement, identify measurement uncertainties and recommend strategies to reduce the uncertainties. The two main results are that the optical design of the CAS-DPOL aerosol spectrometer can lead to an under-counting bias of up to 40% for larger particles and an over-counting bias of 20%-30% for smaller particles. Secondly, depending on how the instrument is mounted on the plane, the sampling can be subject to a significantly larger size selection bias than typically recognized, especially if the mounting leads to irregular sampling conditions. To correct both problems a new correction algorithm is described generalizing the results also to other optical particle counters. Finally, a comparison study is presented showing the effects on mass estimation and radiative forcing for uncorrected and corrected data also stating the resulting uncertainty.

Analysis of reflectance spectra of UV-absorbing aerosol scenes measured by SCIAMACHY

NASA Astrophysics Data System (ADS)

de Graaf, M.; Stammes, P.; Aben, E. A. A.

2007-01-01

Reflectance spectra from 280-1750 nm of typical desert dust aerosol (DDA) and biomass burning aerosol (BBA) scenes over oceans are presented, measured by the space-borne spectrometer Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY). DDA and BBA are both UV-absorbing aerosols, but their effect on the top-of-atmosphere (TOA) reflectance is different due to differences in the way mineral aerosols and smoke reflect and absorb radiation. Mineral aerosols are typically large, inert particles, found in warm, dry continental air. Smoke particles, on the other hand, are usually small particles, although often clustered, chemically very active and highly variable in composition. Moreover, BBA are hygroscopic and over oceans BBA were invariably found in cloudy scenes. TOA reflectance spectra of typical DDA and BBA scenes were analyzed, using radiative transfer simulations, and compared. The DDA spectrum was successfully simulated using a layer with a bimodal size distribution of mineral aerosols in a clear sky. The spectrum of the BBA scene, however, was determined by the interaction between cloud droplets and smoke particles, as is shown by simulations with a model of separate aerosol and cloud layers and models with internally and externally mixed aerosol/cloud layers. The occurrence of clouds in smoke scenes when sufficient water vapor is present usually prevents the detection of optical properties of these aerosol plumes using space-borne sensors. However, the Absorbing Aerosol Index (AAI), a UV color index, is not sensitive to scattering aerosols and clouds and can be used to detect these otherwise obscured aerosol plumes over clouds. The amount of absorption of radiation can be expressed using the absorption optical thickness. The absorption optical thickness in the DDA case was 0.42 (340 nm) and 0.14 (550 nm) for an aerosol layer of optical thickness 1.74 (550 nm). In the BBA case the absorption optical thickness was 0.18 (340 nm) and 0

The physico-chemical evolution of atmospheric aerosols and the gas-particle partitioning of inorganic aerosol during KORUS-AQ

NASA Astrophysics Data System (ADS)

Lee, T.; Park, T.; Lee, J. B.; Lim, Y. J.; Ahn, J.; Park, J. S.; Soo, C. J.; Desyaterik, Y.; Collett, J. L., Jr.

2017-12-01

Aerosols influence climate change directly by scattering and absorption and indirectly by acting as cloud condensation nuclei and some of the effects of aerosols are reduction in visibility, deterioration of human health, and deposition of pollutants to ecosystems. Urban area is large source of aerosols and aerosol precursors. Aerosol sources are both local and from long-range transport. Long-range transport processed aerosol are often dominant sources of aerosol pollution in Korea. To improve our knowledge of aerosol chemistry, Korea and U.S-Air Quality (KORUS-AQ) of Aircraft-based aerosol measurement took place in and around Seoul, Korea during May and June 2016. KORUS-AQ campaigns were conducted to study the chemical characterization and processes of pollutants in the Seoul Metropolitan area to regional scales of Korean peninsula. Aerodyne High Resolution Time of Flight Aerosol Mass Spectrometer (HR-ToF-AMS) was deployed on aircraft platforms on-board DC-8 (NASA) aircraft. We characterized aerosol chemical properties and mass concentrations of sulfate, nitrate, ammonium and organics in polluted air plumes and investigate the spatial and vertical distribution of the species. The results of studies show that organics is predominant in Aerosol and a significant fraction of the organics is oxygenated organic aerosol (OOA) at the high altitude. Both Nitrate and sulfate can partition between the gas and particle phases. The ratios for HNO3/(N(V) (=gaseous HNO3 + particulate Nitrate) and SO2/(SO2+Sulfate) were found to exhibit quite different distributions between the particles and gas phase for the locations during KORUS-AQ campaign, representing potential for formation of additional particulate nitrate and sulfate. The results of those studies can provide highly resolved temporal and spatial air pollutant, which are valuable for air quality model input parameters for aerosol behaviour.

Environmental temperature effect on the far-infrared absorption features of aromatic-based Titan's aerosol analogs

NASA Astrophysics Data System (ADS)

Gautier, Thomas; Trainer, Melissa G.; Loeffler, Mark J.; Sebree, Joshua A.; Anderson, Carrie M.

2017-01-01

Benzene detection has been reported in Titan's atmosphere both in the stratosphere at ppb levels by remote sensing (Coustenis et al., 2007; Vinatier et al., 2007) and in the thermosphere at ppm levels by the Cassini's Ion and Neutral Mass Spectrometer (Waite et al., 2007). This detection supports the idea that aromatic and heteroaromatic reaction pathways may play an important role in Titan's atmospheric chemistry, especially in the formation of aerosols. Indeed, aromatic molecules are easily dissociated by ultraviolet radiation and can therefore contribute significantly to aerosol formation. It has been shown recently that aerosol analogs produced from a gas mixture containing a low concentration of aromatic and/or heteroaromatic molecules (benzene, naphthalene, pyridine, quinoline and isoquinoline) have spectral signatures below 500 cm-1, a first step towards reproducing the aerosol spectral features observed by Cassini's Composite InfraRed Spectrometer (CIRS) in the far infrared (Anderson and Samuelson 2011, and references therein). In this work we investigate the influence of environmental temperature on the absorption spectra of such aerosol samples, simulating the temperature range to which aerosols, once formed, are exposed during their transport through Titan's stratosphere. Our results show that environmental temperature does not have any major effect on the spectral shape of these aerosol analogs in the far-infrared, which is consistent with the CIRS observations.

Airborne measurements of multi-wavelength aerosol optical depth and cloud-transmitted radiances in the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES)

NASA Astrophysics Data System (ADS)

Shinozuka, Y.; Johnson, R. R.; LeBlanc, S. E.; Chang, C. S.; Redemann, J.

2016-12-01

We report on our recent airborne measurements of multi-wavelength aerosol optical depth and cloud-transmitted radiances over the North Atlantic. We ran the Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR) in November 2015 and the 14-channel Ames Airborne Tracking Sunphotometer (AATS-14) in May and June 2016, both aboard the NASA C-130 aircraft. These sunphotometers provide measurements of overlying cirrus and aerosol optical depths of up to about 0.5 and constrain ecosystem and aerosol retrievals from the accompanying nadir-viewing remote sensing instruments. In addition, 4STAR measures hyperspectral transmitted light, which enables the retrieval of cloud optical depth, effective radius, and thermodynamic phase from below cloud. Our measurements contribute to the science objectives of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES), an interdisciplinary investigation resolving key processes controlling marine ecosystems and aerosols that are essential to our understanding of Earth system function and future change.

Coordinated Airborne, Spaceborne, and Ground-Based Measurements of Massive, Thick Aerosol Layers During the Dry Season in Southern Africa

NASA Technical Reports Server (NTRS)

Schmid, B.; Redemann, J.; Russell, P. B.; Hobbs, P. V.; Hlavka, D. L.; McGill, M. J.; Holben, B. N.; Welton, E. J.; Campbell, J.; Torres, O.;

Two-Column Aerosol Project: Aerosol Light Extinction Measurements Field Campaign Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubey, Manvendra; Aiken, Allison; Berg, Larry

We deployed Aerodyne Research Inc.’s first Cavity Attenuated Phase Shift extinction (CAPS PMex) monitor (built by Aerodyne) that measures light extinction by using a visible-light-emitting diode (LED) as a light source, a sample cell incorporating two high-reflectivity mirrors centered at the wavelength of the LED, and a vacuum photodiode detector in Cape Cod in 2012/13 for the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Two-Column Aerosol Project (TCAP). The efficacy of this instrument is based on the fact that aerosols are broadband scatterers and absorbers of light. The input LED is square-wave modulated and passedmore » through the sample cell that distorts it due to exponential decay by aerosol light absorption and scattering; this is measured at the detector. The amount of phase shift of the light at the detector is used to determine the light extinction. This extinction measurement provides an absolute value, requiring no calibration. The goal was to compare the CAPS performance with direct measurements of absorption with ARM’s baseline photoacoustic soot spectrometer (PASS-3) and nephelometer instruments to evaluate its performance.« less

Photoacoustic absorption spectroscopy of single optically trapped aerosol droplets

NASA Astrophysics Data System (ADS)

Covert, Paul A.; Cremer, Johannes W.; Signorell, Ruth

2017-08-01

Photoacoustics have been widely used for the study of aerosol optical properties. To date, these studies have been performed on particle ensembles, with minimal ability to control for particle size. Here, we present our singleparticle photoacoustic spectrometer. The sensitivity and stability of the instrument is discussed, along with results from two experiments that illustrate the unique capabilities of this instrument. In the first experiment, we present a measurement of the particle size-dependence of the photoacoustic response. Our results confirm previous models of aerosol photoacoustics that had yet to be experimentally tested. The second set of results reveals a size-dependence of photochemical processes within aerosols that results from the nanofocusing of light within individual droplets.

A New Method Using Single-Particle Mass Spectrometry Data to Distinguish Mineral Dust and Biological Aerosols

NASA Astrophysics Data System (ADS)

Al-Mashat, H.; Kristensen, L.; Sultana, C. M.; Prather, K. A.

2016-12-01

The ability to distinguish types of particles present within a cloud is important for determining accurate inputs to climate models. The chemical composition of particles within cloud liquid droplets and ice crystals can have a significant impact on the timing, location, and amount of precipitation that falls. Precipitation efficiency is increased by the presence of ice crystals in clouds, and both mineral dust and biological aerosols have been shown to be effective ice nucleating particles (INPs) in the atmosphere. A current challenge in aerosol science is distinguishing mineral dust and biological material in the analysis of real-time, ambient, single-particle mass spectral data. Single-particle mass spectrometers are capable of measuring the size-resolved chemical composition of individual atmospheric particles. However, there is no consistent analytical method for distinguishing dust and biological aerosols. Sampling and characterization of control samples (i.e. of known identity) of mineral dust and bacteria were performed by the Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) as part of the Fifth Ice Nucleation (FIN01) Workshop at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) facility in Karlsruhe, Germany. Using data collected by the ATOFMS of control samples, a new metric has been developed to classify single particles as dust or biological independent of spectral cluster analysis. This method, involving the use of a ratio of mass spectral peak areas for organic nitrogen and silicates, is easily reproducible and does not rely on extensive knowledge of particle chemistry or the ionization characteristics of mass spectrometers. This represents a step toward rapidly distinguishing particle types responsible for ice nucleation activity during real-time sampling in clouds. The ability to distinguish types of particles present within a cloud is important for determining accurate inputs to climate models. The chemical composition of particles

Wavelength dependence of dust aerosol single scattering albedo as observed by the Compact Reconnaissance Imaging Spectrometer

NASA Astrophysics Data System (ADS)

Wolff, M. J.; Smith, M. D.; Clancy, R. T.; Arvidson, R.; Kahre, M.; Seelos, F.; Murchie, S.; Savijärvi, H.

2009-06-01

Observations by the Compact Reconnaissance Imaging Spectrometer (CRISM) onboard the Mars Reconnaissance Orbiter (MRO) over the range 440-2920 nm of the very dusty Martian atmosphere of the 2007 planet-encircling dust event are combined with those made by both Mars Exploration Rovers (MERs) to better characterize the single scattering albedo (ω 0) of Martian dust aerosols. Using the diagnostic geometry of the CRISM emission phase function (EPF) sequences and the “ground truth” connection provided at both MER locations allows one to more effectively isolate the single scattering albedo (ω 0). This approach eliminates a significant portion of the type of uncertainty involved in many of the earlier radiative transfer analyses. Furthermore, the use of a “first principles” or microphysical representation of the aerosol scattering properties offers a direct path to produce a set of complex refractive indices (m = n + ik) that are consistent with the retrieved ω 0 values. We consider a family of effective particle radii: 1.2, 1.4, 1.6, and 1.8 μm. The resulting set of model data comparisons, ω 0, and m are presented along with an assessment of potential sources of error and uncertainty. We discuss our results within the context of previous work, including the apparent dichotomy of the literature values: “dark” (solar band ω 0 = 0.89-0.90) and “bright” (solar band ω 0 = 0.92-0.94). Previous work suggests that a mean radius of 1.8 μm is representative for the conditions sampled by the CRISM observations. Using the m for this case and a smaller effective particle radius more appropriate for diffuse dust conditions (1.4 μm), we examine EPF-derived optical depths relative to the MER 880 nm optical depths. Finally, we explore the potential impact of the resulting brighter solar band ω 0 of 0.94 to atmospheric temperatures in the planetary boundary layer.

Evaluation of the new capture vapourizer for aerosol mass spectrometers (AMS) through laboratory studies of inorganic species

DOE PAGES

Hu, Weiwei; Campuzano-Jost, Pedro; Day, Douglas A.; ...

2017-08-15

Aerosol mass spectrometers (AMSs) and Aerosol Chemical Speciation Monitors (ACSMs) commercialized by Aerodyne are widely used to measure the non-refractory species in submicron particles. With the standard vapourizer (SV) that is installed in all commercial instruments to date, the quantification of ambient aerosol mass concentration requires the use of the collection efficiency (CE) to correct for the loss of particles due to bounce. A new capture vapourizer (CV) has been designed to reduce the need for a bounce-related CE correction. Two high-resolution AMS instruments, one with a SV and one with a CV, were operated side by side in themore » laboratory. Four standard species, NH 4NO 3, NaNO 3, (NH 4) 2SO 4 and NH 4Cl, which typically constitute the majority of the mass of ambient submicron inorganic species, are studied. The effect of vapourizer temperature ( T v ∼ 200–800 °C) on the detected fragments, CE and size distributions are investigated. A T v of 500–550 °C for the CV is recommended. In the CV, CE was identical (around unity) for more volatile species (e.g. NH 4NO 3) and comparable to or higher than the SV for less-volatile species (e.g. (NH 4) 2SO 4), demonstrating an improvement in CE for laboratory inorganic species in the CV. The detected relative intensities of fragments of NO 3 and SO 4 species observed with the CV are different from those observed with the SV, and are consistent with additional thermal decomposition arising from the increased residence time and multiple collisions. Increased residence times with the CV also lead to broader particle size distribution measurements than with the SV. A method for estimating whether pure species will be detected in AMS sizing mode is proposed. Production of CO 2(g) from sampled nitrate on the vapourizer surface, which has been reported for the SV, is negligible for the CV for NH 4NO 3 and comparable to the SV for NaNO 3. . We observe an extremely consistent fragmentation for

Evaluation of the new capture vapourizer for aerosol mass spectrometers (AMS) through laboratory studies of inorganic species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Weiwei; Campuzano-Jost, Pedro; Day, Douglas A.

Aerosol mass spectrometers (AMSs) and Aerosol Chemical Speciation Monitors (ACSMs) commercialized by Aerodyne are widely used to measure the non-refractory species in submicron particles. With the standard vapourizer (SV) that is installed in all commercial instruments to date, the quantification of ambient aerosol mass concentration requires the use of the collection efficiency (CE) to correct for the loss of particles due to bounce. A new capture vapourizer (CV) has been designed to reduce the need for a bounce-related CE correction. Two high-resolution AMS instruments, one with a SV and one with a CV, were operated side by side in themore » laboratory. Four standard species, NH 4NO 3, NaNO 3, (NH 4) 2SO 4 and NH 4Cl, which typically constitute the majority of the mass of ambient submicron inorganic species, are studied. The effect of vapourizer temperature ( T v ∼ 200–800 °C) on the detected fragments, CE and size distributions are investigated. A T v of 500–550 °C for the CV is recommended. In the CV, CE was identical (around unity) for more volatile species (e.g. NH 4NO 3) and comparable to or higher than the SV for less-volatile species (e.g. (NH 4) 2SO 4), demonstrating an improvement in CE for laboratory inorganic species in the CV. The detected relative intensities of fragments of NO 3 and SO 4 species observed with the CV are different from those observed with the SV, and are consistent with additional thermal decomposition arising from the increased residence time and multiple collisions. Increased residence times with the CV also lead to broader particle size distribution measurements than with the SV. A method for estimating whether pure species will be detected in AMS sizing mode is proposed. Production of CO 2(g) from sampled nitrate on the vapourizer surface, which has been reported for the SV, is negligible for the CV for NH 4NO 3 and comparable to the SV for NaNO 3. . We observe an extremely consistent fragmentation for

Secondary Organic Aerosol Formation from Glyoxal: photochemical versus dark uptake and reversible versus irreversible SOA formation

NASA Astrophysics Data System (ADS)

Waxman, E.; Slowik, J. G.; Kampf, C. J.; Timkovsky, J.; Noziere, B.; Praplan, A. P.; Pfaffenberger, L.; Holzinger, R.; Hoffmann, T.; Dommen, J.; Prevot, A. S.; Baltensperger, U.; Volkamer, R.

2011-12-01

Glyoxal forms secondary organic aerosol (SOA) by partitioning to the aerosol aqueous phase according to Henry's law. The subsequent processing by heterogeneous and multiphase reactions shifts the partitioning towards aerosols. Currently it is not well understood whether these reactions result in reversible or irreversible SOA formation, and what parameters influence the rate limiting step of multiphase processing. We conducted a series of simulation chamber experiments at PSI in April and May 2011 to investigate processing under dark conditions, UV and/or visible light irradiated conditions, and in the presence and absence of OH radicals. Experiments used ammonium sulfate or ammonium sulfate/fulvic acid mixtures as seed aerosols, and were conducted between 50% and 85% relative humidity at approximately constant RH over the course of any given experiment. Glyoxal was produced photochemically from acetylene, using HONO photolysis as the OH radical source. Gas-phase glyoxal was measured by the CU LED-Cavity Enhanced-DOAS. The Thermal-Desorption Proton-Transfer-Reaction Mass Spectrometer (TD-PTR-MS) and Ion Chromatography Mass Spectrometer (IC-MS) monitored both gas and aerosol-phase organic reaction products. Particle composition was monitored by High-Resolution Time-of-Flight Aerosol Mass Spectrometry (HR-ToF-AMS), and HPLC-ESI MS/MS and LC-MS analysis of filter samples.

Secondary Organic Aerosol Formation from Glyoxal: photochemical versus dark uptake and reversible versus irreversible SOA formation

NASA Astrophysics Data System (ADS)

Waxman, E.; Slowik, J.; Kampf, C.; Timkovsky, J.; Noziere, B.; Praplan, A.; Pffafenberger, L.; Holzinger, R.; Hoffmann, T.; Dommen, J.; Prevot, A.; Baltensperger, U.; Volkamer, R.

2012-04-01

Glyoxal forms secondary organic aerosol (SOA) by partitioning to the aerosol aqueous phase according to Henry's law. The subsequent processing by heterogeneous and multiphase reactions shifts the partitioning towards aerosols. Currently it is not well understood whether these reactions result in reversible or irreversible SOA formation, and what parameters influence the rate limiting step of multiphase processing. We conducted a series of simulation chamber experiments at PSI in April and May 2011 to investigate processing under dark conditions, UV and/or visible light irradiated conditions, and in the presence and absence of OH radicals. Experiments used ammonium sulfate or ammonium sulfate/fulvic acid mixtures as seed aerosols, and were conducted between 50% and 85% relative humidity at approximately constant RH over the course of any given experiment. Glyoxal was produced photochemically from acetylene, using HONO photolysis as the OH radical source. Gas-phase glyoxal was measured by the CU LED-Cavity Enhanced-DOAS. The Thermal-Desorption Proton-Transfer-Reaction Mass Spectrometer (TD-PTR-MS) and Ion Chromatography Mass Spectrometer (IC-MS) monitored both gas and aerosol-phase organic reaction products. Particle composition was monitored by High-Resolution Time-of-Flight Aerosol Mass Spectrometry (HR-ToF-AMS), and HPLC-ESI MS/MS and LC-MS analysis of filter samples.

Micrometeorological flux measurements of aerosol and gases above Beijing

NASA Astrophysics Data System (ADS)

Nemitz, Eiko; Langford, Ben; Mullinger, Neil; Cowan, Nicholas; Coyle, Mhairi; Acton, William Joe; Lee, James; Fu, Pingqing

2017-04-01

Air pollution is estimated to cause 1.6 million premature deaths in China every year and in the winter 2016/17 Beijing had to issue health alerts and put in place ad hoc limitations on industrial and vehicular activity. Much of this pollution is attributed to emissions from industrial processes and in particular coal combustion. By contrast, the diffuse pollutant sources within the city are less well understood. This includes, e.g., emissions from the Beijing traffic fleet, the sewage system, food preparation, solid fuel combustion in the streets and small industrial processes. Within the framework of a major UK-Chinese collaboration to study air pollution and its impact on human health in Beijing, we therefore measured fluxes of a large range of pollutants from a height of 102 m on the 325 m meteorological tower at the Institute of Atmospheric Physics. Several instruments were mounted at 102 m: fluxes of CO2 and H2O were measured with an infrared gas analyser (LiCOR 7500) and fluxes of ozone with a combination of a relative fast-response ozone analyser (ROFI) and a 2B absolute O3 instrument. Total particle number fluxes were measured with a condensation particle counter (TSI CPC 3785), and size-segregated fluxes over the size range 0.06 to 20 μm with a combination of an optical Ultrafine High Sensitivity Aerosol Spectrometer (UHSAS) and an Aerodynamic Particle Sizer Spectrometer (TSI APS3321). Ammonia (NH3) fluxes were measured for the first time above the urban environment using an Aerodyne compact quantum cascade laser (QCL). In addition, composition resolved aerosol fluxes were measured with an Aerodyne Aerosol Mass Spectrometer (HR-ToF-AMS), operated in a measurement container at the bottom of the tower, which subsampled from a 120 m long copper tube (15 mm OD). The analysis so far suggests that, due to often low wind speeds, fluxes were at times de-coupled from the surface. Fluxes normalised by CO2, a tracer for the amount of fossil fuel consumed, should be

Light absorption by secondary organic aerosol from α-pinene: Effects of oxidants, seed aerosol acidity, and relative humidity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Chen; Gyawali, Madhu; Zaveri, Rahul A.

2013-10-25

It is well known that light absorption from dust and black carbon aerosols has a warming effect on climate while light scattering from sulfate, nitrate, and sea salt aerosols has a cooling effect. However, there are large uncertainties associated with light absorption and scattering by different types of organic aerosols, especially in the near-UV and UV spectral regions. In this paper, we present the results from a systematic laboratory study focused on measuring light absorption by secondary organic aerosols (SOAs) generated from dark α-pinene + O 3 and α-pinene + NO x + O 3 systems in the presence ofmore » neutral and acidic sulfate seed aerosols. Light absorption was monitored using photoacoustic spectrometers at four different wavelengths: 355, 405, 532, and 870 nm. Significant light absorption at 355 and 405 nm was observed for the SOA formed from α-pinene + O 3 + NO 3 system only in the presence of highly acidic sulfate seed aerosols under dry conditions. In contrast, no absorption was observed when the relative humidity was elevated to greater than 27% or in the presence of neutral sulfate seed aerosols. Organic nitrates in the SOA formed in the presence of neutral sulfate seed aerosols were found to be nonabsorbing, while the light-absorbing compounds are speculated to be aldol condensation oligomers with nitroxy organosulfate groups that are formed in highly acidic sulfate aerosols. Finally and overall, these results suggest that dark α-pinene + O 3 and α-pinene + NO x + O 3 systems do not form light-absorbing SOA under typical atmospheric conditions.« less

The Influence of Chemical Composition and Relative Humidity on the Optical Properties of Aerosols During the Southern Oxidant and Aerosol Study (SOAS)

NASA Astrophysics Data System (ADS)

Attwood, A. R.; Washenfelder, R. A.; Brock, C. A.; Brown, S. S.; Hu, W.; Campuzano Jost, P.; Day, D. A.; Palm, B. B.; Simoes de Sa, S.; Jimenez, J. L.

2013-12-01

Atmospheric particles are produced from a wide variety of both anthropogenic and natural sources and play an important role in the Earth's radiative budget by direct scattering and absorption of radiation. To address this impact, in situ measurements of aerosol optical, chemical and hygroscopic properties were performed during the Southern Oxidant and Aerosol Study (SOAS), which took place in the summer of 2013. Ground based measurements of sub-micron aerosol in the southeastern United States were made to investigate the influence of chemical composition and hygroscopicity on aerosol optical properties. We report the wavelength dependence of aerosol extinction cross sections measured with a novel broadband cavity enhanced spectrometer covering a wavelength range of 360-420 nm using two light emitting diodes (LED) and a separate cavity ring down (CRDS) channel. The sensitivity of the relative humidity dependence of extinction based on the type of aerosol present is examined and we show that the optical properties and hygroscopicity of aerosols are greatly influenced by the fraction of sulfate and organics within the particles. Additional data analysis from the SOAS campaign will be presented. The results, thus far, illustrate that the variability in aerosol chemical composition can impact visibility and climate forcing in this region.

Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) Field Campaign Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fast, J. D.; Berg, L. K.; Burleyson, C.

average and soil moisture was low during the late summer IOP. These factors likely influence the occurrence and lifecycle of shallow clouds. Most of the instrumentation was deployed on the ARM Aerial Facility (AAF) Gulfstream 1 (G-1) aircraft, including those that measure atmospheric turbulence, cloud water content and drop size distributions, aerosol precursor gases, aerosol chemical composition and size distributions, and cloud condensation nuclei (CCN) concentrations. The specific instrumentation is listed in Table 1. The team of scientists participating in the G-1 flights were from Pacific Northwest National Laboratory (PNNL), Brookhaven National Laboratory (BNL), and the University of Washington. Routine ARM aerosol measurements made at the surface were supplemented with aerosol microphysical properties measurements, with support from the DOE Environmental Molecular Sciences Laboratory (EMSL) User Facility and the Atmospheric System Radiation (ASR) program. This included deploying a scanning mobility particle sizer (SMPS) to measure aerosol size distribution, a proton transfer reaction-mass spectrometer (PTR-MS) to measure volatile organic compounds, an aerosol mass spectrometer (AMS) to measure bulk aerosol composition, and the single-particle laser ablation time-of-flight mass spectrometer (SPLAT II) to measure single-particle aerosol composition at the SGP site Guest Instrumentation Facility. In this way, characterization of aerosol properties at the surface and on the G-1 were consistent. In addition, the HI-SCALE: Nanoparticle Composition and Precursors add-on campaign was conducted during the second IOP in which several state-of-the-science chemical ionization mass spectrometers were deployed to measure nanoparticle composition and precursors. Scientists participating in the surface measurements were from PNNL, BNL, University California–Irvine, Augsberg College, Colorado University, Aerodyne Inc., and Aerosol Dynamics Inc.« less

Measurements of aerosol chemical composition in boreal forest summer conditions

NASA Astrophysics Data System (ADS)

ńijälä, M.; Junninen, H.; Ehn, M.; Petäjä, T.; Vogel, A.; Hoffmann, T.; Corrigan, A.; Russell, L.; Makkonen, U.; Virkkula, A.; Mäntykenttä, J.; Kulmala, M.; Worsnop, D.

2012-04-01

Boreal forests are an important biome, covering vast areas of the northern hemisphere and affecting the global climate change via various feedbacks [1]. Despite having relatively few anthropogenic primary aerosol sources, they always contain a non-negligible aerosol population [2]. This study describes aerosol chemical composition measurements using Aerodyne Aerosol Mass Spectrometer (C-ToF AMS, [3]), carried out at a boreal forest area in Hyytiälä, Southern Finland. The site, Helsinki University SMEAR II measurement station [4], is situated at a homogeneous Scots pine (Pinus sylvestris) forest stand. In addition to the station's permanent aerosol, gas phase and meteorological instruments, during the HUMPPA (Hyytiälä United Measurements of Photochemistry and Particles in Air) campaign in July 2010, a very comprehensive set of atmospheric chemistry measurement instrumentation was provided by the Max Planck Institute for chemistry, Johannes Gutenberg-University, University of California and the Finnish Meteorological institute. In this study aerosol chemical composition measurements from the campaign are presented. The dominant aerosol chemical species during the campaign were the organics, although periods with elevated amounts of particulate sulfates were also seen. The overall AMS measured particle mass concentrations varied from near zero to 27 μg/m observed during a forest fire smoke episode. The AMS measured aerosol mass loadings were found to agree well with DMPS derived mass concentrations (r2=0.998). The AMS data was also compared with three other aerosol instruments. The Marga instrument [5] was used to provide a quantitative semi-online measurement of inorganic chemical compounds in particle phase. Fourier Transform Infrared Spectroscopy (FTIR) analysis was performed on daily filter samples, enabling the identification and quantification of organic aerosol subspecies. Finally an Atmospheric Pressure Chemical Ionization Ion Trap Mass Spectrometer (APCI

Does the Madden-Julian Oscillation influence aerosol variability?

NASA Astrophysics Data System (ADS)

Tian, Baijun; Waliser, Duane E.; Kahn, Ralph A.; Li, Qinbin; Yung, Yuk L.; Tyranowski, Tomasz; Geogdzhayev, Igor V.; Mishchenko, Michael I.; Torres, Omar; Smirnov, Alexander

2008-06-01

We investigate the modulation of aerosols by the Madden-Julian Oscillation (MJO) using multiple, global satellite aerosol products: aerosol index (AI) from the Total Ozone Mapping Spectrometer (TOMS) on Nimbus-7, and aerosol optical thickness (AOT) from the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua and the Advanced Very High Resolution Radiometer (AVHRR) on NOAA satellites. A composite MJO analysis indicates that large variations in the TOMS AI and MODIS/AVHRR AOT are found over the equatorial Indian and western Pacific Oceans where MJO convection is active, as well as the tropical Africa and Atlantic Ocean where MJO convection is weak but the background aerosol level is high. A strong inverse linear relationship between the TOMS AI and rainfall anomalies, but a weaker, less coherent positive correlation between the MODIS/AVHRR AOT and rainfall anomalies, were found. The MODIS/AVHRR pattern is consistent with ground-based Aerosol Robotic Network data. These results indicate that the MJO and its associated cloudiness, rainfall, and circulation variability systematically influence the variability in remote sensing aerosol retrieval results. Several physical and retrieval algorithmic factors that may contribute to the observed aerosol-rainfall relationships are discussed. Preliminary analysis indicates that cloud contamination in the aerosol retrievals is likely to be a major contributor to the observed relationships, although we cannot exclude possible contributions from other physical mechanisms. Future research is needed to fully understand these complex aerosol-rainfall relationships.

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing.

PubMed

Swarts, Daan C; Jinek, Martin

2018-05-22

Cas9 and Cas12a are multidomain CRISPR-associated nucleases that can be programmed with a guide RNA to bind and cleave complementary DNA targets. The guide RNA sequence can be varied, making these effector enzymes versatile tools for genome editing and gene regulation applications. While Cas9 is currently the best-characterized and most widely used nuclease for such purposes, Cas12a (previously named Cpf1) has recently emerged as an alternative for Cas9. Cas9 and Cas12a have distinct evolutionary origins and exhibit different structural architectures, resulting in distinct molecular mechanisms. Here we compare the structural and mechanistic features that distinguish Cas9 and Cas12a, and describe how these features modulate their activity. We discuss implications for genome editing, and how they may influence the choice of Cas9 or Cas12a for specific applications. Finally, we review recent studies in which Cas12a has been utilized as a genome editing tool. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes. © 2018 Wiley Periodicals, Inc.

[Clustered regularly interspaced short palindromic repeat associated protein genes cas1 and cas2 in Shigella].

PubMed

Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao; Xi, Yuanlin

2014-05-01

To detect the distribution of clustered regularly interspaced short palindromic repeat (CRISPR) associated protein genes cas1 and cas2 in Shigella and to understand the characteristics of CRISPR with relationship between CRISPR and related characteristics on drug resistance. CRISPR associated protein genes cas1 and cas2 in Shigella were detected by PCR, with its products sequenced and compared. The CRISPR-associated protein genes cas1 and cas2 were found in all the 196 Shigella isolates which were isolated at different times and locations in China. Consistencies showed through related sequencing appeared as follows: cas2, cas1 (a) and cas1 (b) were 96.44%, 97.61% and 96.97%, respectively. There were two mutations including 3177129 site(C→G)and 3177126 site (G→C) of cas1 (b) gene in 2003135 strain which were not found in the corresponding sites of Z23 and 2008113. showed that in terms of both susceptibility and antibiotic-resistance, strain 2003135 was stronger than Z23 and 2008113. CRISPR system widely existed in Shigella, with the level of drug resistance in cas1 (b) gene mutant strains higher than in wild strains. Cas1 (b) gene mutation might be one of the reasons causing the different levels of resistance.

The Backscatter Cloud Probe - a compact low-profile autonomous optical spectrometer

NASA Astrophysics Data System (ADS)

Beswick, K.; Baumgardner, D.; Gallagher, M.; Newton, R.

2013-08-01

A compact (500 cm3), lightweight (500 g), near-field, single particle backscattering optical spectrometer is described that mounts flush with the skin of an aircraft and measures the concentration and optical equivalent diameter of particles from 5 to 75 μm. The Backscatter Cloud Probe (BCP) was designed as a real-time qualitative cloud detector primarily for data quality control of trace gas instruments developed for the climate monitoring instrument packages that are being installed on commercial passenger aircraft as part of the European Union In-Service Aircraft for a Global Observing System (IAGOS) program (http://www.iagos.org/). Subsequent evaluations of the BCP measurements on a number of research aircraft, however, have revealed it capable of delivering quantitative particle data products including size distributions, liquid water content and other information on cloud properties. We demonstrate the instrument's capability for delivering useful long-term climatological information, across a wide range of environmental conditions. The BCP has been evaluated by comparing its measurements with those from other cloud particle spectrometers on research aircraft and several BCPs are currently flying on commercial A340/A330 Airbus passenger airliners. The design and calibration of the BCP is described in this presentation, along with an evaluation of measurements made on the research and commercial aircraft. Comparisons of the BCP with two other cloud spectrometers, the Cloud Droplet Probe (CDP) and the Cloud and Aerosol Spectrometer (CAS), show that the BCP size distributions agree well with those from the other two, given the intrinsic limitations and uncertainties related to the three instruments. Preliminary results from more than 7000 h of airborne measurements by the BCP on two Airbus A-340s operating on routine global traffic routes (one Lufthansa, the other China Airlines) show that more than 340 h of

LC-MS-MS-TOF analysis of oxygenated organic compounds in ambient aerosol

NASA Astrophysics Data System (ADS)

Roempp, A.; Moortgat, G.

2003-04-01

Ambient aerosol samples were taken at different sites across Europe. The fine mode aerosol was collected on quartz filters at flow rates of 160 L/min and 500 L/min. These samples were analyzed for organic acids (C>4) by an HPLC system coupled to a hybrid mass spectrometer. The mass spectrometer consists of a quadrupole mass analyzer, a quadrupole collision cell and a time-of-flight mass analyzer (TOF). Analytes were identified by standards when available or MS-MS experiments and exact mass measurements utilizing the high mass resolution of the TOF instrument. Monoterpenes (alpha-pinene, beta-pinene, sabinene, limonene, 3-carene) were ozonolyzed in the laboratory and compared with field samples. Besides the commonly measured organic acids (pinic, pinonic and norpinic acid) sabinic, caric and caronic acid were identified for the first time in ambient aerosol. In addition, nearly all samples showed significant concentrations of newly identified keto dicarboxylic acids (C9 - C12). Laboratory experiments were used to investigate the formation mechanisms of these compounds. By comparing laboratory measurements of wood combustion and field samples from the Eastern Mediterranean region, nitrocatechol was identified as a possible tracer for biomass burning. The data obtained is used to determine the role of biogenic sources in secondary organic aerosol formation.

LASER DESORPTION IONIZATION OF ULTRAFINE AEROSOL PARTICLES. (R823980)

EPA Science Inventory

On-line analysis of ultrafine aerosol particle in the 12 to 150 nm size range is performed by
laser desorption/ionization. Particles are size selected with a differential mobility analyzer and then
sent into a linear time-of-flight mass spectrometer where they are ablated w...

Investigating the Chemical Pathways to PAH- and PANH-Based Aerosols in Titan's Atmospheric chemistry

NASA Technical Reports Server (NTRS)

Sciamma-O'Brien, Ella Marion; Contreras, Cesar; Ricketts, Claire Louise; Salama, Farid

2011-01-01

A complex organic chemistry between Titan's two main constituents, N2 and CH4, leads to the production of more complex molecules and subsequently to solid organic aerosols. These aerosols are at the origin of the haze layers giving Titan its characteristic orange color. In situ measurements by the Ion Neutral Mass Spectrometer (INMS) and Cassini Plasma Spectrometer (CAPS) instruments onboard Cassini have revealed the presence of large amounts of neutral, positively and negatively charged heavy molecules in the ionosphere of Titan. In particular, benzene (C6H6) and toluene (C6H5CH3), which are critical precursors of polycyclic aromatic hydrocarbon (PAH) compounds, have been detected, suggesting that PAHs might play a role in the production of Titan s aerosols. Moreover, results from numerical models as well as laboratory simulations of Titan s atmospheric chemistry are also suggesting chemical pathways that link the simple precursor molecules resulting from the first steps of the N2-CH4 chemistry (C2H2, C2H4, HCN ...) to benzene, and to PAHs and nitrogen-containing PAHs (or PANHs) as precursors to the production of solid aerosols.

Single particle characterization using a light scattering module coupled to a time-of-flight aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Cross, E. S.; Onasch, T. B.; Canagaratna, M.; Jayne, J. T.; Kimmel, J.; Yu, X.-Y.; Alexander, M. L.; Worsnop, D. R.; Davidovits, P.

2008-12-01

We present the first single particle results obtained using an Aerodyne time-of-flight aerosol mass spectrometer coupled with a light scattering module (LS-ToF-AMS). The instrument was deployed at the T1 ground site approximately 40 km northeast of the Mexico City Metropolitan Area (MCMA) as part of the MILAGRO field study in March of 2006. The instrument was operated as a standard AMS from 12-30 March, acquiring average chemical composition and size distributions for the ambient aerosol, and in single particle mode from 27-30 March. Over a 75-h sampling period, 12 853 single particle mass spectra were optically triggered, saved, and analyzed. The correlated optical and chemical detection allowed detailed examination of single particle collection and quantification within the LS-ToF-AMS. The single particle data enabled the mixing states of the ambient aerosol to be characterized within the context of the size-resolved ensemble chemical information. The particulate mixing states were examined as a function of sampling time and most of the particles were found to be internal mixtures containing many of the organic and inorganic species identified in the ensemble analysis. The single particle mass spectra were deconvolved, using techniques developed for ensemble AMS data analysis, into HOA, OOA, NH4NO3, (NH4)2SO4, and NH4Cl fractions. Average single particle mass and chemistry measurements are shown to be in agreement with ensemble MS and PTOF measurements. While a significant fraction of ambient particles were internal mixtures of varying degrees, single particle measurements of chemical composition allowed the identification of time periods during which the ambient ensemble was externally mixed. In some cases the chemical composition of the particles suggested a likely source. Throughout the full sampling period, the ambient ensemble was an external mixture of combustion-generated HOA particles from local sources (e.g. traffic), with number concentrations peaking

Determination of mixing state and sources of wintertime organic aerosol in Paris using single particle mass spectrometry

NASA Astrophysics Data System (ADS)

Healy, R. M.; Sciare, J.; Poulain, L.; Wiedensohler, A.; Jeong, C.; McGuire, M.; Evans, G. J.; McGillicuddy, E.; O'Connor, I. P.; Sodeau, J. R.; Wenger, J.

2012-12-01

The size-resolved chemical composition of single particles at an urban background site in Paris, France, was determined using an Aerosol Time-Of-Flight Mass Spectrometer (ATOFMS) as part of the MEGAPOLI winter campaign in January/February 2010. A variety of mixing states were identified for organic aerosol by mass spectral clustering and apportioned to both fossil fuel and biomass burning sources. The ATOFMS data were scaled in order to produce mass concentration estimates for each organic aerosol particle type identified. Potassium-containing organic aerosol internally mixed with nitrate, associated with local wood burning, was observed to dominate during periods characterised by marine air masses. Sulfate-rich potassium-containing organic aerosol, associated with transboundary transport of biomass burning emissions, dominated during periods influenced by continental air masses. The scaled total mass concentration for potassium-containing particles was well correlated (R2 = 0.79) with concurrent measurements of potassium mass concentration measured with a Particle-Into-Liquid-Sampler (PILS). Another organic particle type, also containing potassium but rich in trimethylamine and sulfate, was detected exclusively during continental air mass events. These particles are postulated to have accumulated gas phase trimethylamine through heterogeneous reaction before arriving at the sampling site. Potential source regions for transboundary organic aerosols have been investigated using the potential source contribution function (PSCF). Comparison with aerosol mass spectrometer (AMS) measurements will also be discussed.

Laboratory Studies of Temperature and Relative Humidity Dependence of Aerosol Nucleation during the TANGENT 2017 IOP Study

NASA Astrophysics Data System (ADS)

Ouyang, Q.; Tiszenkel, L.; Stangl, C. M.; Krasnomowitz, J.; Johnston, M. V.; Lee, S.

2017-12-01

In this poster, we will present recent measurements of temperature and relative humidity dependence of aerosol nucleation of sulfuric acid under the conditions representative of the ground level to the free troposphere. Aerosol nucleation is critically dependent on temperature, but the current global aerosol models use nucleation algorithms that are independent of temperature and relative humidity due to the lack of experimental data. Thus, these models fail to simulate nucleation in a wide range of altitude and latitude conditions. We are currently conducting the Tandem Aerosol Nucleation and Growth Environment Tube (TANGENT) the intense observation period (IOP) experiments to investigate the aerosol nucleation and growth properties independently, during nucleation and growth. Nucleation takes place from sulfuric acid, water and some base compounds in a fast flow nucleation tube (FT-1). Nucleation precursors are detected with two chemical ionization mass spectrometers (CIMS) and newly nucleated particles are measured with a particle size magnifier (PSM) and a scanning mobility particle sizers (SMPS). Then these particles grow further in the second flow tube (FT-2) in the presence of oxidants of biogenic organic compounds. Chemical compositions of grown particles are further analyzed with a nano-aerosol mass spectrometer (NAMS). Our experimental results will provide a robust algorithm for aerosol nucleation and growth rates as a function of temperature and relative humidity.

Application of FIGAERO (Filter Inlet for Gases and AEROsol) coupled to a high resolution time of flight chemical ionization mass spectrometer to field and chamber organic aerosol: Implications for carboxylic acid formation and gas-particle partitioning from monoterpene oxidation

NASA Astrophysics Data System (ADS)

Lopez-Hilfiker, F.; Mohr, C.; Ehn, M.; Rubach, F.; Mentel, T. F.; Kleist, E.; Wildt, J.; Thornton, J. A.

2013-12-01

We present measurements of a large suite of gas and particle phase carboxylic acid containing compounds made with a Filter Inlet for Gas and AEROsol (FIGAERO) coupled to a high resolution time of flight chemical ionization mass spectrometer (HR-ToF-CIMS) developed at the University of Washington. A prototype operated with acetate negative ion proton transfer chemistry was deployed on the Julich Plant Atmosphere Chamber to study a-pinene oxidation, and a modified version was deployed at the SMEAR II forest station in Hyytiälä, Finland and SOAS, in Brent Alabama. We focus here on results from JPAC and Hyytiälä, where we utilized the same ionization method most selective towards carboxylic acids. In all locations, 100's of organic acid compounds were observed in the gas and particles and many of the same composition acids detected in the gas-phase were detected in the particles upon temperature programmed thermal desorption. Particulate organics detected by FIGAERO are highly correlated with organic aerosol mass measured by an AMS, providing additional volatility and molecular level information about collected aerosol. The fraction of a given compound measured in the particle phase follows expected trends with elemental composition, but many compounds would not be well described by an absorptive partitioning model assuming unity activity coefficients. Moreover the detailed structure in the thermal desorption signals reveals a contribution from thermal decomposition of large molecular weight organics and or oligomers with implications for partitioning measurements and model validation

El Chichon and 'mystery cloud' aerosols between 30 and 55 km Global observations from the SME visible spectrometer

NASA Astrophysics Data System (ADS)

Clancy, R. T.

1986-09-01

Visible limb radiances measured by the Solar Mesosphere Explorer (SME) are used to obtain volume scattering ratios for aerosol loading in the 30-55 km altitude range of the stratosphere. Global maps of these ratios are presented for the period January 1982 to August 1984. Significant aerosol scattering from the 'mystery cloud' and El Chichon aerosol layers are found above 30 km. A timescale of approximately 2 months between the appearance of the aerosol at 30.5 km and at 37.5 km is consistent with vertical transport of aerosol or vapor by eddy diffusion above 30 km. An anticorrelation exists between aerosol scattering and stratospheric temperatures. Periods of lower stratospheric temperatures may account for the formation of aerosol between 40 and 55 km altitude.

El Chichon and 'mystery cloud' aerosols between 30 and 55 km Global observations from the SME visible spectrometer

NASA Technical Reports Server (NTRS)

Clancy, R. T.

1986-01-01

Visible limb radiances measured by the Solar Mesosphere Explorer (SME) are used to obtain volume scattering ratios for aerosol loading in the 30-55 km altitude range of the stratosphere. Global maps of these ratios are presented for the period January 1982 to August 1984. Significant aerosol scattering from the 'mystery cloud' and El Chichon aerosol layers are found above 30 km. A timescale of approximately 2 months between the appearance of the aerosol at 30.5 km and at 37.5 km is consistent with vertical transport of aerosol or vapor by eddy diffusion above 30 km. An anticorrelation exists between aerosol scattering and stratospheric temperatures. Periods of lower stratospheric temperatures may account for the formation of aerosol between 40 and 55 km altitude.

MAESTRO Measurements of Atmospheric Aerosol

NASA Astrophysics Data System (ADS)

McElroy, Tom; Drummond, James; Zou, Jason

2014-05-01

MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) is now in its 11th year on orbit as part of the Atmospheric Chemistry Experiment on the Canadian Space Agency's SCISAT satellite. MAESTRO data analysis has been dogged by a deficiency in accurate timing between the measurements made by the partner instrument, the ACE-FTS (Atmospheric Chemistry Experiment, Fourier Transform Spectrometer), that provides the atmospheric pressure-temperature profile and observation tangent altitudes used in the MAESTRO data analysis. Attempts have been made to use apparent air column density and oxygen A-band absorption as a mechanism to line up the tangent heights, but to no avail. A new product is now being produced, based on matching the modeled ozone slant columns from the ACE-FTS retrievals with the MAESTRO slant column measurements. The approach is very promising and indicates that a valuable product from the MAESTRO wavelength-dependent aerosol extinction likely result. The usefulness of the profile matching technique will be demonstrated and some aerosol absorption profiles will be presented in comparison with measurements made by the ACE Imager aerosol profile results. While the process optimizes the comparison between ACE-FTS ozone profile data and that from MAESTRO, it does not detract from the higher vertical resolution information provided by MAESTRO.

Characterization of fresh and aged organic aerosol emissions from meat charbroiling

NASA Astrophysics Data System (ADS)

Kaltsonoudis, Christos; Kostenidou, Evangelia; Louvaris, Evangelos; Psichoudaki, Magda; Tsiligiannis, Epameinondas; Florou, Kalliopi; Liangou, Aikaterini; Pandis, Spyros N.

2017-06-01

Cooking emissions can be a significant source of fine particulate matter in urban areas. In this study the aerosol- and gas-phase emissions from meat charbroiling were characterized. Greek souvlakia with pork were cooked using a commercial charbroiler and a fraction of the emissions were introduced into a smog chamber where after a characterization phase they were exposed to UV illumination and oxidants. The particulate and gas phases were characterized by a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) and a proton-transfer-reaction mass spectrometer (PTR-MS) correspondingly. More than 99 % of the aerosol emitted was composed of organic compounds, while black carbon (BC) contributed 0.3 % and the inorganic species less than 0.5 % of the total aerosol mass. The initial O : C ratio was approximately 0.09 and increased up to 0.30 after a few hours of chemical aging (exposures of 1010 molecules cm-3 s for OH and 100 ppb h for ozone). The initial and aged AMS spectra differed considerably (θ = 27°). Ambient measurements were also conducted during Fat Thursday in Patras, Greece, when traditionally meat is charbroiled everywhere in the city. Positive matrix factorization (PMF) revealed that cooking organic aerosol (COA) reached up to 85 % of the total OA from 10:00 to 12:00 LST that day. The ambient COA factor in two major Greek cities had a mass spectrum during spring and summer similar to the aged meat charbroiling emissions. In contrast, the ambient COA factor during winter resembled strongly the fresh laboratory meat charbroiling emissions.

Measurements of Organic Composition of Aerosol and Rainwater Samples Using Offline Aerosol Mass Spectrometry

NASA Astrophysics Data System (ADS)

OBrien, R. E.; Ridley, K. J.; Canagaratna, M. R.; Croteau, P.; Budisulistiorini, S. H.; Cui, T.; Green, H. S.; Surratt, J. D.; Jayne, J. T.; Kroll, J. H.

2016-12-01

A thorough understanding of the sources, evolution, and budgets of atmospheric organic aerosol requires widespread measurements of the amount and chemical composition of atmospheric organic carbon in the condensed phase (within particles and water droplets). Collecting such datasets requires substantial spatial and temporal (long term) coverage, which can be challenging when relying on online measurements by state-of-the-art research-grade instrumentation (such as those used in atmospheric chemistry field studies). Instead, samples are routinely collected using relatively low-cost techniques, such as aerosol filters, for offline analysis of their chemical composition. However, measurements made by online and offline instruments can be fundamentally different, leading to disparities between data from field studies and those from more routine monitoring. To better connect these two approaches, and take advantage of the benefits of each, we have developed a method to introduce collected samples into online aerosol instruments using nebulization. Because nebulizers typically require tens to hundreds of milliliters of solution, limiting this technique to large samples, we developed a new, ultrasonic micro-nebulizer that requires only small volumes (tens of microliters) of sample for chemical analysis. The nebulized (resuspended) sample is then sent into a high-resolution Aerosol Mass Spectrometer (AMS), a widely-used instrument that provides key information on the chemical composition of aerosol particulate matter (elemental ratios, carbon oxidation state, etc.), measurements that are not typically made for collected atmospheric samples. Here, we compare AMS data collected using standard on-line techniques with our offline analysis, demonstrating the utility of this new technique to aerosol filter samples. We then apply this approach to organic aerosol filter samples collected in remote regions, as well as rainwater samples from across the US. This data provides

Real-Time Detection Method And System For Identifying Individual Aerosol Particles

DOEpatents

Gard, Eric Evan; Fergenson, David Philip

2005-10-25

A method and system of identifying individual aerosol particles in real time. Sample aerosol particles are compared against and identified with substantially matching known particle types by producing positive and negative test spectra of an individual aerosol particle using a bipolar single particle mass spectrometer. Each test spectrum is compared to spectra of the same respective polarity in a database of predetermined positive and negative spectra for known particle types and a set of substantially matching spectra is obtained. Finally the identity of the individual aerosol particle is determined from the set of substantially matching spectra by determining a best matching one of the known particle types having both a substantially matching positive spectrum and a substantially matching negative spectrum associated with the best matching known particle type.

Aerosol chemical composition in cloud events by high resolution time-of-flight aerosol mass spectrometry.

PubMed

Hao, Liqing; Romakkaniemi, Sami; Kortelainen, Aki; Jaatinen, Antti; Portin, Harri; Miettinen, Pasi; Komppula, Mika; Leskinen, Ari; Virtanen, Annele; Smith, James N; Sueper, Donna; Worsnop, Douglas R; Lehtinen, Kari E J; Laaksonen, Ari

2013-03-19

This study presents results of direct observations of aerosol chemical composition in clouds. A high-resolution time-of-flight aerosol mass spectrometer was used to make measurements of cloud interstitial particles (INT) and mixed cloud interstitial and droplet residual particles (TOT). The differences between these two are the cloud droplet residuals (RES). Positive matrix factorization analysis of high-resolution mass spectral data sets and theoretical calculations were performed to yield distributions of chemical composition of the INT and RES particles. We observed that less oxidized hydrocarbon-like organic aerosols (HOA) were mainly distributed into the INT particles, whereas more oxidized low-volatile oxygenated OA (LVOOA) mainly in the RES particles. Nitrates existed as organic nitrate and in chemical form of NH(4)NO(3). Organic nitrates accounted for 45% of total nitrates in the INT particles, in clear contrast to 26% in the RES particles. Meanwhile, sulfates coexist in forms of acidic NH(4)HSO(4) and neutralized (NH(4))(2)SO(4). Acidic sulfate made up 64.8% of total sulfates in the INT particles, much higher than 10.7% in the RES particles. The results indicate a possible joint effect of activation ability of aerosol particles, cloud processing, and particle size effects on cloud formation.

Regional Aerosol Forcing over India: Preliminary Results from the South West Asian Aerosol-Monsoon Interactions (SWAAMI) Aircraft Experiment

NASA Astrophysics Data System (ADS)

Morgan, W.; Brooks, J.; Fox, C.; Haslett, S.; Liu, D.; Kompalli, S. K.; Pathak, H.; Manoj, M. R.; Allan, J. D.; Haywood, J. M.; Highwood, E.; Langridge, J.; Nanjundaiah, R. S.; Krishnamoorthy, K.; Babu, S. S.; Satheesh, S. K.; Turner, A. G.; Coe, H.

2016-12-01

Aerosol particles from multiple sources across the Indian subcontinent build up to form a dense and extensive haze across the region in advance of the monsoon. These aerosols are thought to perturb the regional radiative balance and hydrological cycle, which may have a significant impact on the monsoon circulation, as well as influencing the associated cloud and rainfall of the system. However the nature and magnitude of such impacts are poorly understood or constrained. Major uncertainties relevant to the regional aerosol burden include its vertical distribution, the relative contribution of different pollution sources and natural emissions and the role of absorbing aerosol species (black carbon and mineral dust). The South West Asian Aerosol-Monsoon Interactions (SWAAMI) project sought to address these major uncertainties by conducting an airborne experiment during June/July 2016 on-board the UK Facility for Airborne Atmospheric Measurement (FAAM) BAe-146 research aircraft. Based out of Lucknow in the), The aircraft conducted multiple flights from Lucknow in the heart of the Indo-Gangetic Plain (IGP) in advance of the monsoon and during the onset phase. The spatial and vertical distribution of aerosol was evaluated across northern India, encompassing drier desert-like regions to the west, heavily populated urban and industrial centres over the IGP and air masses in outflow regions to the south-east towards the Bay of Bengal. Principal measurements included aerosol chemical composition using an Aerodyne Aerosol Mass Spectrometer and a DMT Single Particle Soot Photometer, alongside a Leosphere backscatter LIDAR. Sulphate was a major contributor to the aerosol burden across India, while the organic aerosol was elevated and more dominant over the most polluted regions of the IGP. Substantial aerosol concentrations were frequently observed up to altitudes of approximately 6km, with notable changes in aerosol chemical and physical properties when comparing different

Spectral signatures of polar stratospheric clouds and sulfate aerosol

NASA Technical Reports Server (NTRS)

Massie, S. T.; Bailey, P. L.; Gille, J. C.; Lee, E. C.; Mergenthaler, J. L.; Roche, A. E.; Kumer, J. B.; Fishbein, E. F.; Waters, J. W.; Lahoz, W. A.

1994-01-01

Multiwavelength observations of Antarctic and midlatitude aerosol by the Cryogenic Limb Array Etalon Spectrometer (CLAES) experiment on the Upper Atmosphere Research Satellite (UARS) are used to demonstrate a technique that identifies the location of polar stratospheric clouds. The technique discussed uses the normalized area of the triangle formed by the aerosol extinctions at 925, 1257, and 1605/cm (10.8, 8.0, and 6.2 micrometers) to derive a spectral aerosol measure M of the aerosol spectrum. Mie calculations for spherical particles and T-matrix calculations for spheriodal particles are used to generate theoretical spectral extinction curves for sulfate and polar stratospheric cloud particles. The values of the spectral aerosol measure M for the sulfate and polar stratospheric cloud particles are shown to be different. Aerosol extinction data, corresponding to temperatures between 180 and 220 K at a pressure of 46 hPa (near 21-km altitude) for 18 August 1992, are used to demonstrate the technique. Thermodynamic calculations, based upon frost-point calculations and laboratory phase-equilibrium studies of nitric acid trihydrate, are used to predict the location of nitric acid trihydrate cloud particles.

Aerosols and Clouds: In Cahoots to Change Climate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berg, Larry

Key knowledge gaps persist despite advances in the scientific understanding of how aerosols and clouds evolve and affect climate. The Two-Column Aerosol Project, or TCAP, was designed to provide a detailed set of observations to tackle this area of unknowns. Led by PNNL atmospheric scientist Larry Berg, ARM's Climate Research Facility was deployed in Cape Cod, Massachusetts for the 12-month duration of TCAP, which came to a close in June 2013. "We are developing new tools to look at particle chemistry, like our mass spectrometer used in TCAP that can tell us the individual chemical composition of an aerosol," saidmore » Berg. "Then, we'll run our models and compare it with the data that we have to make sure we're getting correct answers and make sure our climate models are reflecting the best information."« less

Aerosols and Clouds: In Cahoots to Change Climate

ScienceCinema

Berg, Larry

2018-01-16

Key knowledge gaps persist despite advances in the scientific understanding of how aerosols and clouds evolve and affect climate. The Two-Column Aerosol Project, or TCAP, was designed to provide a detailed set of observations to tackle this area of unknowns. Led by PNNL atmospheric scientist Larry Berg, ARM's Climate Research Facility was deployed in Cape Cod, Massachusetts for the 12-month duration of TCAP, which came to a close in June 2013. "We are developing new tools to look at particle chemistry, like our mass spectrometer used in TCAP that can tell us the individual chemical composition of an aerosol," said Berg. "Then, we'll run our models and compare it with the data that we have to make sure we're getting correct answers and make sure our climate models are reflecting the best information."

Aerosol and Surface Parameter Retrievals for a Multi-Angle, Multiband Spectrometer

NASA Technical Reports Server (NTRS)

Broderick, Daniel

2012-01-01

This software retrieves the surface and atmosphere parameters of multi-angle, multiband spectra. The synthetic spectra are generated by applying the modified Rahman-Pinty-Verstraete Bidirectional Reflectance Distribution Function (BRDF) model, and a single-scattering dominated atmosphere model to surface reflectance data from Multiangle Imaging SpectroRadiometer (MISR). The aerosol physical model uses a single scattering approximation using Rayleigh scattering molecules, and Henyey-Greenstein aerosols. The surface and atmosphere parameters of the models are retrieved using the Lavenberg-Marquardt algorithm. The software can retrieve the surface and atmosphere parameters with two different scales. The surface parameters are retrieved pixel-by-pixel while the atmosphere parameters are retrieved for a group of pixels where the same atmosphere model parameters are applied. This two-scale approach allows one to select the natural scale of the atmosphere properties relative to surface properties. The software also takes advantage of an intelligent initial condition given by the solution of the neighbor pixels.

Molecular Mechanisms of RNA-Targeting by Cas13-containing Type VI CRISPR-Cas Systems.

PubMed

O'Connell, Mitchell

2018-06-22

Prokaryotic adaptive immune systems use CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) and CRISPR associated (Cas) proteins for RNA-guided cleavage of foreign genetic elements. The focus of this review, Type VI CRISPR-Cas systems, include a single protein known as Cas13 (formerly C2c2), that when assembled with a crRNA forms a crRNA-guided RNA-targeting effector complex. Type VI CRISPR-Cas systems can be divided into four subtypes (A-D) based on Cas13 phylogeny. All Cas13 proteins studied to date possess two enzymatically distinct ribonuclease activities that are required for optimal interference. One RNase is responsible for pre-crRNA processing to form mature Type VI interference complexes, while the other RNase activity provided by the two HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) domains, is required for degradation of target RNA during viral interference. In this review, I will compare and contrast what is known about the molecular architecture and behavior of Type VI (A-D) CRISPR-Cas13 interference complexes, how this allows them to carry out their RNA-targeting function, how Type VI accessory proteins are able to modulate Cas13 activity, and how together all of these features have led to the rapid development of a range of RNA-targeting applications. Throughout I will also discuss some of the outstanding questions regarding Cas13's molecular behavior, and its role in bacterial adaptive immunity and RNA-targeting applications. Copyright © 2018. Published by Elsevier Ltd.

Vertical Transport of Aerosol Particles across Mountain Topography near the Los Angeles Basin

NASA Astrophysics Data System (ADS)

Murray, J. J.; Schill, S.; Freeman, S.; Bertram, T. H.; Lefer, B. L.

2015-12-01

Transport of aerosol particles is known to affect air quality and is largely dependent on the characteristic topography of the surrounding region. To characterize this transport, aerosol number distributions were collected with an Ultra-High Sensitivity Aerosol Spectrometer (UHSAS, DMT) during the 2015 NASA Student Airborne Research Program (SARP) in and around the Los Angeles Basin in Southern California. Increases in particle number concentration and size were observed over mountainous terrain north of Los Angeles County. Chemical analysis and meteorological lagrangian trajectories suggest orographic lifting processes, known as the "chimney effect". Implications for spatial transport and distribution will be discussed.

Secondary organic aerosol formation from low-NO(x) photooxidation of dodecane: evolution of multigeneration gas-phase chemistry and aerosol composition.

PubMed

Yee, Lindsay D; Craven, Jill S; Loza, Christine L; Schilling, Katherine A; Ng, Nga Lee; Canagaratna, Manjula R; Ziemann, Paul J; Flagan, Richard C; Seinfeld, John H

2012-06-21

The extended photooxidation of and secondary organic aerosol (SOA) formation from dodecane (C(12)H(26)) under low-NO(x) conditions, such that RO(2) + HO(2) chemistry dominates the fate of the peroxy radicals, is studied in the Caltech Environmental Chamber based on simultaneous gas and particle-phase measurements. A mechanism simulation indicates that greater than 67% of the initial carbon ends up as fourth and higher generation products after 10 h of reaction, and simulated trends for seven species are supported by gas-phase measurements. A characteristic set of hydroperoxide gas-phase products are formed under these low-NO(x) conditions. Production of semivolatile hydroperoxide species within three generations of chemistry is consistent with observed initial aerosol growth. Continued gas-phase oxidation of these semivolatile species produces multifunctional low volatility compounds. This study elucidates the complex evolution of the gas-phase photooxidation chemistry and subsequent SOA formation through a novel approach comparing molecular level information from a chemical ionization mass spectrometer (CIMS) and high m/z ion fragments from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). Combination of these techniques reveals that particle-phase chemistry leading to peroxyhemiacetal formation is the likely mechanism by which these species are incorporated in the particle phase. The current findings are relevant toward understanding atmospheric SOA formation and aging from the "unresolved complex mixture," comprising, in part, long-chain alkanes.

Black carbon in aerosol during BIBLE B

NASA Astrophysics Data System (ADS)

Liley, J. Ben; Baumgardner, D.; Kondo, Y.; Kita, K.; Blake, D. R.; Koike, M.; Machida, T.; Takegawa, N.; Kawakami, S.; Shirai, T.; Ogawa, T.

2003-02-01

The Biomass Burning and Lightning Experiment (BIBLE) A and B campaigns over the tropical western Pacific during springtime deployed a Gulfstream-II aircraft with systems to measure ozone and numerous precursor species. Aerosol measuring systems included a MASP optical particle counter, a condensation nucleus (CN) counter, and an absorption spectrometer for black carbon. Aerosol volume was very low in the middle and upper troposphere during both campaigns, and during BIBLE A, there was little aerosol enhancement in the boundary layer away from urban areas. In BIBLE B, there was marked aerosol enhancement in the lowest 3 km of the atmosphere. Mixing ratios of CN in cloud-free conditions in the upper troposphere were in general higher than in the boundary layer, indicating new particle formation from gaseous precursors. High concentrations of black carbon were observed during BIBLE B, with mass loadings up to 40 μg m-3 representing as much as one quarter of total aerosol mass. Strong correlations with hydrocarbon enhancement allow the determination of a black carbon emission ratio for the fires at that time. Expressed as elemental carbon, it is about 0.5% of carbon dioxide and 6% of carbon monoxide emissions from the same fires, comparable to methane production, and greater than that of other hydrocarbons.

Black carbon in aerosol during BIBLE B

NASA Astrophysics Data System (ADS)

Liley, J. Ben; Baumgardner, D.; Kondo, Y.; Kita, K.; Blake, D. R.; Koike, M.; Machida, T.; Takegawa, N.; Kawakami, S.; Shirai, T.; Ogawa, T.

2002-02-01

The Biomass Burning and Lightning Experiment (BIBLE) A and B campaigns over the tropical western Pacific during springtime deployed a Gulfstream-II aircraft with systems to measure ozone and numerous precursor species. Aerosol measuring systems included a MASP optical particle counter, a condensation nucleus (CN) counter, and an absorption spectrometer for black carbon. Aerosol volume was very low in the middle and upper troposphere during both campaigns, and during BIBLE A, there was little aerosol enhancement in the boundary layer away from urban areas. In BIBLE B, there was marked aerosol enhancement in the lowest 3 km of the atmosphere. Mixing ratios of CN in cloud-free conditions in the upper troposphere were in general higher than in the boundary layer, indicating new particle formation from gaseous precursors. High concentrations of black carbon were observed during BIBLE B, with mass loadings up to 40 μg m-3 representing as much as one quarter of total aerosol mass. Strong correlations with hydrocarbon enhancement allow the determination of a black carbon emission ratio for the fires at that time. Expressed as elemental carbon, it is about 0.5% of carbon dioxide and 6% of carbon monoxide emissions from the same fires, comparable to methane production, and greater than that of other hydrocarbons.

Real-time detection method and system for identifying individual aerosol particles

DOEpatents

Gard, Eric E [San Francisco, CA; Coffee, Keith R [Patterson, CA; Frank, Matthias [Oakland, CA; Tobias, Herbert J [Kensington, CA; Fergenson, David P [Alamo, CA; Madden, Norm [Livermore, CA; Riot, Vincent J [Berkeley, CA; Steele, Paul T [Livermore, CA; Woods, Bruce W [Livermore, CA

2007-08-21

An improved method and system of identifying individual aerosol particles in real time. Sample aerosol particles are collimated, tracked, and screened to determine which ones qualify for mass spectrometric analysis based on predetermined qualification or selection criteria. Screening techniques include one or more of determining particle size, shape, symmetry, and fluorescence. Only qualifying particles passing all screening criteria are subject to desorption/ionization and single particle mass spectrometry to produce corresponding test spectra, which is used to determine the identities of each of the qualifying aerosol particles by comparing the test spectra against predetermined spectra for known particle types. In this manner, activation cycling of a particle ablation laser of a single particle mass spectrometer is reduced.

Aircraft measurements of aerosol properties during GoAmazon - G1 and HALO inter-comparison

NASA Astrophysics Data System (ADS)

Mei, F.; Cecchini, M. A.; Wang, J.; Tomlinson, J. M.; Comstock, J. M.; Hubbe, J. M.; Pekour, M. S.; Machado, L.; Wendisch, M.; Longo, K.; Martin, S. T.; Schmid, B.; Weinzierl, B.; Krüger, M. L.; Zöger, M.

2015-12-01

Currently, the indirect effects of atmospheric aerosols remain the most uncertain components in forcing of climate change over the industrial period (IPCC, 2013). This large uncertainty is partially a result of our incomplete understanding of the ability of particles to form cloud droplets under atmospherically relevant supersaturations. One objective of the US Department of Energy (DOE) Green Ocean Amazon Project (GoAmazon2014/5) is to understand the influence of the emission from Manaus, a tropical megacity, on aerosol size, concentration, and chemical composition, and their impact on cloud condensation nuclei (CCN) spectrum. The GoAmazon2014/5 study was an international campaign with the collaboration efforts from US, Brazil and Germany. During the intensive operation period, in the dry season (Sep. 1st - Oct. 10th, 2014), aerosol concentration, size distributions, and CCN spectra, both under pristine conditions and inside the Manaus plume, were characterized in-situ from the DOE Gulfstream-1 (G-1) research aircraft and German HALO aircraft during 4 coordinated flights on Sep. 9th, Sep. 16th, Sep 21st and Oct. 1st, 2014. During those four flights, aerosol number concentrations and CCN concentrations at two supersaturations (0.25% and 0.5%) were measured by condensation particle counters (CPCs) and a DMT dual column CCN counter onboard both G-1 and HALO. Aerosol size distribution was also measured by a Fast Integrated Mobility Spectrometer (FIMS) aboard the G-1 and is compared with the size distribution from Ultra High Sensitivity Aerosol Spectrometer - Airborne (UHSAS-A, DMT), which were deployed both on the G-1 and the HALO. Good agreement between the aerosol properties measured from the two aircraft has been achieved. The vertical profiles of aerosol size distribution and CCN spectrum will be discussed.

Seasonal dependence of aerosol processing in urban Philadelphia

NASA Astrophysics Data System (ADS)

Avery, A. M.; Waring, M. S.; DeCarlo, P. F.

2017-12-01

Urban aerosols pose an important threat to human health due to the conflation of emissions and concentrated population exposed. Winter and summer aerosol and trace gas measurements were taken in downtown Philadelphia in 2016. Measurements included aerosol composition and size with an Aerodyne Aerosol Mass Spectrometer (AMS), particle size distributions with an SMPS, and an aethalometer. Trace gas measurements of O3, NO, CH4, CO, and CO2 were taken concurrently. Sampling in seasonal extremes provided contrast in aerosol and trace gas composition, aerosol processing, and emission factors. Inorganic aerosol components contributed approximately 60% of the submicron aerosol mass, while summertime aerosol composition was roughly 70% organic matter. Positive Matrix Factorization (PMF) on the organic aerosol (OA) matrix revealed three factors in common in each season, including an oxygenated organic aerosol (OOA) factor with different temporal behavior in each season. In summertime, OOA varied diurnally with ozone and daytime temperature, but in the wintertime, it was anti-correlated with ozone and temperature, and instead trended with calculated liquid water, indicating a seasonally-dependent processing of organic aerosol in Philadelphia's urban environment. Due to the inorganic dominant winter aerosol, liquid water much higher (2.65 μg/m3) in winter than in summer (1.54 μg/m3). Diurnally varying concentrations of background gas phase species (CH4, CO2) were higher in winter and varied less as a result of boundary layer conditions; ozone was also higher in background in winter than summer. Winter stagnation events with low windspeed showed large buildup of trace gases CH4, CO, CO2, and NO. Traffic related aerosol was also elevated with black carbon and hydrocarbon-like OA (HOA) plumes of each at 3-5 times higher than the winter the average value for each. Winter ratios of HOA to black carbon were significantly higher in the winter than the summer due to lower

Primary and secondary contributions to aerosol light scattering and absorption in Mexico City during the MILAGRO 2006 campaign

NASA Astrophysics Data System (ADS)

Paredes-Miranda, G.; Arnott, W. P.; Jimenez, J. L.; Aiken, A. C.; Gaffney, J. S.; Marley, N. A.

2009-06-01

A photoacoustic spectrometer, a nephelometer, an aethalometer, and an aerosol mass spectrometer were used to measure at ground level real-time aerosol light absorption, scattering, and chemistry at an urban site located in North East Mexico City (Instituto Mexicano del Petroleo, Mexican Petroleum Institute, denoted by IMP), as part of the Megacity Impact on Regional and Global Environments field experiment, MILAGRO, in March 2006. Photoacoustic and reciprocal nephelometer measurements at 532 nm accomplished with a single instrument compare favorably with conventional measurements made with an aethalometer and a TSI nephelometer. The diurnally averaged single scattering albedo at 532 nm was found to vary from 0.60 to 0.85 with the peak value at midday and the minimum value at 07:00 a.m. local time, indicating that the Mexico City plume is likely to have a net warming effect on local climate. The peak value is associated with strong photochemical generation of secondary aerosol. It is estimated that the photochemical production of secondary aerosol (inorganic and organic) is approximately 75% of the aerosol mass concentration and light scattering in association with the peak single scattering albedo. A strong correlation of aerosol scattering at 532 nm and total aerosol mass concentration was found, and an average mass scattering efficiency factor of 3.8 m2/g was determined. Comparisons of photoacoustic and aethalometer light absorption with oxygenated organic aerosol concentration (OOA) indicate a very small systematic bias of the filter based measurement associated with OOA and the peak aerosol single scattering albedo.

Primary and secondary contributions to aerosol light scattering and absorption in Mexico City during the MILAGRO 2006 campaign

NASA Astrophysics Data System (ADS)

Paredes-Miranda, G.; Arnott, W. P.; Jimenez, J. L.; Aiken, A. C.; Gaffney, J. S.; Marley, N. A.

2008-09-01

A photoacoustic spectrometer, a nephelometer, an aetholemeter, and an aerosol mass spectrometer were used to measure at ground level real-time aerosol light absorption, scattering, and chemistry at an urban site located in north east Mexico City (Instituto Mexicano del Petroleo, Mexican Petroleum Institute, denoted by IMP), as part of the Megacity Impact on Regional and Global Environments field experiment, MILAGRO, in March 2006. Photoacoustic and reciprocal nephelometer measurements at 532 nm accomplished with a single instrument compare favorably with conventional measurements made with an aethelometer and a TSI nephelometer. The diurnally averaged single scattering albedo at 532 nm was found to vary from 0.60 to 0.85 with the peak value at midday and the minimum value at 7 a.m. local time, indicating that the Mexico City plume is likely to have a net warming effect on local climate. The peak value is associated with strong photochemical generation of secondary aerosol. It is estimated that the same-day photochemical production of secondary aerosol (inorganic and organic) is approximately 40 percent of the aerosol mass concentration and light scattering in association with the peak single scattering albedo. A strong correlation of aerosol scattering at 532 nm and total aerosol mass concentration was found, and an average mass scattering efficiency factor of 3.8 m2/g was determined. Comparisons of photoacoustic and aethalometer light absorption with oxygenated organic aerosol concentration (OOA) indicate a very small systematic bias of the filter based measurement associated with OOA and the peak aerosol single scattering albedo.

Particulate contamination spectrometer. Volume 1: Technical report

NASA Technical Reports Server (NTRS)

Schmitt, R. J.; Boyd, B. A.; Linford, R. M. F.

1975-01-01

A laser particulate spectrometer (LPS) system was developed to measure the size and speed distributions of particulate (dusts, aerosols, ice particles, etc.) contaminants. Detection of the particulates was achieved by means of light scattering and extinction effects using a single laser beam to cover a size range of 0.8 to 275 microns diameter and a speed range of 0.2 to 20 meter/second. The LPS system was designed to operate in the high vacuum environment of a space simulation chamber with cold shroud temperatures ranging from 77 to 300 K.

Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System.

PubMed

Ka, Donghyun; Lee, Hasup; Jung, Yi-Deun; Kim, Kyunggon; Seok, Chaok; Suh, Nayoung; Bae, Euiyoung

2016-01-05

CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploiting CRISPR/Cas systems for biotechnology

PubMed Central

Sampson, Timothy R.; Weiss, David S.

2015-01-01

The Cas9 endonuclease is the central component of the Type II CRISPR/Cas system, a prokaryotic adaptive restriction system against invading nucleic acids, such as those originating from bacteriophages and plasmids. Recently, this RNA-directed DNA endonuclease has been harnessed to target DNA sequences of interest. Here, we review the development of Cas9 as an important tool to not only edit the genomes of a number of different prokaryotic and eukaryotic species, but also as an efficient system for site-specific transcriptional repression or activation. Additionally, a specific Cas9 protein has been observed to target an RNA substrate, suggesting that Cas9 may have the ability to be programmed to target RNA as well. Cas proteins from other CRISPR/Cas subtypes may also be exploited in this regard. Thus, CRISPR/Cas systems represent an effective and versatile biotechnological tool, which will have significant impact on future advancements in genome engineering. PMID:24323919

Exploiting CRISPR/Cas systems for biotechnology.

PubMed

Sampson, Timothy R; Weiss, David S

2014-01-01

The Cas9 endonuclease is the central component of the Type II CRISPR/Cas system, a prokaryotic adaptive restriction system against invading nucleic acids, such as those originating from bacteriophages and plasmids. Recently, this RNA-directed DNA endonuclease has been harnessed to target DNA sequences of interest. Here, we review the development of Cas9 as an important tool to not only edit the genomes of a number of different prokaryotic and eukaryotic species, but also as an efficient system for site-specific transcriptional repression or activation. Additionally, a specific Cas9 protein has been observed to target an RNA substrate, suggesting that Cas9 may have the ability to be programmed to target RNA as well. Cas proteins from other CRISPR/Cas subtypes may also be exploited in this regard. Thus, CRISPR/Cas systems represent an effective and versatile biotechnological tool, which will have significant impact on future advancements in genome engineering. © 2014 WILEY Periodicals, Inc.

Classification of organic aerosol in the atmosphere over Seoul based on chemical group separation using two dimensional gas chromatography-time of flight mass spectrometry (GC×GC TOFMS) data

NASA Astrophysics Data System (ADS)

Jeon, S.; Lim, H. B.; Choi, N.; Lee, J.; Ahn, Y. K.; Kim, Y. P.

2016-12-01

Organic aerosols contain thousands of organic compounds and contribute to 20-90% of the total fine aerosol mass. For analyzing organic aerosols, a wide range of analytical techniques have been used such as gas chromatography mass spectrometer (GC/MS), liquid chromatography mass spectrometer (LC/MS), aerosol mass spectrometer (AMS), etc. Among them, comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometer (GCxGC/TOF-MS) can provide higher chemical resolution than AMS and analyze more mass fractions of organic aerosols than GC/MS. In this study, we suggest a new data processing method using GCxGC/TOF-MS data for analyzing organic compounds in the ambient aerosols. TSP samples were collected on the roof of the Asan engineering building, Ewha Womans University, Seoul, South Korea (37.56 °N, 126.94 °E, 20 m above ground level). A total of 67 samples were obtained during summer (August 2013) and winter (January and February 2014) with a PUF sampler (Tisch, TE-1000) on quartz fiber filter. Filters were extracted using accelerated solvent extractor with a mixture of dichloromethane and methanol (3:1, v/v). Total extracts were blown down to 0.5 mL using a nitrogen evaporator (Turbo Vap Ⅱ, caliper Life Sciences). Organic compounds in the TSP samples were separated into 6 chemical groups, depending on their retention time in two dimensions for their volatility and polarity. All area of peaks in each group was summed and variance of total area in each group was compared depending on season and diurnal cycle.

Vacuum FTIR observation on hygroscopic properties and phase transition of malonic acid aerosols

NASA Astrophysics Data System (ADS)

Shao, Xu; Zhang, Yun; Pang, Shu-Feng; Zhang, Yun-Hong

2017-02-01

A novel approach based on a combination of a pulse relative humidity (RH) controlling system and a rapid scan vacuum FTIR spectrometer was utilized to investigate the hygroscopic property and phase transition of malonic acid (MA) aerosols. By using this approach, both water vapor amount around the aerosols and water content within aerosols with sub-second time resolution were obtained. Based on the features of FTIR absorbing bands, it can be known that the evolution of hydrogen-bonding structures of malonic acid aerosols took place from (H2O)n-MA to MA-MA accompanying with phase transition in the dehumidifying process. And in present paper, the stepwise efflorescence of MA aerosols and nucleation rates at different RHs are first reported. Our observation has shown that the efflorescence of MA started at ∼17% RH and the nucleation rates increased with decreasing RH.

Ultra-Stable Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (5STAR)

NASA Technical Reports Server (NTRS)

Dunagan, Stephen E.; Johnson, Roy R.; Redemann, Jens; Holben, Brent N.; Schmidt, Beat; Flynn, Connor Joseph; Fahey, Lauren; LeBlanc, Samuel; Liss, Jordan; Kacenelenbogen, Meloe S.;

Field Studies of Broadband Aerosol Optical Extinction in the Ultraviolet Spectral Region

NASA Astrophysics Data System (ADS)

Washenfelder, R. A.; Attwood, A.; Brock, C. A.; Brown, S. S.

2013-12-01

Aerosols influence the Earth's radiative budget by scattering and absorbing incoming solar radiation. The optical properties of aerosols vary as a function of wavelength, but few measurements have reported the wavelength dependence of aerosol extinction cross sections and complex refractive indices. In the case of brown carbon, its wavelength-dependent absorption in the ultraviolet spectral region has been suggested as an important component of aerosol radiative forcing. We describe a new field instrument to measure aerosol optical extinction as a function of wavelength, using cavity enhanced spectroscopy with a broadband light source. The instrument consists of two broadband channels which span the 360-390 and 385-420 nm spectral regions using two light emitting diodes (LED) and a grating spectrometer with charge-coupled device (CCD) detector. We deployed this instrument during the Fire Lab at Missoula Experiment during Fall 2012 to measure biomass burning aerosol, and again during the Southern Oxidant and Aerosol Study in summer 2013 to measure organic aerosol in the Southeastern U.S. In both field experiments, we determined aerosol optical extinction as a function of wavelength and can interpret this together with size distribution and composition measurements to characterize the aerosol optical properties and radiative forcing.

Validation of LIRIC aerosol concentration retrievals using airborne measurements during a biomass burning episode over Athens

NASA Astrophysics Data System (ADS)

Kokkalis, Panagiotis; Amiridis, Vassilis; Allan, James D.; Papayannis, Alexandros; Solomos, Stavros; Binietoglou, Ioannis; Bougiatioti, Aikaterini; Tsekeri, Alexandra; Nenes, Athanasios; Rosenberg, Philip D.; Marenco, Franco; Marinou, Eleni; Vasilescu, Jeni; Nicolae, Doina; Coe, Hugh; Bacak, Asan; Chaikovsky, Anatoli

2017-01-01

In this paper we validate the Lidar-Radiometer Inversion Code (LIRIC) retrievals of the aerosol concentration in the fine mode, using the airborne aerosol chemical composition dataset obtained over the Greater Athens Area (GAA) in Greece, during the ACEMED campaign. The study focuses on the 2nd of September 2011, when a long-range transported smoke layer was observed in the free troposphere over Greece, in the height range from 2 to 3 km. CIMEL sun-photometric measurements revealed high AOD ( 0.4 at 532 nm) and Ångström exponent values ( 1.7 at 440/870 nm), in agreement with coincident ground-based lidar observations. Airborne chemical composition measurements performed over the GAA, revealed increased CO volume concentration ( 110 ppbv), with 57% sulphate dominance in the PM1 fraction. For this case, we compare LIRIC retrievals of the aerosol concentration in the fine mode with the airborne Aerosol Mass Spectrometer (AMS) and Passive Cavity Aerosol Spectrometer Probe (PCASP) measurements. Our analysis shows that the remote sensing retrievals are in a good agreement with the measured airborne in-situ data from 2 to 4 km. The discrepancies observed between LIRIC and airborne measurements at the lower troposphere (below 2 km), could be explained by the spatial and temporal variability of the aerosol load within the area where the airborne data were averaged along with the different time windows of the retrievals.

On the accuracy of aerosol photoacoustic spectrometer calibrations using absorption by ozone

NASA Astrophysics Data System (ADS)

Davies, Nicholas W.; Cotterell, Michael I.; Fox, Cathryn; Szpek, Kate; Haywood, Jim M.; Langridge, Justin M.

2018-04-01

In recent years, photoacoustic spectroscopy has emerged as an invaluable tool for the accurate measurement of light absorption by atmospheric aerosol. Photoacoustic instruments require calibration, which can be achieved by measuring the photoacoustic signal generated by known quantities of gaseous ozone. Recent work has questioned the validity of this approach at short visible wavelengths (404 nm), indicating systematic calibration errors of the order of a factor of 2. We revisit this result and test the validity of the ozone calibration method using a suite of multipass photoacoustic cells operating at wavelengths 405, 514 and 658 nm. Using aerosolised nigrosin with mobility-selected diameters in the range 250-425 nm, we demonstrate excellent agreement between measured and modelled ensemble absorption cross sections at all wavelengths, thus demonstrating the validity of the ozone-based calibration method for aerosol photoacoustic spectroscopy at visible wavelengths.

Real-Time Characterization of Aerosol Particle Composition above the Urban Canopy in Beijing: Insights into the Interactions between the Atmospheric Boundary Layer and Aerosol Chemistry.

PubMed

Sun, Yele; Du, Wei; Wang, Qingqing; Zhang, Qi; Chen, Chen; Chen, Yong; Chen, Zhenyi; Fu, Pingqing; Wang, Zifa; Gao, Zhiqiu; Worsnop, Douglas R

2015-10-06

Despite extensive efforts into the characterization of air pollution during the past decade, real-time characterization of aerosol particle composition above the urban canopy in the megacity Beijing has never been performed to date. Here we conducted the first simultaneous real-time measurements of aerosol composition at two different heights at the same location in urban Beijing from December 19, 2013 to January 2, 2014. The nonrefractory submicron aerosol (NR-PM1) species were measured in situ by a high-resolution aerosol mass spectrometer at near-ground level and an aerosol chemical speciation monitor at 260 m on a 325 m meteorological tower in Beijing. Secondary aerosol showed similar temporal variations between ground level and 260 m, whereas much weaker correlations were found for the primary aerosol. The diurnal evolution of the ratios and correlations of aerosol species between 260 m and the ground level further illustrated a complex interaction between vertical mixing processes and local source emissions on aerosol chemistry in the atmospheric boundary layer. As a result, the aerosol compositions at the two heights were substantially different. Organic aerosol (OA), mainly composed of primary OA (62%), at the ground level showed a higher contribution to NR-PM1 (65%) than at 260 m (54%), whereas a higher concentration and contribution (15%) of nitrate was observed at 260 m, probably due to the favorable gas-particle partitioning under lower temperature conditions. In addition, two different boundary layer structures were observed, each interacting differently with the evolution processes of aerosol chemistry.

Reactive uptake of HOCl to laboratory generated sea salt particles and nascent sea-spray aerosol

NASA Astrophysics Data System (ADS)

Campbell, N. R.; Ryder, O. S.; Bertram, T. H.

2013-12-01

Field observations suggest that the reactive uptake of HOCl on marine aerosol particles is an important source of chlorine radicals, particularly under low NOx conditions. However to date, laboratory measurements disagree on the magnitude of the reactive uptake coefficient for HOCl by a factor of 5 (γ(HOCl) ranges between 0.0004 and 0.0018), and there are no measurements of γ(HOCl) on nascent sea-spray aerosol. Here, we present measurements of the reactive uptake of HOCl to laboratory generated sodium chloride and sea-spray aerosol particles generated in a novel Marine Aerosol Reference Tank (MART), coupled to an entrained aerosol flow reactor and Chemical Ionization Mass Spectrometer (CIMS). Measurements of γ(HOCl) retrieved here are compared against those in the literature, and the role of organic coatings on nascent sea-spray aerosol is explored.

Characterization of the sources and processes of organic and inorganic aerosols in New York City with a high-resolution time-of-flight aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Sun, Y.-L.; Zhang, Q.; Schwab, J. J.; Demerjian, K. L.; Chen, W.-N.; Bae, M.-S.; Hung, H.-M.; Hogrefe, O.; Frank, B.; Rattigan, O. V.; Lin, Y.-C.

2010-10-01

Submicron aerosol particles (PM1) were measured in-situ using a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) during the summer 2009 Field Intensive Study at Queens College in New York City. Organic aerosol (OA) and sulfate are the two dominant species, accounting for 54% and 24%, respectively, of total PM1 mass on average. The average mass size distribution of OA presents a small mode peaking at ~150 nm (Dva) in addition to an accumulation mode (~550 nm) that is internally mixed with sulfate, nitrate, and ammonium. The diurnal cycles of sulfate and OA both show pronounced peaks between 01:00-02:00 p.m. EST due to photochemical production. The average (±1σ) oxygen-to-carbon (O/C), hydrogen-to-carbon (H/C), and nitrogen-to-carbon (N/C) ratios of OA in NYC are 0.36 (±0.09), 1.49 (±0.08), and 0.012(±0.005), respectively, corresponding to an average organic mass-to-carbon (OM/OC) ratio of 1.62(±0.11). Positive matrix factorization (PMF) of the high resolution mass spectra identified five OA components: a hydrocarbon-like OA (HOA), two types of oxygenated OA (OOA) including a low-volatility OOA (LV-OOA) and a semi-volatile OOA (SV-OOA), a cooking-emission related OA (COA), and a unique nitrogen-enriched OA (NOA). HOA appears to represent primary OA (POA) from urban traffic emissions. It comprises primarily of reduced species (H/C=1.83; O/C=0.06) and shows a mass spectral pattern very similar to those of POA from fossil fuel combustion, and correlates tightly with traffic emission tracers including elemental carbon and NOx. LV-OOA, which is highly oxidized (O/C=0.63) and correlates well with sulfate, appears to be representative for regional, aged secondary OA (SOA). SV-OOA, which is less oxidized (O/C=0.38) and correlates well with non-refractory chloride, likely represents less photo-chemically aged, semi-volatile SOA. COA shows a similar spectral pattern to the reference spectra of POA from cooking emissions and a distinct diurnal pattern

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

USDA-ARS?s Scientific Manuscript database

The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

Changes in organic aerosol composition with aging inferred from aerosol mass spectra

NASA Astrophysics Data System (ADS)

Ng, N. L.; Canagaratna, M. R.; Jimenez, J. L.; Chhabra, P. S.; Seinfeld, J. H.; Worsnop, D. R.

2011-07-01

Organic aerosols (OA) can be separated with factor analysis of aerosol mass spectrometer (AMS) data into hydrocarbon-like OA (HOA) and oxygenated OA (OOA). We develop a new method to parameterize H:C of OOA in terms of f43 (ratio of m/z 43, mostly C2H3O+, to total signal in the component mass spectrum). Such parameterization allows for the transformation of large database of ambient OOA components from the f44 (mostly CO2+, likely from acid groups) vs. f43 space ("triangle plot") (Ng et al., 2010) into the Van Krevelen diagram (H:C vs. O:C) (Van Krevelen, 1950). Heald et al. (2010) examined the evolution of total OA in the Van Krevelen diagram. In this work total OA is deconvolved into components that correspond to primary (HOA and others) and secondary (OOA) organic aerosols. By deconvolving total OA into different components, we remove physical mixing effects between secondary and primary aerosols which allows for examination of the evolution of OOA components alone in the Van Krevelen space. This provides a unique means of following ambient secondary OA evolution that is analogous to and can be compared with trends observed in chamber studies of secondary organic aerosol formation. The triangle plot in Ng et al. (2010) indicates that f44 of OOA components increases with photochemical age, suggesting the importance of acid formation in OOA evolution. Once they are transformed with the new parameterization, the triangle plot of the OOA components from all sites occupy an area in Van Krevelen space which follows a ΔH:C/ΔO:C slope of ~ -0.5. This slope suggests that ambient OOA aging results in net changes in chemical composition that are equivalent to the addition of both acid and alcohol/peroxide functional groups without fragmentation (i.e. C-C bond breakage), and/or the addition of acid groups with fragmentation. These results provide a framework for linking the bulk aerosol chemical composition evolution to molecular-level studies.

[Detection of CRSPR-Cas system in Streptococcus thermophiles].

PubMed

Li, Wan; Liang, Hongzhang; Zhang, Danqing; Wang, Nana; Tang, Yaru; Li, Bailiang; Huo, Guicheng

2016-04-14

We aimed to detect the CRSPR-Cas system of six Streptococcus thermophilus. Bioinformatics method was used to predict CRSPR-Cas system of nine S. thermophilus that published in National Center for Biotechnology Information. Four primers were designed according to the flanking sequences of standard strains and the CRISPR-Cas system of six S. thermophilus have been detected by PCR method. S. thermophilus S4 had a Cas9 gene, others all had Cas9 gene, Cas10 gene and Cas9* gene. In addition, 79 and KLDS3.0207 still had Cas3 gene. Signature genes amplification of CRSPR-Cas system could predict the type of CRSPR-Cas system in unsequenced strains, these findings will help establish the foundation for the study of CRSPR-Cas system in lactic acid bacteria.

Inter-Comparison of ILAS-II Version 1.4 Aerosol Extinction Coefficient at 780 nm with SAGE II, SAGE III, and POAM III Aerosol Data

NASA Technical Reports Server (NTRS)

Saitoh, Naoko; Hayashida, S.; Sugita, T.; Nakajima, H.; Yokota, T.; Hayashi, M.; Shiraishi, K.; Kanzawa, H.; Ejiri, M. K.; Irie, H.;

Variability of Ambient Aerosol in the Mexico City Metropolian Area

NASA Astrophysics Data System (ADS)

Onasch, T. B.; Worsnop, D. R.; Canagaratna, M.; Jayne, J. T.; Herndon, S.; Mortimer, P.; Kolb, C. E.; Rogers, T.; Knighton, B.; Dunlea, E.; Marr, L.; de Foy, B.; Molina, M.; Molina, L.; Salcedo, D.; Dzepina, K.; Jimenez, J. L.

2004-12-01

The spatial and temporal variations of the ambient aerosol in the Mexico City Metropolitan area was characterized during the springs of 2002 and 2003 using a mobile laboratory equipped with gas and particulate measurement instrumentation. The laboratory was operated at various fixed sites locations in and at the edge of the metropolitan area (Xalostoc, Merced, Cenica, Pedregal, and Santa Ana). Size-resolved aerosol mass and chemical composition was measured with an aerosol mass spectrometer and selected trace gas species (low mass organic compounds, NO, NO2, NOy, O3, SO2, CH2O, NH3, CO2) were measured using a proton transfer reaction mass spectrometer and various optical systems. The aerosol was predominantly organic in composition with lesser amounts of ammonium nitrate, sulfate, and chloride. The organic component was composed of mixed primary and secondary organic compounds. The mass loading and chemical composition of the aerosol was influenced by local and regional air pollution sources and the meteorology in Mexico City. Most urban sites were influenced by a strong diurnal particulate mass trend indicative of primary organic emissions from traffic during early morning and subsequently oxidized/processed organics and ammonium nitrate particles starting in the mid-morning (~9 AM) and continuing throughout the day. Morning traffic-related primary organic emissions were strongest at La Merced (center of Mexico City, located near a busy food market), more subdued at other fixed sites further from the city center, and varied depending upon the day of week and holiday schedules. Particle-bound polycyclic aromatic hydrocarbons were observed within Mexico City fixed sites and were correlated with traffic organic PM emissions. Oxidized organic and ammonium nitrate events occurred during mid-morning at all city sites and were well correlated with gas phase photochemical activity. The daily ammonium nitrate aerosol event occurred later at sites near the city limits

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease.

PubMed

Ivanov, Yury V; Shariat, Nikki; Register, Karen B; Linz, Bodo; Rivera, Israel; Hu, Kai; Dudley, Edward G; Harvill, Eric T

2015-10-26

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR. The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR. Here we describe a novel Type II-C CRISPR and its associated genes-cas1, cas2, and cas9-in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies.

Synergic use of TOMS and Aeronet Observations for Characterization of Aerosol Absorption

NASA Technical Reports Server (NTRS)

Torres, O.; Bhartia, P. K.; Dubovik, O.; Holben, B.; Siniuk, A.

2003-01-01

The role of aerosol absorption on the radiative transfer balance of the earth-atmosphere system is one of the largest sources of uncertainty in the analysis of global climate change. Global measurements of aerosol single scattering albedo are, therefore, necessary to properly assess the radiative forcing effect of aerosols. Remote sensing of aerosol absorption is currently carried out using both ground (Aerosol Robotic Network) and space (Total Ozone Mapping Spectrometer) based observations. The satellite technique uses measurements of backscattered near ultraviolet radiation. Carbonaceous aerosols, resulting from the combustion of biomass, are one of the most predominant absorbing aerosol types in the atmosphere. In this presentation, TOMS and AERONET retrievals of single scattering albedo of carbonaceous aerosols, are compared for different environmental conditions: agriculture related biomass burning in South America and Africa and peat fires in Eastern Europe. The AERONET and TOMS derived aerosol absorption information are in good quantitative agreement. The most absorbing smoke is detected over the African Savanna. Aerosol absorption over the Brazilian rain forest is less absorbing. Absorption by aerosol particles resulting from peat fires in Eastern Europe is weaker than the absorption measured in Africa and South America. This analysis shows that the near UV satellite method of aerosol absorption characterization has the sensitivity to distinguish different levels of aerosol absorption. The analysis of the combined AERONET-TOMS observations shows a high degree of synergy between satellite and ground based observations.

Broadband Measurement of Aerosol Extinction in the Visible Range

NASA Astrophysics Data System (ADS)

He, Quanfu; Bluvshtein, Nir; Segev, Lior; Flores, Michel; Rudich, Yinon; Washenfelder, Rebecca; Brown, Steven

2017-04-01

Atmospheric aerosols influence the Earth's radiative budget directly by scattering and absorbing incoming solar radiation. Aerosol direct forcing remains one of the largest uncertainties in quantifying the role that aerosols play in the Earth's radiative budget. The optical properties of aerosols vary as a function of wavelength, but few measurements reported the wavelength dependence of aerosol extinction cross section and complex refractive indices, particularly in the blue and visible spectral range. There is also currently a large gap in our knowledge of how the optical properties evolve as a function of atmospheric aging in the visible spectrum. In this study, we constructed a new and novel laboratory instrument to measure aerosol extinction as a function of wavelength, using cavity enhanced spectroscopy with a white light source. This broadband cavity enhanced spectroscopy (BBCES) covers the 395-700 nm spectral region using a broadband light source and a grating spectrometer with charge-coupled device detector (CCD). We evaluated this BBCES by measuring extinction cross section for aerosols that are pure scattering, slightly absorbing and strongly absorbing atomized from standard materials. We also retrieved the refractive indices from the measured extinction cross sections. Secondary organic aerosols from biogenic and anthropogenic precursors were "aged" to differential time scales (1 to 10 days) in an Oxidation Flow Reactor (OFR) under the combined influence of OH, O3 and UV light. The new BBCES was used to online measure the extinction cross sections of the SOA. This talk will provide a comprehensive understanding of aerosol optical properties alerting during aging process in the 395 - 700 nm spectrum.

Autonomous marine hyperspectral radiometers for determining solar irradiances and aerosol optical properties

NASA Astrophysics Data System (ADS)

Wood, John; Smyth, Tim J.; Estellés, Victor

2017-05-01

We have developed two hyperspectral radiometer systems which require no moving parts, shade rings or motorised tracking, making them ideally suited for autonomous use in the inhospitable remote marine environment. Both systems are able to measure direct and diffuse hyperspectral irradiance in the wavelength range 350-1050 nm at 6 nm (Spectrometer 1) or 3.5 nm (Spectrometer 2) resolution. Marine field trials along a 100° transect (between 50° N and 50° S) of the Atlantic Ocean resulted in close agreement with existing commercially available instruments in measuring (1) photosynthetically available radiation (PAR), with both spectrometers giving regression slopes close to unity (Spectrometer 1: 0.960; Spectrometer 2: 1.006) and R2 ˜ 0.96; (2) irradiant energy, with R2 ˜ 0.98 and a regression slope of 0.75 which can be accounted for by the difference in wavelength integration range; and (3) hyperspectral irradiance where the agreement on average was between 2 and 5 %. Two long duration land-based field campaigns of up to 18 months allowed both spectrometers to be well calibrated. This was also invaluable for empirically correcting for the wider field of view (FOV) of the spectrometers in comparison with the current generation of sun photometers ( ˜ 7.5° compared with ˜ 1°). The need for this correction was also confirmed and independently quantified by atmospheric radiative transfer modelling and found to be a function of aerosol optical depth (AOD) and solar zenith angle. Once Spectrometer 2 was well calibrated and the FOV effect corrected for, the RMSE in retrievals of AOD when compared with a CIMEL sun photometer were reduced to ˜ 0.02-0.03 with R2 > 0.95 at wavelengths 440, 500, 670 and 870 nm. Corrections for the FOV as well as ship motion were applied to the data from the marine field trials. This resulted in AOD500 nm ranging between 0.05 in the clear background marine aerosol regions and ˜ 0.5 within the Saharan dust plume. The RMSE between the

All-in-One CRISPR-Cas9/FokI-dCas9 Vector-Mediated Multiplex Genome Engineering in Cultured Cells.

PubMed

Sakuma, Tetsushi; Sakamoto, Takuya; Yamamoto, Takashi

2017-01-01

CRISPR-Cas9 enables highly convenient multiplex genome engineering in cultured cells, because it utilizes generic Cas9 nuclease and an easily customizable single-guide RNA (sgRNA) for site-specific DNA double-strand break induction. We previously established a multiplex CRISPR-Cas9 assembly system for constructing an all-in-one vector simultaneously expressing multiple sgRNAs and Cas9 nuclease or other Cas9 variants including FokI-dCas9, which supersedes the wild-type Cas9 with regard to high specificity. In this chapter, we describe a streamlined protocol to design and construct multiplex CRISPR-Cas9 or FokI-dCas9 vectors, to introduce them into cultured cells by lipofection or electroporation, to enrich the genomically edited cells with a transient puromycin selection, to validate the mutation efficiency by Surveyor nuclease assay, and to perform off-target analyses. We show that our protocol enables highly efficient multiplex genome engineering even in hard-to-transfect HepG2 cells.

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.

PubMed

Yamada, Mari; Watanabe, Yuto; Gootenberg, Jonathan S; Hirano, Hisato; Ran, F Ann; Nakane, Takanori; Ishitani, Ryuichiro; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2017-03-16

The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems. The CjCas9 guide RNA contains a triple-helix structure, which is distinct from known RNA triple helices, thereby expanding the natural repertoire of RNA triple helices. Furthermore, unlike the other Cas9 orthologs, CjCas9 contacts the nucleotide sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif. Collectively, these findings improve our mechanistic understanding of the CRISPR-Cas9 systems and may facilitate Cas9 engineering. Copyright © 2017 Elsevier Inc. All rights reserved.

A Broad-Spectrum Inhibitor of CRISPR-Cas9.

PubMed

Harrington, Lucas B; Doxzen, Kevin W; Ma, Enbo; Liu, Jun-Jie; Knott, Gavin J; Edraki, Alireza; Garcia, Bianca; Amrani, Nadia; Chen, Janice S; Cofsky, Joshua C; Kranzusch, Philip J; Sontheimer, Erik J; Davidson, Alan R; Maxwell, Karen L; Doudna, Jennifer A

2017-09-07

CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9. Copyright © 2017 Elsevier Inc. All rights reserved.

Annotation and Classification of CRISPR-Cas Systems

PubMed Central

Makarova, Kira S.; Koonin, Eugene V.

2018-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods. PMID:25981466

Annotation and Classification of CRISPR-Cas Systems.

PubMed

Makarova, Kira S; Koonin, Eugene V

2015-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.

Formation of secondary organic aerosol coating on black carbon particles near vehicular emissions

NASA Astrophysics Data System (ADS)

Lee, Alex K. Y.; Chen, Chia-Li; Liu, Jun; Price, Derek J.; Betha, Raghu; Russell, Lynn M.; Zhang, Xiaolu; Cappa, Christopher D.

2017-12-01

Black carbon (BC) emitted from incomplete combustion can result in significant impacts on air quality and climate. Understanding the mixing state of ambient BC and the chemical characteristics of its associated coatings is particularly important to evaluate BC fate and environmental impacts. In this study, we investigate the formation of organic coatings on BC particles in an urban environment (Fontana, California) under hot and dry conditions using a soot-particle aerosol mass spectrometer (SP-AMS). The SP-AMS was operated in a configuration that can exclusively detect refractory BC (rBC) particles and their coatings. Using the -log(NOx / NOy) ratio as a proxy for photochemical age of air masses, substantial formation of secondary organic aerosol (SOA) coatings on rBC particles was observed due to active photochemistry in the afternoon, whereas primary organic aerosol (POA) components were strongly associated with rBC from fresh vehicular emissions in the morning rush hours. There is also evidence that cooking-related organic aerosols were externally mixed from rBC. Positive matrix factorization and elemental analysis illustrate that most of the observed SOA coatings were freshly formed, providing an opportunity to examine SOA coating formation on rBCs near vehicular emissions. Approximately 7-20 wt % of secondary organic and inorganic species were estimated to be internally mixed with rBC on average, implying that rBC is unlikely the major condensation sink of SOA in this study. Comparison of our results to a co-located standard high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) measurement suggests that at least a portion of SOA materials condensed on rBC surfaces were chemically different from oxygenated organic aerosol (OOA) particles that were externally mixed with rBC, although they could both be generated from local photochemistry.

Naturally occurring off-switches for CRISPR-Cas9

PubMed Central

Pawluk, April; Amrani, Nadia; Zhang, Yan; Garcia, Bianca; Hidalgo-Reyes, Yurima; Lee, Jooyoung; Edraki, Alireza; Shah, Megha; Sontheimer, Erik J.; Maxwell, Karen L.; Davidson, Alan R.

2017-01-01

Summary CRISPR-Cas9 technology would be enhanced by the ability to inhibit Cas9 function spatially, temporally, or conditionally. Previously, we discovered small proteins encoded by bacteriophages that inhibit the CRISPR-Cas systems of their host bacteria. These “anti-CRISPRs” were specific to type I CRISPR-Cas systems that do not employ the Cas9 protein. We posited that nature would also yield Cas9 inhibitors in response to the evolutionary arms race between bacteriophages and their hosts. Here, we report the discovery of three distinct families of anti-CRISPRs that specifically inhibit the CRISPR-Cas9 system of Neisseria meningitidis. We show that these proteins bind directly to N. meningitidis Cas9 (NmeCas9), and can be used as potent inhibitors of genome editing by this system in human cells. These anti-CRISPR proteins now enable “off-switches” for CRISPR-Cas9 activity, and provide a genetically-encodable means to inhibit CRISPR-Cas9 genome editing in eukaryotes. PMID:27984730

ultra-Stable Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (5STAR)

NASA Astrophysics Data System (ADS)

Dunagan, S. E.; Johnson, R. R.; Redemann, J.; Holben, B. N.; Schmid, B.; Flynn, C. J.; Fahey, L.; LeBlanc, S. E.; Liss, J.; Kacenelenbogen, M. S.; Segal-Rosenhaimer, M.; Shinozuka, Y.; Dahlgren, R. P.; Pistone, K.; Karol, Y.

2017-12-01

The Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR) combines airborne sun tracking and sky scanning with diffraction spectroscopy to improve knowledge of atmospheric constituents and their links to air pollution and climate. Direct beam hyperspectral measurement of optical depth improves retrievals of gas constituents and determination of aerosol properties. Sky scanning enhances retrievals of aerosol type and size distribution. Hyperspectral cloud-transmitted radiance measurements enable the retrieval of cloud properties from below clouds. These measurements tighten the closure between satellite and ground-based measurements. 4STAR incorporates a modular sun-tracking/ sky-scanning optical head with optical fiber signal transmission to rack mounted spectrometers, permitting miniaturization of the external optical tracking head, and future detector evolution. 4STAR has supported a broad range of flight experiments since it was first flown in 2010. This experience provides the basis for a series of improvements directed toward reducing measurement uncertainty and calibration complexity, and expanding future measurement capabilities, to be incorporated into a new 5STAR instrument. A 9-channel photodiode radiometer with AERONET-matched bandpass filters will be incorporated to improve calibration stability. A wide dynamic range tracking camera will provide a high precision solar position tracking signal as well as an image of sky conditions around the solar axis. An ultrasonic window cleaning system design will be tested. A UV spectrometer tailored for formaldehyde and SO2 gas retrievals will be added to the spectrometer enclosure. Finally, expansion capability for a 4 channel polarized radiometer to measure the Stokes polarization vector of sky light will be incorporated. This paper presents initial progress on this next-generation 5STAR instrument. Keywords: atmosphere; climate; pollution; radiometry; technology; hyperspectral; fiber optic

Cluster analysis of the organic peaks in bulk mass spectra obtained during the 2002 New England Air Quality Study with an Aerodyne aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.; Middlebrook, A. M.

2006-06-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter most probably originating from both, anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent as much as 5 µg/m3 organic aerosol mass - 17% of the total organic mass - that can be attributed to biogenic sources. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Online investigations on ozonation products of pyrene and benz[ a]anthracene particles with a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer

NASA Astrophysics Data System (ADS)

Gao, Shaokai; Zhang, Yang; Meng, Junwang; Shu, Jinian

The reaction products of ozone with pyrene and benz[ a]anthracene absorbed on azelaic acid particles under the pseudo-first-order reaction conditions have been investigated with a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS). The pyrene and benz[ a]anthracene particles with the initial concentrations of ˜1 mg m -3 are respectively exposed to ˜22 ppm ozone in a reaction chamber with a volume of ˜180 L. The time-of-flight mass spectra of the particulate ozonides are obtained. The assignments of the mass spectra reveal that 4-carboxy-5-phenanthrene-carboxyaldehyde (71%) and hydroxypyrene (23%) are the main solid state ozonides of pyrene, while 2-(2-formyl)phenyl-3-naphthoic acid (35%), hydroxybenz[ a]anthrone (30%), and benz[ a]anthracene-7,12-dione (18%) are the main solid state ozonides of benz[ a]anthracene. The pathways of the ozonations are proposed in the paper.

Photochemical Aging of Organic Aerosols: A Laboratory Study

NASA Astrophysics Data System (ADS)

Papanastasiou, Dimitrios K.; Kostenidou, Evangelia; Gkatzelis, Georgios I.; Psichoudaki, Magdalini; Louvaris, Evangelos; Pandis, Spyros N.

2014-05-01

-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) were used to measure the organic aerosol mass production and oxidation degree (O:C ratio) following OH aging. A thermodenuder system was used to measure the volatility distribution change as organic aerosol aged upon continuous oxidation. Organic gas phase species were characterized with a Proton Transfer Reaction - Mass Spectrometer (PTR-MS) while NOx and O3 were measured with the use of corresponding analyzers. Results from this study show that organic mass production occurs upon exposure to OH radicals indicating that continuous OH aging of semi-volatile is probably responsible for at least some of the gap between observed and modeled OA levels in the atmosphere. Additionally, this chemical aging process leads to a decrease in volatility and an increase in O:C ratio while the level of change in both properties depends on OH exposure. The atmospheric implications of this study are discussed.

ARM - Midlatitude Continental Convective Clouds - Ultra High Sensitivity Aerosol Spectrometer(tomlinson-uhsas)

DOE Data Explorer

Tomlinson, Jason; Jensen, Mike

2012-02-28

Ultra High Sensitivity Aerosol Spectrometer (UHSASA) A major component of the Mid-latitude Continental Convective Clouds Experiment (MC3E) field campaign was the deployment of an enhanced radiosonde array designed to capture the vertical profile of atmospheric state variables (pressure, temperature, humidity wind speed and wind direction) for the purpose of deriving the large-scale forcing for use in modeling studies. The radiosonde array included six sites (enhanced Central Facility [CF-1] plus five new sites) launching radiosondes at 3-6 hour sampling intervals. The network will cover an area of approximately (300)2 km2 with five outer sounding launch sites and one central launch location. The five outer sounding launch sites are: S01 Pratt, KS [ 37.7oN, 98.75oW]; S02 Chanute, KS [37.674, 95.488]; S03 Vici, Oklahoma [36.071, -99.204]; S04 Morris, Oklahoma [35.687, -95.856]; and S05 Purcell, Oklahoma [34.985, -97.522]. Soundings from the SGP Central Facility during MC3E can be retrieved from the regular ARM archive. During routine MC3E operations 4 radiosondes were launched from each of these sites (approx. 0130, 0730, 1330 and 1930 UTC). On days that were forecast to be convective up to four additional launches were launched at each site (approx. 0430, 1030, 1630, 2230 UTC). There were a total of approximately 14 of these high frequency launch days over the course of the experiment. These files contain brightness temperatures observed at Purcell during MC3E. The measurements were made with a 5 channel (22.235, 23.035, 23.835, 26.235, 30.000GHz) microwave radiometer at one minute intervals. The results have been separated into daily files and the day of observations is indicated in the file name. All observations were zenith pointing. Included in the files are the time variables base_time and time_offset. These follow the ARM time conventions. Base_time is the number seconds since January 1, 1970 at 00:00:00 for the first data point of the file and time_offset is

CRISPR-Cas: Adapting to change.

PubMed

Jackson, Simon A; McKenzie, Rebecca E; Fagerlund, Robert D; Kieper, Sebastian N; Fineran, Peter C; Brouns, Stan J J

2017-04-07

Bacteria and archaea are engaged in a constant arms race to defend against the ever-present threats of viruses and invasion by mobile genetic elements. The most flexible weapons in the prokaryotic defense arsenal are the CRISPR-Cas adaptive immune systems. These systems are capable of selective identification and neutralization of foreign DNA and/or RNA. CRISPR-Cas systems rely on stored genetic memories to facilitate target recognition. Thus, to keep pace with a changing pool of hostile invaders, the CRISPR memory banks must be regularly updated with new information through a process termed CRISPR adaptation. In this Review, we outline the recent advances in our understanding of the molecular mechanisms governing CRISPR adaptation. Specifically, the conserved protein machinery Cas1-Cas2 is the cornerstone of adaptive immunity in a range of diverse CRISPR-Cas systems. Copyright © 2017, American Association for the Advancement of Science.

Aerosol chemical composition at Cabauw, The Netherlands as observed in two intensive periods in May 2008 and March 2009

NASA Astrophysics Data System (ADS)

Mensah, A. A.; Holzinger, R.; Otjes, R.; Trimborn, A.; Mentel, Th. F.; ten Brink, H.; Henzing, B.; Kiendler-Scharr, A.

2012-05-01

Observations of aerosol chemical composition in Cabauw, the Netherlands, are presented for two intensive measurement periods in May 2008 and March 2009. Sub-micron aerosol chemical composition was measured by an Aerodyne Aerosol Mass Spectrometer (AMS) and is compared to observations from aerosol size distribution measurements as well as composition measurements with a Monitor for AeRosol and GAses (MARGA) based instrument and a Thermal-Desorption Proton-Transfer-Reaction Mass-Spectrometer (TD-PTR-MS). An overview of the data is presented and the data quality is discussed. In May 2008 enhanced pollution was observed with organics contributing 40% to the PM1 mass. In contrast the observed average mass loading was lower in March 2009 and a dominance of ammonium nitrate (42%) was observed. The semi-volatile nature of ammonium nitrate is evident in the diurnal cycles with maximum concentrations observed in the morning hours in May 2008 and little diurnal variation observed in March 2009. Size dependent composition data from AMS measurements are presented and show a dominance of organics in the size range below 200 nm. A higher O:C ratio of the organics is observed for May 2008 than for March 2009. Together with the time series of individual tracer ions this shows the dominance of OOA over HOA in May 2008.

Aerosol Vacuum-Assisted Plasma Ionization (Aero-VaPI) Coupled to Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Blair, Sandra L.; Ng, Nga L.; Zambrzycki, Stephen C.; Li, Anyin; Fernández, Facundo M.

2018-02-01

In this communication, we report on the real-time analysis of organic aerosol particles by Vacuum-assisted Plasma Ionization-Mass Spectrometry (Aero-VaPI-MS) using a home-built VaPI ion source coupled to a Synapt G2-S HDMS ion mobility-mass spectrometry (IM-MS) system. Standards of organic molecules of interest in prebiotic chemistry were used to generate aerosols. Monocaprin and decanoic acid aerosol particles were successfully detected in both the positive and negative ion modes, respectively. A complex aerosol mixture of different sizes of polymers of L-malic acid was also examined through ion mobility (IM) separations, resulting in the detection of polymers of up to eight monomeric units. This noncommercial plasma ion source is proposed as a low cost alternative to other plasma ionization platforms used for aerosol analysis, and a higher-performance alternative to more traditional aerosol mass spectrometers. VaPI provides robust online ionization of organics in aerosols without extensive ion activation, with the coupling to IM-MS providing higher peak capacity and excellent mass accuracy. [Figure not available: see fulltext.

New CRISPR-Cas systems from uncultivated microbes

NASA Astrophysics Data System (ADS)

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

2017-02-01

CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

Development and first application of an Aerosol Collection Module (ACM) for quasi online compound specific aerosol measurements

NASA Astrophysics Data System (ADS)

Hohaus, Thorsten; Kiendler-Scharr, Astrid; Trimborn, Dagmar; Jayne, John; Wahner, Andreas; Worsnop, Doug

2010-05-01

experiment course. The SOA was simultaneously characterized by an aerosol mass spectrometer (AMS). The ACM-GC-MS results will be compared with PMF analysis of the AMS organic aerosol. The correlation of specific compounds with PMF factors will be discussed together with future applications of the ACM-GC-MS system for ambient aerosol measurements. Acknowledgement This work was supported by the US Environmental Protection Agency (EPA Grant No. RD-83107701-0) and the Department of Energy (DOE SBIR Grant No. DE-FG02-05ER84269). References Intergovernmental Panel on Climate Change (IPCC): Climate Change 2007, Cambridge University Press, UK, 2007 Hallquist et al., The formation, properties and impact of secondary organic aerosol: current and emerging issues, Atmos. Chem. Phys, Vol.9, 5155-5236, 2009

Naturally Occurring Off-Switches for CRISPR-Cas9.

PubMed

Pawluk, April; Amrani, Nadia; Zhang, Yan; Garcia, Bianca; Hidalgo-Reyes, Yurima; Lee, Jooyoung; Edraki, Alireza; Shah, Megha; Sontheimer, Erik J; Maxwell, Karen L; Davidson, Alan R

2016-12-15

CRISPR-Cas9 technology would be enhanced by the ability to inhibit Cas9 function spatially, temporally, or conditionally. Previously, we discovered small proteins encoded by bacteriophages that inhibit the CRISPR-Cas systems of their host bacteria. These "anti-CRISPRs" were specific to type I CRISPR-Cas systems that do not employ the Cas9 protein. We posited that nature would also yield Cas9 inhibitors in response to the evolutionary arms race between bacteriophages and their hosts. Here, we report the discovery of three distinct families of anti-CRISPRs that specifically inhibit the CRISPR-Cas9 system of Neisseria meningitidis. We show that these proteins bind directly to N. meningitidis Cas9 (NmeCas9) and can be used as potent inhibitors of genome editing by this system in human cells. These anti-CRISPR proteins now enable "off-switches" for CRISPR-Cas9 activity and provide a genetically encodable means to inhibit CRISPR-Cas9 genome editing in eukaryotes. VIDEO ABSTRACT. Copyright © 2016 Elsevier Inc. All rights reserved.

Salting Constants of Small Organic Molecules in Aerosol-Relevant Salts and Application to Aerosol Formation in the Southeastern United States

NASA Astrophysics Data System (ADS)

Waxman, E.; Carlton, A. M. G.; Ziemann, P. J.; Volkamer, R. M.

2014-12-01

Secondary organic aerosol (SOA) formation from small water-soluble molecules such as glyoxal and methyl glyoxal is a topic of emerging interest. Results from recent field campaigns, e.g. Waxman et al. (2013, GRL) and Knote et al. (2014, ACP), show that these molecules can form significant SOA mass as a result of 'salting-in'. Salting-in happens when a molecule's solubility increases with salt concentration and salting-out is the reverse. Salting effects modify the solubility exponentially with increasing salt concentration, and thus the effective Henry's law constant can strongly modify partitioning, and multiphase chemical reaction rates in aerosol water. Moreover, the solubility in aerosol water cannot easily inferred based on the solubility in cloud water, as the salting effects could change the solubility by a factor of 104 or more. In this work, we have devised and applied a novel experimental setup to measure salting constants using an ion trap mass spectrometer. We focus on small, water soluble molecules like methyl glyoxal and similar compounds and measure salting constants for aerosol-relevant salts including ammonium sulfate, ammonium nitrate, and sodium chloride. The Setschenow salting-constant values are then used to parameterize the effects of salting in CMAQ. We present a series of sensitivity studies of the effects that inorganic aerosols have on the SOA formation from small soluble molecules in the southeastern United States.

The Retrieval of Aerosol Optical Thickness Using the MERIS Instrument

NASA Astrophysics Data System (ADS)

Mei, L.; Rozanov, V. V.; Vountas, M.; Burrows, J. P.; Levy, R. C.; Lotz, W.

2015-12-01

Retrieval of aerosol properties for satellite instruments without shortwave-IR spectral information, multi-viewing, polarization and/or high-temporal observation ability is a challenging problem for spaceborne aerosol remote sensing. However, space based instruments like the MEdium Resolution Imaging Spectrometer (MERIS) and the successor, Ocean and Land Colour Instrument (OLCI) with high calibration accuracy and high spatial resolution provide unique abilities for obtaining valuable aerosol information for a better understanding of the impact of aerosols on climate, which is still one of the largest uncertainties of global climate change evaluation. In this study, a new Aerosol Optical Thickness (AOT) retrieval algorithm (XBAER: eXtensible Bremen AErosol Retrieval) is presented. XBAER utilizes the global surface spectral library database for the determination of surface properties while the MODIS collection 6 aerosol type treatment is adapted for the aerosol type selection. In order to take the surface Bidirectional Reflectance Distribution Function (BRDF) effect into account for the MERIS reduce resolution (1km) retrieval, a modified Ross-Li mode is used. The AOT is determined in the algorithm using lookup tables including polarization created using Radiative Transfer Model SCIATRAN3.4, by minimizing the difference between atmospheric corrected surface reflectance with given AOT and the surface reflectance calculated from the spectral library. The global comparison with operational MODIS C6 product, Multi-angle Imaging SpectroRadiometer (MISR) product, Advanced Along-Track Scanning Radiometer (AATSR) aerosol product and the validation using AErosol RObotic NETwork (AERONET) show promising results. The current XBAER algorithm is only valid for aerosol remote sensing over land and a similar method will be extended to ocean later.

Secondary Organic Aerosol Formation in the Captive Aerosol Growth and Evolution (CAGE) Chambers during the Southern Oxidant and Aerosol Study (SOAS) in Centreville, AL

NASA Astrophysics Data System (ADS)

Leong, Y.; Karakurt Cevik, B.; Hernandez, C.; Griffin, R. J.; Taylor, N.; Matus, J.; Collins, D. R.

2013-12-01

Secondary organic aerosol (SOA) represents a large portion of sub-micron particulate matter on a global scale. The composition of SOA and its formation processes are heavily influenced by anthropogenic and biogenic activity. Volatile organic compounds (VOCs) that are emitted naturally from forests or from human activity serve as precursors to SOA formation. Biogenic SOA (BSOA) is formed from biogenic VOCs and is prevalent in forested regions like the Southeastern United States. The formation and enhancement of BSOA under anthropogenic influences such as nitrogen oxides (NOx), sulfur dioxide (SO2), and oxygen radicals are still not well understood. The lack of information on anthropogenic BSOA enhancement and the reversibility of SOA formation could explain the underprediction of SOA in current models. To address some of these gaps in knowledge, this study was conducted as part of the Southern Oxidant and Aerosol Study (SOAS) in Centreville, AL during the summer of 2013. SOA growth experiments were conducted in two Captive Aerosol Growth and Evolution (CAGE) outdoor chambers located at the SEARCH site. Ambient trace gas concentrations were maintained in these chambers using semi-permeable gas-exchange membranes, while studying the growth of injected monodisperse seed aerosol. The control chamber was operated under ambient conditions; the relative humidity and oxidant and NOx levels were perturbed in the second chamber. This design allows experiments to capture the natural BSOA formation processes in the southeastern atmosphere and to study the influence of anthropogenic activity on aerosol chemistry. Chamber experiments were periodically monitored with physical and chemical instrumentation including a scanning mobility particle sizer (SMPS), a cloud condensation nuclei counter (CCNC), a humidified tandem differential mobility analyzer (H-TDMA), and an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). The CAGE experiments focused on SOA

Photochemical aging of light-absorbing secondary organic aerosol material.

PubMed

Sareen, Neha; Moussa, Samar G; McNeill, V Faye

2013-04-11

Dark reactions of methylglyoxal with NH4(+) in aqueous aerosols yield light-absorbing and surface-active products that can influence the physical properties of the particles. Little is known about how the product mixture and its optical properties will change due to photolysis as well as oxidative aging by O3 and OH in the atmosphere. Here, we report the results of kinetics and product studies of the photochemical aging of aerosols formed by atomizing aqueous solutions of methylglyoxal and ammonium sulfate. Experiments were performed using aerosol flow tube reactors coupled with an aerosol chemical ionization mass spectrometer (Aerosol-CIMS) for monitoring gas- and particle-phase compositions. Particles were also impacted onto quartz windows in order to assess changes in their UV-visible absorption upon oxidation. Photooxidation of the aerosols leads to the formation of small, volatile organic acids including formic acid, acetic acid, and glyoxylic acid. The atmospheric lifetime of these species during the daytime is predicted to be on the order of minutes, with photolysis being an important mechanism of degradation. The lifetime with respect to O3 oxidation was observed to be on the order of hours. O3 oxidation also leads to a net increase in light absorption by the particles due to the formation of additional carbonyl compounds. Our results are consistent with field observations of high brown carbon absorption in the early morning.

Apportionment of urban aerosol sources in Chongqing (China) using synergistic on-line techniques

NASA Astrophysics Data System (ADS)

Chen, Yang; Yang, Fumo

2016-04-01

The sources of ambient fine particulate matter (PM2.5) during wintertime at a background urban location in Chongqing (southwestern China) have been determined. Aerosol chemical composition analyses were performed using multiple on-line techniques, such as single particle aerosol mass spectrometer (SPAMS) for single particle chemical composition, on-line elemental carbon-organic carbon analyzer (on-line OC-EC), on-line X-ray fluorescence (XRF) for elements, and in-situ Gas and Aerosol Compositions monitor (IGAC) for water-soluble ions in PM2.5. All the datasets from these techniques have been adjusted to a 1-h time resolution for receptor model input. Positive matrix factorization (PMF) has been used for resolving aerosol sources. At least six sources, including domestic coal burning, biomass burning, dust, traffic, industrial and secondary/aged factors have been resolved and interpreted. The synergistic on-line techniques were helpful for identifying aerosol sources more clearly than when only employing the results from the individual techniques. This results are useful for better understanding of aerosol sources and atmospheric processes.

Preliminary observations of organic gas-particle partitioning from biomass combustion smoke using an aerosol mass spectrometer

Treesearch

T. Lee; S. M. Kreidenweis; J. L. Collett; A. P. Sullivan; C. M. Carrico; J. L. Jimenez; M. Cubison; S. Saarikoski; D. R. Worsnop; T. B. Onasch; E. Fortner; W. C. Malm; E. Lincoln; Cyle Wold; WeiMin Hao

2010-01-01

Aerosols play important roles in adverse health effects, indirect and direct forcing of Earth’s climate, and visibility degradation. Biomass burning emissions from wild and prescribed fires can make a significant contribution to ambient aerosol mass in many locations and seasons. In order to better understand the chemical properties of particles produced by combustion...

Global measurements of coarse-mode aerosol size distributions - first results from the Atmospheric Tomography Mission (ATom)

NASA Astrophysics Data System (ADS)

Weinzierl, B.; Dollner, M.; Schuh, H.; Brock, C. A.; Bui, T. V.; Gasteiger, J.; Froyd, K. D.; Schwarz, J. P.; Spanu, A.; Murphy, D. M.; Katich, J. M.; Kupc, A.; Williamson, C.

2016-12-01

Although coarse-mode aerosol (>1 µm diameter), composed mainly of mineral dust and sea-salt, is highly abundant over large regions of the world, these particles form a particularly poorly understood and characterized subset of atmospheric aerosol constituents. The NASA-sponsored Atmospheric Tomography Mission (ATom) is an unprecedented field program that investigates how human emissions affect air quality and climate change. ATom provides a singular opportunity to characterize the global coarse-mode size distribution by continuously profiling between 0.2 and 13 km with the NASA DC-8 research aircraft while traveling from the high Arctic down south the middle of the Pacific Ocean, to the Southern Ocean and back north over the Atlantic Ocean basin in four seasons. For ATom, the DC-8 aircraft has been equipped with multiple instruments to observe the composition of the air. The coarse mode and cloud particle size distribution is measured in-situ with a Cloud, Aerosol, and Precipitation Spectrometer (CAPS) mounted under the wing of the DC-8 research aircraft. The CAPS consists of an optical spectrometer providing size distributions in the size range between 0.5 and 50 µm and an imager detecting number concentration, size and shape of particles between 15 and 930 µm diameter. Early ATom flights indicated complicated vertical layering: over the sea, we regularly observed sea salt aerosol which extended from the ground up to 0.6-1 km altitude. In addition - depending on the location of the measurements - we frequently found layers with coarse mode aerosol originating from deserts and biomass burning aerosol aloft. In this study, we will present first results of coarse mode aerosol observations from the entire first ATom deployment in summer 2016. We will show vertical profiles of coarse mode aerosol number concentration, discuss their interhemispheric differences, and look into the question how frequently coarse-mode aerosol is externally mixed with submicron black

Biomass burning and biogenic aerosols in northern Australia during the SAFIRED campaign

NASA Astrophysics Data System (ADS)

Milic, Andelija; Mallet, Marc D.; Cravigan, Luke T.; Alroe, Joel; Ristovski, Zoran D.; Selleck, Paul; Lawson, Sarah J.; Ward, Jason; Desservettaz, Maximilien J.; Paton-Walsh, Clare; Williams, Leah R.; Keywood, Melita D.; Miljevic, Branka

2017-03-01

There is a lack of knowledge of how biomass burning aerosols in the tropics age, including those in the fire-prone Northern Territory in Australia. This paper reports chemical characterization of fresh and aged aerosols monitored during the 1-month-long SAFIRED (Savannah Fires in the Early Dry Season) field study, with an emphasis on the chemical signature and aging of organic aerosols. The campaign took place in June 2014 during the early dry season when the surface measurement site, the Australian Tropical Atmospheric Research Station (ATARS), located in the Northern Territory, was heavily influenced by thousands of wild and prescribed bushfires. ATARS was equipped with a wide suite of instrumentation for gaseous and aerosol characterization. A compact time-of-flight aerosol mass spectrometer was deployed to monitor aerosol chemical composition. Approximately 90 % of submicron non-refractory mass was composed of organic material. Ozone enhancement in biomass burning plumes indicated increased air mass photochemistry. The diversity in biomass burning emissions was illustrated through variability in chemical signature (e.g. wide range in f44, from 0.06 to 0.18) for five intense fire events. The background particulate loading was characterized using positive matrix factorization (PMF). A PMF-resolved BBOA (biomass burning organic aerosol) factor comprised 24 % of the submicron non-refractory organic aerosol mass, confirming the significance of fire sources. A dominant PMF factor, OOA (oxygenated organic aerosol), made up 47 % of the sampled aerosol, illustrating the importance of aerosol aging in the Northern Territory. Biogenic isoprene-derived organic aerosol factor was the third significant fraction of the background aerosol (28 %).

Characterization of particulate products for aging of ethylbenzene secondary organic aerosol in the presence of ammonium sulfate seed aerosol.

PubMed

Huang, Mingqiang; Zhang, Jiahui; Cai, Shunyou; Liao, Yingmin; Zhao, Weixiong; Hu, Changjin; Gu, Xuejun; Fang, Li; Zhang, Weijun

2016-09-01

Aging of secondary organic aerosol (SOA) particles formed from OH- initiated oxidation of ethylbenzene in the presence of high mass (100-300μg/m(3)) concentrations of (NH4)2SO4 seed aerosol was investigated in a home-made smog chamber in this study. The chemical composition of aged ethylbenzene SOA particles was measured using an aerosol laser time-of-flight mass spectrometer (ALTOFMS) coupled with a Fuzzy C-Means (FCM) clustering algorithm. Experimental results showed that nitrophenol, ethyl-nitrophenol, 2,4-dinitrophenol, methyl glyoxylic acid, 5-ethyl-6-oxo-2,4-hexadienoic acid, 2-ethyl-2,4-hexadiendioic acid, 2,3-dihydroxy-5-ethyl-6-oxo-4-hexenoic acid, 1H-imidazole, hydrated N-glyoxal substituted 1H-imidazole, hydrated glyoxal dimer substituted imidazole, 1H-imidazole-2-carbaldehyde, N-glyoxal substituted hydrated 1H-imidazole-2-carbaldehyde and high-molecular-weight (HMW) components were the predominant products in the aged particles. Compared to the previous aromatic SOA aging studies, imidazole compounds, which can absorb solar radiation effectively, were newly detected in aged ethylbenzene SOA in the presence of high concentrations of (NH4)2SO4 seed aerosol. These findings provide new information for discussing aromatic SOA aging mechanisms. Copyright © 2016. Published by Elsevier B.V.

RNA targeting with CRISPR-Cas13.

PubMed

Abudayyeh, Omar O; Gootenberg, Jonathan S; Essletzbichler, Patrick; Han, Shuo; Joung, Julia; Belanto, Joseph J; Verdine, Vanessa; Cox, David B T; Kellner, Max J; Regev, Aviv; Lander, Eric S; Voytas, Daniel F; Ting, Alice Y; Zhang, Feng

2017-10-12

RNA has important and diverse roles in biology, but molecular tools to manipulate and measure it are limited. For example, RNA interference can efficiently knockdown RNAs, but it is prone to off-target effects, and visualizing RNAs typically relies on the introduction of exogenous tags. Here we demonstrate that the class 2 type VI RNA-guided RNA-targeting CRISPR-Cas effector Cas13a (previously known as C2c2) can be engineered for mammalian cell RNA knockdown and binding. After initial screening of 15 orthologues, we identified Cas13a from Leptotrichia wadei (LwaCas13a) as the most effective in an interference assay in Escherichia coli. LwaCas13a can be heterologously expressed in mammalian and plant cells for targeted knockdown of either reporter or endogenous transcripts with comparable levels of knockdown as RNA interference and improved specificity. Catalytically inactive LwaCas13a maintains targeted RNA binding activity, which we leveraged for programmable tracking of transcripts in live cells. Our results establish CRISPR-Cas13a as a flexible platform for studying RNA in mammalian cells and therapeutic development.

New CRISPR–Cas systems from uncultivated microbes

DOE PAGES

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; ...

2016-12-22

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less

New CRISPR–Cas systems from uncultivated microbes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less

MGS TES Measurements of Dust and Ice Aerosol Behaviors

NASA Astrophysics Data System (ADS)

Clancy, R. T.; Wolff, M. J.; Christensen, P. R.

2000-10-01

The Thermal Emission Spectrometer (TES, Christensen et al., Science, v279, 1692-1697, 1998) on board the Mars Global Surveyor obtains simultaneous solar band and thermal IR spectral emission-phase-function (EPF) observations with global spatial coverage and continuous seasonal sampling. These measurements allow the first comprehensive study of the coupled visible scattering and thermal IR absorption properties of Mars atmospheric aerosols, a fundamental requirement towards defining opacities, particle sizes, and particle shapes for separable dust and water ice aerosol components. Furthermore, TES limb sounding at solar band and IR wavelengths may be analyzed in the context of these EPF column determinations to constrain the distinctive vertical profile behaviors of dust and ice clouds. We present initial radiative transfer analyses of TES visible and IR EPFs, which indicate surprisingly complex dust and ice aerosol behaviors over all latitudes and seasons. Distinctive backscattering peaks of variable intensity are observed for several types of water ice clouds, along with evidence for ice-coated dust aerosols. We will present a broad spatial and temporal sampling of solar band and spectral IR results for Mars atmospheric ice and dust aerosols observed over the 1998-2000 period. This research is supported by the MGS Participating Scientist and MED Science Data Analysis programs.

Vacuum FTIR study on the hygroscopicity of magnesium acetate aerosols

NASA Astrophysics Data System (ADS)

Wang, Na; Cai, Chen; He, Xiang; Pang, Shu-Feng; Zhang, Yun-Hong

2018-03-01

Hygroscopicity and volatility of secondary organic aerosol (SOA) are two important properties, which determine the composition, concentration, size, phase state of SOA and thus chemical and optical properties for SOA. In this work, magnesium acetate (Mg(Ac)2) aerosol was used as a simple SOA model in order to reveal relationship between hygroscopicity and volatility. A novel approach was set up based on a combination of a vacuum FTIR spectrometer and a home-made relative humidity (RH) controlling system. The striking advantage of this approach was that the RH and the compositions of aerosols could be obtained from a same IR spectrum, which guaranteed the synchronism between RH and spectral features on a sub-second scale. At the constant RH of 90% and 80% for 3000 s, the water content within Mg(Ac)2 aerosol particles decreased about 19.0% and 9.4% while there were 13.4% and 6.0% of acetate loss. This was attributed to a cooperation between volatile of acetic acid and Mg2 + hydrolysis in Mg(Ac)2 aerosols, which greatly suppressed the hygroscopicity of Mg(Ac)2 aerosols. When the RH changed with pulsed mode between 70% and 90%, hygroscopicity relaxation was observed for Mg(Ac)2 aerosols. Diffuse coefficient of water in the relaxation process was estimated to be 5 × 10- 12 m2·s- 1 for the Mg(Ac)2 aerosols. Combining the IR spectra analysis, the decrease in the diffuse coefficient of water was due to the formation of magnesium hydroxide accompanying acetic acid evaporation in the aerosols.

Optical extinction of highly porous aerosol following atmospheric freeze drying

NASA Astrophysics Data System (ADS)

Adler, Gabriela; Haspel, Carynelisa; Moise, Tamar; Rudich, Yinon

2014-06-01

Porous glassy particles are a potentially significant but unexplored component of atmospheric aerosol that can form by aerosol processing through the ice phase of high convective clouds. The optical properties of porous glassy aerosols formed from a freeze-dry cycle simulating freezing and sublimation of ice particles were measured using a cavity ring down aerosol spectrometer (CRD-AS) at 532 nm and 355 nm wavelength. The measured extinction efficiency was significantly reduced for porous organic and mixed organic-ammonium sulfate particles as compared to the extinction efficiency of the homogeneous aerosol of the same composition prior to the freeze-drying process. A number of theoretical approaches for modeling the optical extinction of porous aerosols were explored. These include effective medium approximations, extended effective medium approximations, multilayer concentric sphere models, Rayleigh-Debye-Gans theory, and the discrete dipole approximation. Though such approaches are commonly used to describe porous particles in astrophysical and atmospheric contexts, in the current study, these approaches predicted an even lower extinction than the measured one. Rather, the best representation of the measured extinction was obtained with an effective refractive index retrieved from a fit to Mie scattering theory assuming spherical particles with a fixed void content. The single-scattering albedo of the porous glassy aerosols was derived using this effective refractive index and was found to be lower than that of the corresponding homogeneous aerosol, indicating stronger relative absorption at the wavelengths measured. The reduced extinction and increased absorption may be of significance in assessing direct, indirect, and semidirect forcing in regions where porous aerosols are expected to be prevalent.

Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish.

PubMed

Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

2018-03-02

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites ( tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. Copyright © 2018 Hu et al.

Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish

PubMed Central

Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

2018-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites (tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. PMID:29295818

Structure and Engineering of Francisella novicida Cas9

PubMed Central

Hirano, Hisato; Gootenberg, Jonathan S.; Horii, Takuro; Abudayyeh, Omar O.; Kimura, Mika; Hsu, Patrick D.; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-01-01

Summary The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA, and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5′-NGG-3′ PAM, and used the structural information to create a variant that can recognize the more relaxed 5′-YG-3′ PAM. Furthermore, we demonstrated that pre-assembled FnCas9 ribonucleoprotein complexes can be microinjected into mouse zygotes to edit endogenous sites with the 5′-YG-3′ PAMs, thus expanding the target space of the CRISPR-Cas9 toolbox. PMID:26875867

Structure and Engineering of Francisella novicida Cas9.

PubMed

Hirano, Hisato; Gootenberg, Jonathan S; Horii, Takuro; Abudayyeh, Omar O; Kimura, Mika; Hsu, Patrick D; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-02-25

The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5'-NGG-3' PAM, and used the structural information to create a variant that can recognize the more relaxed 5'-YG-3' PAM. Furthermore, we demonstrated that the FnCas9-ribonucleoprotein complex can be microinjected into mouse zygotes to edit endogenous sites with the 5'-YG-3' PAM, thus expanding the target space of the CRISPR-Cas9 toolbox. Copyright © 2016 Elsevier Inc. All rights reserved.

Vacuum FTIR Observation on the Dynamic Hygroscopicity of Aerosols under Pulsed Relative Humidity.

PubMed

Leng, Chun-Bo; Pang, Shu-Feng; Zhang, Yun; Cai, Chen; Liu, Yong; Zhang, Yun-Hong

2015-08-04

A novel approach based on a combination of a pulse RH controlling system and a rapid scan vacuum FTIR spectrometer (PRHCS-RSVFTIR) was utilized to investigate dynamic hygroscopicity of two atmospheric aerosols: ammonium sulfate ((NH4)2SO4) and magnesium sulfate (MgSO4). In this approach, rapid-scan infrared spectra of water vapor and aerosols were obtained to determine relative humidity (RH) in sample cell and hygroscopic property of aerosols with a subsecond time resolution. Heterogeneous nucleation rates of (NH4)2SO4 were, for the first time, measured under low RH conditions (<35% RH). In addition, studies of MgSO4 aerosols revealed that water mass transport may be limited by different processes depending on RH values (surface limited at 40% < RH < 52% and bulk phase limited at RH < 40%). Furthermore, we are also the first to report water diffusion constants in micron size MgSO4 aerosols at very low RH values. Our results have shown that the PRHCS-RSVFTIR is well-suited for determination of hygroscopicity of atmospheric aerosols and water transport and nucleation kinetics of liquid aerosols.

Measurement of Fukushima Aerosol Debris in Sequim and Richland, WA and Ketchikan, AK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miley, Harry S.; Bowyer, Ted W.; Engelmann, Mark D.

2013-05-01

Aerosol collections were initiated at several locations by PNNL shortly after the Great East Japan Earthquake of May 2011. Aerosol samples were transferred to laboratory high-resolution gamma spectrometers for analysis. Similar to treaty monitoring stations operating across the Northern hemisphere, iodine and other isotopes which could be volatilized at high temperature were detected. Though these locations are not far apart, they have significant variations with respect to water, mountain-range placement, and local topography. Variation in computed source terms will be shown to bound the variability of this approach to source estimation.

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.

PubMed

Zhang, Quan; Ye, Yuzhen

2017-02-06

The CRISPR-Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR-Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don't contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems.

A new application of hierarchical cluster analysis to investigate organic peaks in bulk mass spectra obtained with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Middlebrook, A. M.; Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Modification, calibration, and performance of the Ultra-High Sensitivity Aerosol Spectrometer for particle size distribution and volatility measurements during the Atmospheric Tomography Mission (ATom) airborne campaign

NASA Astrophysics Data System (ADS)

Kupc, Agnieszka; Williamson, Christina; Wagner, Nicholas L.; Richardson, Mathews; Brock, Charles A.

2018-01-01

Atmospheric aerosol is a key component of the chemistry and climate of the Earth's atmosphere. Accurate measurement of the concentration of atmospheric particles as a function of their size is fundamental to investigations of particle microphysics, optical characteristics, and chemical processes. We describe the modification, calibration, and performance of two commercially available, Ultra-High Sensitivity Aerosol Spectrometers (UHSASs) as used on the NASA DC-8 aircraft during the Atmospheric Tomography Mission (ATom). To avoid sample flow issues related to pressure variations during aircraft altitude changes, we installed a laminar flow meter on each instrument to measure sample flow directly at the inlet as well as flow controllers to maintain constant volumetric sheath flows. In addition, we added a compact thermodenuder operating at 300 °C to the inlet line of one of the instruments. With these modifications, the instruments are capable of making accurate (ranging from 7 % for Dp < 0.07 µm to 1 % for Dp > 0.13 µm), precise (< ±1.2 %), and continuous (1 Hz) measurements of size-resolved particle number concentration over the diameter range of 0.063-1.0 µm at ambient pressures of > 1000 to 225 hPa, while simultaneously providing information on particle volatility.We assessed the effect of uncertainty in the refractive index (n) of ambient particles that are sized by the UHSAS assuming the refractive index of ammonium sulfate (n = 1.52). For calibration particles with n between 1.44 and 1.58, the UHSAS diameter varies by +4/-10 % relative to ammonium sulfate. This diameter uncertainty associated with the range of refractive indices (i.e., particle composition) translates to aerosol surface area and volume uncertainties of +8.4/-17.8 and +12.4/-27.5 %, respectively. In addition to sizing uncertainty, low counting statistics can lead to uncertainties of < 20 % for aerosol surface area and < 30 % for volume with 10 s time resolution. The UHSAS reduction in

Observation and analysis of aerosol optical properties and aerosol growth in two New Year celebrations in Manila Observatory (14.64N, 127.07E)

NASA Astrophysics Data System (ADS)

Lagrosas, N.; Bautista, D. L. B.; Miranda, J. P.

2016-12-01

Aerosol optical properties and growth were measured during 2014 and 2016 New Year celebrations at Manila Observatory, Philippines. Measurements were done using a USB2000 spectrometer from 22:00 of 31 December 2013 to 03:00 of 01 January 2014 and from 18:00 of 31 December 2015 to 05:30 01 January 2016. A xenon lamp was used as a light source 150m from the spectrometer. Fireworks and firecrackers were the main sources of aerosols during these festivities. Data were collected every 60s and 10s for 2014 and 2016 respectively. The aerosol volume size distribution was derived using the parametric inversion method proposed by Kaijser (1983). The method is performed by selecting 8 wavelengths from 387.30nm to 600.00nm. The reference intensities were obtained when firework activities were considerably low and the air was assumed to be relatively clean. Using Mie theory and assuming that the volume size distribution is a linear combination of 33 bimodal lognormal distribution functions with geometric mean radii between 0.003um and 1.2um, a least-square minimization process was implemented between measured optical depths and computed optical depths. The 2016 New Year distribution showed mostly a unimodal size distribution (mean radius = 0.3um) from 23:00 to 05:30 (Fig. 1a). The mean Angstrom coefficient value during the same time interval was approximately 0.75. This could be attributed to a constant RH (100%) during this time interval. A bimodal distribution was observed when RH value was 94% from 18:30 to 21:30. The transition to a unimodal distribution was observed at 21:00 when the RH value changes from 94% to 100%. In contrast to the 2016 New Year celebration, the 2014 size distribution was bimodal from 23:30 to 02:30 (Fig 1b). The bimodal distribution is the result of firework activities before New Year. Aerosol growth was evident when the size distribution became unimodal after 02:30 (mean radius = 1.1um). The mean Angstrom coefficient, when the size distribution is

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins.

PubMed

Rauch, Benjamin J; Silvis, Melanie R; Hultquist, Judd F; Waters, Christopher S; McGregor, Michael J; Krogan, Nevan J; Bondy-Denomy, Joseph

2017-01-12

Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a countermeasure, numerous phages are known that produce proteins to block the function of class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages. More than half of L. monocytogenes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR-Cas9 inactivation. Two of these inhibitors also blocked the widely used Streptococcus pyogenes Cas9 when assayed in Escherichia coli and human cells. These natural Cas9-specific "anti-CRISPRs" present tools that can be used to regulate the genome engineering activities of CRISPR-Cas9. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantification of Semi-Volatile gas-phase Organic Compounds (SVOCs) & Organic Aerosol species and the role of SVOCs in Secondary Organic Aerosol formation

NASA Astrophysics Data System (ADS)

Khan, M. H.; Holzinger, R.

2013-12-01

A Thermal-Desorption Proton-Transfer-Reaction Mass-Spectrometer (TD-PTR-MS) with different sampling systems (multi-stage denuder for gas phase and impact on a collector for aerosol phase) has been deployed in summer 2013 during the Southern Oxidant and Aerosol Study (SOAS) at the SEARCH ground site, Centreville, Alabama for in-situ gas phase and aerosol measurements on an hourly time resolution. A bunch of DB-1 column (0.53 mm x 5.0 μm) is used in the denuder for capturing the bulk of SVOCs and a collection-thermal-desorption (CTD) cell is used for collecting aerosol particles. Several hundreds semivolatile organic compounds (SVOCs) in gas phase and aerosol phases have been detected. The high mass resolution capabilities of ~5000, low detection limit (<0.05 pptv for gas species, <0.01 ng m-3 for aerosol species) and good physical and chemical characterization of SVOCs with the TD-PTR-MS allows constraining both, the quantity and the chemical composition. The SEARCH site was highly impacted by Biogenic Volatile Organic Compounds (BVOCs) and occasionally influenced by anthropogenic pollution. BVOCs and their oxidation products are capable of partitioning into the particle phase, so their simultaneous quantification in both phases has been used to determine the gas/particle-phase partitioning. Our results show the expected diurnal variation based on the changes of air temperature for many species. The results from this study give valuable insights into sources and processing of Secondary Organic Aerosols (SOAs) that can be used to improve parameterization algorithms in regional and global climate models.

Titan aerosol and gas experiment for the Huygens Probe

NASA Technical Reports Server (NTRS)

Carle, G. C.; Kojiro, D. R.; Oberbeck, V.; Ohara, B. J.; Pollack, J. B.; Valentin, J. R.; Bar-Nun, A.; Cohen, M. J.; Ferris, J. P.; Greenberg, J. M.

1991-01-01

The Cassini Mission is a joint undertaking of NASA and the European Space Agency (ESA) to explore the Saturnian System with a Saturn Orbiter and a Titan Probe. The launch vehicle and the Saturn Orbiter are the responsibility of NASA while the Huygens Probe (detachable Titan Probe) is the responsibility of ESA. The spacecraft will be launched in 1996 and the Huygens Probe will arrive at Titan in 2003. The Cassini Mission-Huygens Probe provides a unique opportunity to obtain detailed information about the atmosphere and, possibly, the surface of Titan. Titan possesses a substantial nitrogen atmosphere containing methane and many other organic compounds. Aerosols play an important role in the atmospheric processes on Titan. The Huygens Probe offers an opportunity to determine how organic particles are formed and grow which will clarify their role on Earth. A powerful analytical instrument, capable of addressing the above technology and other science questions, was recently proposed for the Huygens Probe. It is comprised of an aerosol and gas sampler and processor, and a gas chromatograph-ion mobility spectrometer. The instrument will be able to measure complex organics that make up the collected aerosols to the approximate 1 ppm level. Gases will be measured to approximately 10 ppb. Because the Titan atmosphere is expected to be quite complex, a gas chromatograph-ion mobility spectrometer is used to provide unequivocal identification of the components of the analytes. Further details of the science question to be investigated and the proposed instrument are described. The expected results and their implications are also addressed.

The spectroscopic search for the trace aerosols in the planetary atmospheres - the results of numerical simulations

NASA Astrophysics Data System (ADS)

Blecka, Maria I.

2010-05-01

The passive remote spectrometric methods are important in examinations the atmospheres of planets. The radiance spectra inform us about values of thermodynamical parameters and composition of the atmospheres and surfaces. The spectral technology can be useful in detection of the trace aerosols like biological substances (if present) in the environments of the planets. We discuss here some of the aspects related to the spectroscopic search for the aerosols and dust in planetary atmospheres. Possibility of detection and identifications of biological aerosols with a passive InfraRed spectrometer in an open-air environment is discussed. We present numerically simulated, based on radiative transfer theory, spectroscopic observations of the Earth atmosphere. Laboratory measurements of transmittance of various kinds of aerosols, pollens and bacterias were used in modeling.

Aromatic Structure in Simulates Titan Aerosol

NASA Technical Reports Server (NTRS)

Trainer, Melissa G.; Loeffler, M. J.; Anderson, C. M.; Hudson, R. L.; Samuelson, R. E.; Moore, M. A.

2011-01-01

Observations of Titan by the Cassini Composite Infrared Spectrometer (CIRS) between 560 and 20 per centimeter (approximately 18 to 500 micrometers) have been used to infer the vertical variations of Titan's ice abundances, as well as those of the aerosol from the surface to an altitude of 300 km [1]. The aerosol has a broad emission feature centered approximately at 140 per centimeter (71 micrometers). As seen in Figure 1, this feature cannot be reproduced using currently available optical constants from laboratory-generated Titan aerosol analogs [2]. The far-IR is uniquely qualified for investigating low-energy vibrational motions within the lattice structures of COITIDlex aerosol. The feature observed by CIRS is broad, and does not likely arise from individual molecules, but rather is representative of the skeletal movements of macromolecules. Since Cassini's arrival at Titan, benzene (C6H6) has been detected in the atmosphere at ppm levels as well as ions that may be polycyclic aromatic hydrocarbons (PAHs) [3]. We speculate that the feature may be a blended composite that can be identified with low-energy vibrations of two-dimensional lattice structures of large molecules, such as PAHs or nitrogenated aromatics. Such structures do not dominate the composition of analog materials generated from CH4 and N2 irradiation. We are performing studies forming aerosol analog via UV irradiation of aromatic precursors - specifically C6H6 - to understand how the unique chemical architecture of the products will influence the observable aerosol characteristics. The optical and chemical properties of the aromatic analog will be compared to those formed from CH4/N2 mixtures, with a focus on the as-yet unidentified far-IR absorbance feature. Preliminary results indicate that the photochemically-formed aromatic aerosol has distinct chemical composition, and may incorporate nitrogen either into the ring structure or adjoined chemical groups. These compositional differences are

Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.

PubMed

Oliveros, Juan C; Franch, Mònica; Tabas-Madrid, Daniel; San-León, David; Montoliu, Lluis; Cubas, Pilar; Pazos, Florencio

2016-07-08

The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Gas phase emissions from cooking processes and their secondary aerosol production potential

NASA Astrophysics Data System (ADS)

Klein, Felix; Platt, Stephen; Bruns, Emily; Termime-roussel, Brice; Detournay, Anais; Mohr, Claudia; Crippa, Monica; Slowik, Jay; Marchand, Nicolas; Baltensperger, Urs; Prevot, Andre; El Haddad, Imad

2014-05-01

Long before the industrial evolution and the era of fossil fuels, high concentrations of aerosol particles were alluded to in heavily populated areas, including ancient Rome and medieval London. Recent radiocarbon measurements (14C) conducted in modern megacities came as a surprise: carbonaceous aerosol (mainly organic aerosol, OA), a predominant fraction of particulate matter (PM), remains overwhelmingly non-fossil despite extensive fossil fuel combustion. Such particles are directly emitted (primary OA, POA) or formed in-situ in the atmosphere (secondary OA, SOA) via photochemical reactions of volatile organic compounds (VOCs). Urban levels of non-fossil OA greatly exceed the levels measured in pristine environments strongly impacted by biogenic emissions, suggesting a contribution from unidentified anthropogenic non-fossil sources to urban OA. Positive matrix factorization (PMF) techniques applied to ambient aerosol mass spectrometer (AMS, Aerodyne) data identify primary cooking emissions (COA) as one of the main sources of primary non-fossil OA in major cities like London (Allan et al., 2010), New York (Sun et al., 2011) and Beijing (Huang et al., 2010). Cooking processes can also emit VOCs that can act as SOA precursors, potentially explaining in part the high levels of oxygenated OA (OOA) identified by the AMS in urban areas. However, at present, the chemical nature of these VOCs and their secondary aerosol production potential (SAPP) remain virtually unknown. The approach adopted here involves laboratory quantification of PM and VOC emission factors from the main primary COA emitting processes and their SAPP. Primary emissions from deep-fat frying, vegetable boiling, vegetable frying and meat cooking for different oils, meats and vegetables were analysed under controlled conditions after ~100 times dilution. A high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) and a high resolution proton transfer time-of-flight mass spectrometer (PTR

Long-term variations of aerosol optical depth and aerosol radiative forcing over Iran based on satellite and AERONET data.

PubMed

Arkian, F; Nicholson, S E

2017-12-01

In this study, three different sensors of satellites including the Moderate Resolution Imaging Spectroradiometer (MODIS), Multi-angle Imaging SpectroRadiometer (MISR), and Total Ozone Mapping Spectrometer (TOMS) were used to study spatial and temporal variations of aerosols over ten populated cities in Iran. Also, the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model was used for analyzing the origins of air masses and their trajectory in the area. An increasing trend in aerosol concentration was observed in the most studied cities in Iran during 1979-2016. The cities in the western part of Iran had the highest annual mean of aerosol concentration. The highest aerosol optical depth (AOD) value (0.76 ± 0.51) was recorded in May 2012 over Ahvaz, and the lowest value (0.035 ± 0.27) was recorded in December 2013 over Tabriz. After Ahvaz, the highest AOD value was found over Tehran (annual mean 0.11 ± 0.20). The results show that AOD increases with increasing industrial activities, but the increased frequency of aerosols due to land degradation and desertification is more powerful in Iran. The trajectory analysis by the HYSPLIT model showed that the air masses come from Egypt, Syria, and Lebanon and passed over the Iraq and then reached to Iran during summer. Aerosol radiative forcing (ARF) has been analyzed for Zanjan (Aerosol Robotic Network site) during 2010-2013. The ARF at surface and top of the atmosphere was found to be ranging from - 79 to - 10W m -2 (average - 33.45 W m -2 ) and from - 25 to 6 W m -2 (average - 12.80 W m -2 ), respectively.

Changes in organic aerosol composition with aging inferred from aerosol mass spectra

NASA Astrophysics Data System (ADS)

Ng, N. L.; Canagaratna, M. R.; Jimenez, J. L.; Chhabra, P. S.; Seinfeld, J. H.; Worsnop, D. R.

2011-03-01

Organic aerosols (OA) can be separated with factor analysis of aerosol mass spectrometer (AMS) data into hydrocarbon-like OA (HOA) and oxygenated OA (OOA). We develop a new method to parameterize H:C of OOA in terms of f43 (ratio of m/z 43, mostly C2H3O+, to total signal in the component mass spectrum). Such parameterization allows the transformation of large database of ambient OOA components from the f44 (mostly CO2+, likely from acid groups) vs. f43 space ("triangle plot") (Ng et al., 2010) into the Van Krevelen diagram (H:C vs. O:C). Heald et al. (2010) suggested that the bulk composition of OA line up in the Van Krevelen diagram with a slope ~ -1; such slope can potentially arise from the physical mixing of HOA and OOA, and/or from chemical aging of these components. In this study, we find that the OOA components from all sites occupy an area in the Van Krevelen space, with the evolution of OOA following a shallower slope of ~ -0.5, consistent with the additions of both acid and alcohol functional groups without fragmentation, and/or the addition of acid groups with C-C bond breakage. The importance of acid formation in OOA evolution is consistent with increasing f44 in the triangle plot with photochemical age. These results provide a framework for linking the bulk aerosol chemical composition evolution to molecular-level studies.

Spaceborne Remote Sensing of Aerosol Type: Global Distribution, Model Evaluation and Translation into Chemical Speciation

NASA Astrophysics Data System (ADS)

Kacenelenbogen, M. S.; Tan, Q.; Johnson, M. S.; Burton, S. P.; Redemann, J.; Hasekamp, O. P.; Dawson, K. W.; Hair, J. W.; Ferrare, R. A.; Butler, C. F.; Holben, B. N.; Beyersdorf, A. J.; Ziemba, L. D.; Froyd, K. D.; Dibb, J. E.; Shingler, T.; Sorooshian, A.; Jimenez, J. L.; Campuzano Jost, P.; Jacob, D.; Kim, P. S.; Travis, K.; Lacagnina, C.

2016-12-01

It is essential to evaluate and refine aerosol classification methods applied to passive satellite remote sensing. We have developed an aerosol classification algorithm (called Specified Clustering and Mahalanobis Classification, SCMC) that assigns an aerosol type to multi-parameter retrievals by spaceborne, airborne or ground-based passive remote sensing instruments [1]. The aerosol types identified by our scheme are pure dust, polluted dust, urban-industrial/developed economy, urban-industrial/developing economy, dark biomass smoke, light biomass smoke and pure marine. We apply the SCMC method to inversions from the ground-based AErosol RObotic NETwork (AERONET [2]) and retrievals from the space-borne Polarization and Directionality of Earth's Reflectances instrument (POLDER, [3]). The POLDER retrievals that we use differ from the standard POLDER retrievals [4] as they make full use of multi-angle, multispectral polarimetric data [5]. We analyze agreement in the aerosol types inferred from both AERONET and POLDER and evaluate GEOS-Chem [6] simulations over the globe. Finally, we use in-situ observations from the SEAC4RS airborne field experiment to bridge the gap between remote sensing-inferred qualitative SCMC aerosol types and their corresponding quantitative chemical speciation. We apply the SCMC method to airborne in-situ observations from the NASA Langley Aerosol Research Group Experiment (LARGE, [7]) and the Differential Aerosol Sizing and Hygroscopicity Spectrometer Probe (DASH-SP, [8]) instruments; we then relate each coarsely defined SCMC type to a sum of percentage of individual aerosol species, using in-situ observations from the Particle Analysis by Laser Mass Spectrometry (PALMS, [9]), the Soluble Acidic Gases and Aerosol (SAGA, [10]), and the High - Resolution Time - of - Flight Aerosol Mass Spectrometer (HR ToF AMS, [11]). [1] Russell P. B., et al., JGR, 119.16 (2014) [2] Holben B. N., et al., RSE, 66.1 (1998) [3] Tanré D., et al., AMT, 4.7 (2011

Atmospheric soundings by SPICAM occultation observations: aerosol and ozone vertical profiles

NASA Astrophysics Data System (ADS)

Montmessin, F.

2005-12-01

The SPICAM instrument is a highly versatile, dual spectrometer probing both the UV and the NIR spectral region and is currently flying around Mars onboard Mars Express. Since the beginning of MEx operations, SPICAM has collected about thousand atmospheric profiles while observing in a solar or a stellar occultation mode. UV spectra bear the signatures of several species; i.e carbon dioxide, ozone and aerosols, while infrared spectra potentially bring information on atmospheric condensates and on water vapor. This presentation will focus on the measured aerosol, ozone and water vapor profiles. For the aerosol, we will emphasize the numerous observations made in the polar night and will also discuss some high altitude clouds discovered in the southern hemisphere. Ozone and water vapor profiles will be presented along with some General Circulation Model comparisons. This work has been supported by CNES.

CAS-Induced Difficulties in Learning Mathematics?

ERIC Educational Resources Information Center

Jankvist, Uffe Thomas; Misfeldt, Morten

2015-01-01

In recent years computer algebra systems (CAS) have become an integrated part of the upper secondary school mathematics program. Despite the many positive possibilities of CAS, there also seems to be a flip side of the coin in relation to actual difficulties in learning mathematics, not least because a strong dependence on CAS for mathematical…

Secondary organic aerosol formation from primary aliphatic amines with NO3 radical

NASA Astrophysics Data System (ADS)

Malloy, Q. G. J.; Qi, Li; Warren, B.; Cocker, D. R., III; Erupe, M. E.; Silva, P. J.

2009-03-01

Primary aliphatic amines are an important class of nitrogen containing compounds emitted from automobiles, waste treatment facilities and agricultural animal operations. A series of experiments conducted at the UC-Riverside/CE-CERT Environmental Chamber is presented in which oxidation of methylamine, ethylamine, propylamine, and butylamine with O3 and NO3 have been investigated. Very little aerosol formation is observed in the presence of O3 only. However, after addition of NO, and by extension NO3, large aerosol mass yields (~44% for butylamine) are seen. Aerosol generated was determined to be organic in nature due to the small fraction of NO and NO2 in the total signal (<1% for all amines tested) as detected by an aerosol mass spectrometer (AMS). We propose a reaction mechanism between carbonyl containing species and the parent amine leading to formation of particulate imine products. These findings can have significant impacts on rural communities with elevated nighttime PM loadings, when significant levels of NO3 exist.

Secondary organic aerosol formation from primary aliphatic amines with NO3 radical

NASA Astrophysics Data System (ADS)

Malloy, Q. G. J.; Qi, Li; Warren, B.; Cocker, D. R., III; Erupe, M. E.; Silva, P. J.

2008-07-01

Primary aliphatic amines are an important class of nitrogen containing compounds found to be emitted from automobiles, waste treatment facilities and agricultural animal operations. A series of experiments conducted at the UC-Riverside/CE-CERT Environmental Chamber is presented in which oxidation of methylamine, ethylamine, propylamine, and butylamine with NO3 has been investigated. Very little aerosol formation is observed in the presence of O3 only. However, after addition of NO, and by extension NO3, large yields of aerosol mass loadings (~44% for butylamine) are seen. Aerosol generated was determined to be organic in nature due to the small fraction of NO and NO2 in the total signal (<17% for all amines tested) as detected by an aerosol mass spectrometer (AMS). We propose a reaction mechanism between carbonyl containing species and the parent amine leading to formation of particulate imine products. These findings can have significant impacts on rural communities and lead to elevated nighttime PM loadings, when significant levels on NO3 exist.

[CAS General Standards 2012

ERIC Educational Resources Information Center

Council for the Advancement of Standards in Higher Education, 2011

2011-01-01

The mission of the Council for the Advancement of Standards in Higher Education (CAS) is to promote the improvement of programs and services to enhance the quality of student learning and development. CAS is a consortium of professional associations who work collaboratively to develop and promulgate standards and guidelines and to encourage…

X-ray spectrum of Cassiopeia A measured with the Einstein SSS. [Solid State Spectrometer

NASA Technical Reports Server (NTRS)

Becker, R. H.; Smith, B. W.; White, N. E.; Holt, S. S.; Boldt, E. A.; Mushotzky, R. F.; Serlemitsos, P. J.

1979-01-01

The solid state spectrometer (SSS) on the Einstein Observatory observed the X-ray spectrum of Cas A between 0.8 and 4.5 keV with a FWHM energy resolution of 160 eV. Line emission consistent with transitions of helium-like ions of Si, S, and Ar was well defined. Comparison between the data and the emission expected from a gas containing two distinct thermal components requires additional line emission from Mg, Al, Ca, and Fe. These results are discussed in the context of both equilibrium and nonequilibrium situations.

Secondary Organic Aerosol Formation and Aging in a Flow Reactor in the Forested Southeast US during SOAS

NASA Astrophysics Data System (ADS)

Hu, W.; Palm, B. B.; Hacker, L.; Campuzano Jost, P.; Day, D. A.; de Sá, S. S.; Ayres, B. R.; Draper, D.; Fry, J.; Ortega, A. M.; Kiendler-Scharr, A.; Pajunoja, A.; Virtanen, A.; Krechmer, J.; Canagaratna, M. R.; Thompson, S.; Yatavelli, R. L. N.; Stark, H.; Worsnop, D. R.; Martin, S. T.; Farmer, D.; Brown, S. S.; Jimenez, J. L.

2015-12-01

A major field campaign (Southern Oxidant and Aerosol Study, SOAS) was conducted in summer 2013 in a forested area in Centreville Supersite, AL (SEARCH network) in the southeast U.S. To investigate secondary organic aerosol (SOA) formation from biogenic volatile organic compounds (BVOCs), 3 oxidation flow reactors (OFR) were used to expose ambient air to oxidants and their output was analyzed by state-of-the-art gas and aerosol instruments including a High-Resolution Aerosol Mass Spectrometer (HR-AMS), a HR Proton-Transfer Reaction Time-of-Flight Mass Spectrometer (PTR-TOFMS), and Two HR-TOF Chemical Ionization Mass Spectrometers (HRToF-CIMS). Ambient air was exposed 24/7 to variable concentrations of each of the 3 main atmospheric oxidants (OH, NO3 radicals and O3) to investigate the oxidation of BVOCs (including isoprene derived epoxydiols, IEPOX) and SOA formation and aging. Effective OH exposures up to 1×1013 molec cm-3 s were achieved, equivalent to over a month of aging in the atmosphere. Multiple oxidation products from isoprene and monoterpenes including small gas-phase acids were observed in OH OFR. High SOA formation of up to 12 μg m-3 above ambient concentrations of 5 μg m-3 was observed under intermediate OH exposures, while very high OH exposures led to destruction of ~30% of ambient OA, indicating shifting contributions of functionalization vs. fragmentation, consistent with results from urban and terpene-dominated environments. The highest SOA enhancements were 3-4 times higher than ambient OA. More SOA is typically formed during nighttime when terpenes are higher and photochemistry is absent, and less during daytime when isoprene is higher, although the IEPOX pathway is suppressed in the OFR. SOA is also observed after exposure of ambient air to O3 or NO3, although the amounts and oxidation levels were lower than for OH. Formation of organic nitrates in the NO3 reaction will also be discussed.A major field campaign (Southern Oxidant and Aerosol

Light Source Effects on Aerosol Photoacoustic Spectroscopy Measurements

PubMed Central

Radney, James G.; Zangmeister, Christopher D.

2016-01-01

Photoacoustic spectroscopy measurements of flame-generated soot aerosol coated with small amounts of water yielded absorption enhancements that were dependent on the laser used: quasi-continuous wave (Q-CW, ≈ 650 ps pulse duration and 78 MHz repetition rate) versus continuous wave (CW). Water coating thickness was controlled by exposing the aerosol to a set relative humidity (RH). At ≈ 85 % RH, the mass of the soot particles increased by an amount comparable to a monolayer of water being deposited and enhanced the measured absorption by 36 % and 15 % for the Q-CW and CW lasers, respectively. Extinction measurements were also performed using a cavity ring-down spectrometer (extinction equals the sum of absorption and scattering) with a CW laser and negligible enhancement was observed at all RH. These findings demonstrate that source choice can impact measurements of aerosols with volatile coatings and that the absorption enhancements at high RH previously measured by Radney and Zangmeister (2015) [1] are the result of laser source used (Q-CW) and not from an increase in the particle absorption cross section. PMID:28066027

Using CRISPR-Cas systems as antimicrobials.

PubMed

Bikard, David; Barrangou, Rodolphe

2017-06-01

Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered using phages or phagemids as vectors. These principles establish CRISPR-Cas systems as potent and programmable antimicrobials, and open new avenues for the development of CRISPR-based tools for selective removal of bacterial pathogens and precise microbiome composition alteration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of the organic matter in submicron urban aerosols using a Thermo-Desorption Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (TD-PTR-TOF-MS)

NASA Astrophysics Data System (ADS)

Salvador, Christian Mark; Ho, T.-T.; Chou, Charles C.-K.; Chen, M.-J.; Huang, W.-R.; Huang, S.-H.

2016-09-01

Organic matter is the most complicated and unresolved major component of atmospheric aerosol particles. Its sources and global budget are still highly uncertain and thereby necessitate further research efforts with state-of-the-art instrument. This study employed a Thermo-Desorption Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (TD-PTR-TOF-MS) for characterization of ambient organic aerosols. First, five authentic standard substances, which include phthalic acid, levoglucosan, arabitol, cis-pinonic acid and glutaric acid, were utilized to examine the response of the instrument. The results demonstrated the linearity of the TD-PTR-TOF-MS signals against a range of mass loading of specific species on filters. However, it was found that significant fragmentation happened to those challenging compounds, although the proton-transfer-reaction (PTR) was recognized as a soft ionization technique. Consequently, quantitative characterization of aerosols with the TD-PTR-TOF-MS depended on the availability of the fragmentation pattern in mass spectra and the recovery rate with the quantification ion peak(s). The instrument was further deployed to analyze a subset of submicron aerosol samples collected at the TARO (Taipei Aerosol and Radiation Observatory) in Taipei, Taiwan during August 2013. The results were compared with the measurements from a conventional DRI thermo-optical carbon analyzer. The inter-comparison indicated that the TD-PTR-TOF-MS underestimated the mass of total organic matter (TOM) in aerosol samples by 27%. The underestimation was most likely due to the thermo-decomposition during desorption processes and fragmentation in PTR drift tube, where undetectable fragments were formed. Besides, condensation loss of low vapor pressure species in the transfer components was also responsible for the underestimation to a certain degree. Nevertheless, it was showed that the sum of the mass concentrations of the major detected ion peaks correlated strongly

Effects of local meteorology and aerosols on ozone and nitrogen dioxide retrievals from OMI and pandora spectrometers in Maryland, USA during DISCOVER-AQ 2011.

PubMed

Reed, Andra J; Thompson, Anne M; Kollonige, Debra E; Martins, Douglas K; Tzortziou, Maria A; Herman, Jay R; Berkoff, Timothy A; Abuhassan, Nader K; Cede, Alexander

An analysis is presented for both ground- and satellite-based retrievals of total column ozone and nitrogen dioxide levels from the Washington, D.C., and Baltimore, Maryland, metropolitan area during the NASA-sponsored July 2011 campaign of D eriving I nformation on S urface CO nditions from Column and VER tically Resolved Observations Relevant to A ir Q uality (DISCOVER-AQ). Satellite retrievals of total column ozone and nitrogen dioxide from the Ozone Monitoring Instrument (OMI) on the Aura satellite are used, while Pandora spectrometers provide total column ozone and nitrogen dioxide amounts from the ground. We found that OMI and Pandora agree well (residuals within ±25 % for nitrogen dioxide, and ±4.5 % for ozone) for a majority of coincident observations during July 2011. Comparisons with surface nitrogen dioxide from a Teledyne API 200 EU NO x Analyzer showed nitrogen dioxide diurnal variability that was consistent with measurements by Pandora. However, the wide OMI field of view, clouds, and aerosols affected retrievals on certain days, resulting in differences between Pandora and OMI of up to ±65 % for total column nitrogen dioxide, and ±23 % for total column ozone. As expected, significant cloud cover (cloud fraction >0.2) was the most important parameter affecting comparisons of ozone retrievals; however, small, passing cumulus clouds that do not coincide with a high (>0.2) cloud fraction, or low aerosol layers which cause significant backscatter near the ground affected the comparisons of total column nitrogen dioxide retrievals. Our results will impact post-processing satellite retrieval algorithms and quality control procedures.

Evaluation of Meteorological and Aerosol Sensing with small Unmanned Aerial Systems

NASA Astrophysics Data System (ADS)

Claussen, Johanna; Möhler, Ottmar; Leisner, Thomas; Brooks, Ian; Norris, Sarah; Brooks, Barbara; Hill, Martin; Haunold, Werner; Schrod, Jann; Danielczok, Anja

2013-04-01

Atmospheric aerosols have a large impact on the climate system due to their influence on the global radiation budget. Local aerosol sources such as vegetation, (bare) soil or industrial sites have to be quantified with high resolution data to validate aerosol transport models and improve the input for high resolution weather models. Our goal is to evaluate the use of Unmanned Aerial Systems (UAS) as a method for acquisition of high resolution meteorological and aerosol data. During the INUIT measurement campaign in August 2012 at mount Großer Feldberg near Frankfurt, Germany, several flights with different sensor packages were carried out. We measured basic meteorological parameters such as temperature, relative humidity and air pressure with miniaturized onboard sensors. In addition, the Compact Lightweight Aerosol Spectrometer Probe (CLASP) for aerosol size distribution measurement or the Electrostatic Aerosol Collector (EAC) for aerosol sample collection was installed on board. CLASP measures aerosol particles with diameters from 0.17 μm to 9.5 μm in up to 32 channels at a frequency of 10 Hz. The EAC collects air samples at 2 l/min onto a sample holder. After the flight the ice nuclei on the sample holder are activated and counted in the isothermal static diffusion chamber FRIDGE. The results from the INUIT campaign and additional calibration laboratory measurements show that UAS are a valuable platform for miniaturized sensors. The number of ice nuclei was determined with the EAC at 200m above ground level and compared to the reference measurement on the ground.

Evolution and classification of the CRISPR-Cas systems

PubMed Central

S. Makarova, Kira; H. Haft, Daniel; Barrangou, Rodolphe; J. J. Brouns, Stan; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; J. M. Mojica, Francisco; I. Wolf, Yuri; Yakunin, Alexander F.; van der Oost, John; V. Koonin, Eugene

2012-01-01

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a `polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci. PMID:21552286

Light Absorption of Brown Carbon Aerosol in the Pearl River Delta Region of China

NASA Astrophysics Data System (ADS)

Huang, X.

2015-12-01

X.F. Huang, J.F. Yuan, L.M. Cao, J. Cui, C.N. Huang, Z.J. Lan and L.Y. He Key Laboratory for Urban Habitat Environmental Science and Technology, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, ChinaCorresponding author. Tel.: +86 755 26032532; fax: +86 755 26035332. E-mail address: huangxf@pku.edu.cn (X. F. Huang). Abstract: The strong spectral dependence of light absorption of brown carbon (BrC) aerosol has been recognized in recent decades. The Absorption Angstrom Exponent (AAE) of ambient aerosol was widely used in previous studies to attribute light absorption of brown carbon at shorter wavelengths, with a theoretical assumption that the AAE of black carbon (BC) aerosol equals to unit. In this study, the AAE method was improved by statistical extrapolation based on ambient measurements in the polluted seasons in typical urban and rural areas in the Pearl River Delta (PRD) region of China. A three-wavelength photoacoustic soot spectrometer (PASS-3) and an aerosol mass spectrometer (AMS) were used to explore the relationship between the ambient measured AAE and the ratio of organic aerosol to BC aerosol, in order to extract the more realistic AAE by pure BC aerosol, which were found to be 0.86, 0.82 and 1.02 at 405nm and 0.70, 0.71, and 0.86 at 532nm in the campaigns of urban-winter, urban-fall, and rural-fall, respectively. Roadway tunnel experiment results further supported the effectiveness of the obtained AAE for pure BC aerosol. In addition, biomass burning experiments proved higher spectral dependence of more-BrC environment and further verified the reliability of the instruments' response. Then, the average light absorption contribution of BrC aerosol was calculated to be 11.7, 6.3 and 12.1% (with total relative uncertainty of 7.5, 6.9 and 10.0%) at 405nm and 10.0, 4.1 and 5.5% (with total relative uncertainty of 6.5, 8.6 and 15.4%) at 532nm of the three campaigns, respectively. These results indicate that the

CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein.

PubMed

Tang, Lichun; Zeng, Yanting; Du, Hongzi; Gong, Mengmeng; Peng, Jin; Zhang, Buxi; Lei, Ming; Zhao, Fang; Wang, Weihua; Li, Xiaowei; Liu, Jianqiao

2017-06-01

Previous works using human tripronuclear zygotes suggested that the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system could be a tool in correcting disease-causing mutations. However, whether this system was applicable in normal human (dual pronuclear, 2PN) zygotes was unclear. Here we demonstrate that CRISPR/Cas9 is also effective as a gene-editing tool in human 2PN zygotes. By injection of Cas9 protein complexed with the appropriate sgRNAs and homology donors into one-cell human embryos, we demonstrated efficient homologous recombination-mediated correction of point mutations in HBB and G6PD. However, our results also reveal limitations of this correction procedure and highlight the need for further research.

In Situ Single Particle Measurement of Atmospheric Aging of Carbonaceous Aerosols During CARES

NASA Astrophysics Data System (ADS)

Cahill, J. F.; Suski, K.; Hubbe, J.; Shilling, J.; Zaveri, R. A.; Springston, S. R.; Prather, K. A.

2011-12-01

Atmospheric aging of aerosols through photochemistry, heterogeneous reactions and aqueous processing can change their physical and chemical properties, impacting their gas uptake, radiative forcing, and activation of cloud nuclei. Understanding the timescale and magnitude of this aging process is essential for accurate aerosol-climate modeling and predictions. An aircraft aerosol time-of-flight mass spectrometer (A-ATOFMS) measured single particle mixing state during the Carbonaceous Aerosols and Radiative Effects Study (CARES) in the summer of 2010 over Sacramento, CA. On 6/23/10, flights in the morning and afternoon performed pseudo-Lagrangian sampling of the Sacramento urban plume. Carbonaceous particles from these flights were classified into 'aged' and 'fresh' classes based on their mixing state, with aged particles having more secondary species, such as nitrate and sulfate. In the morning flight, a clear decreasing trend in the ratio of fresh/aged particle types was seen as the flight progressed, whereas in the afternoon flight, the ratio was essentially constant. These data show that in the morning carbonaceous aerosols can become heavily oxidized in a few hours. Further analysis of particle mixing state and the timescale of carbonaceous aerosol aging will be presented

Chemical, physical, and optical evolution of biomass burning aerosols: a case study

NASA Astrophysics Data System (ADS)

Adler, G.; Flores, J. M.; Abo Riziq, A.; Borrmann, S.; Rudich, Y.

2011-02-01

In-situ chemical composition measurements of ambient aerosols have been used for characterizing the evolution of submicron aerosols from a large anthropogenic biomass burning (BB) event in Israel. A high resolution Time of Flight Aerosol Mass Spectrometer (HR-RES-TOF-AMS) was used to follow the chemical evolution of BB aerosols during a night-long, extensive nationwide wood burning event and during the following day. While these types of extensive BB events are not common in this region, burning of agricultural waste is a common practice. The aging process of the BB aerosols was followed through their chemical, physical and optical properties. Mass spectrometric analysis of the aerosol organic component showed that aerosol aging is characterized by shifting from less oxidized fresh BB aerosols to more oxidized aerosols. Evidence for aerosol aging during the day following the BB event was indicated by an increase in the organic mass, its oxidation state, the total aerosol concentration, and a shift in the modal particle diameter. The effective broadband refractive index (EBRI) was derived using a white light optical particle counter (WELAS). The average EBRI for a mixed population of aerosols dominated by open fires was m = 1.53(±0.03) + 0.07i(±0.03), during the smoldering phase of the fires we found the EBRI to be m = 1.54(±0.01) + 0.04i(±0.01) compared to m = 1.49(±0.01) + 0.02i(±0.01) of the aged aerosols during the following day. This change indicates a decrease in the overall aerosol absorption and scattering. Elevated levels of particulate Polycyclic Aromatic Hydrocarbons (PAHs) were detected during the entire event, which suggest possible implications for human health during such extensive event.

Measuring Aerosol Optical Properties with the Ozone Monitoring Instrument (OMI)

NASA Technical Reports Server (NTRS)

Veefkind, J. P.; Torres, O.; Syniuk, A.; Decae, R.; deLeeuw, G.

2003-01-01

The Ozone Monitoring Instrument (OMI) is the Dutch-Finnish contribution to the NASA EOS-Aura mission scheduled for launch in January 2004. OM1 is an imaging spectrometer that will measure the back-scattered Solar radiance between 270 an 500 nm. With its relatively high spatial resolution (13x24 sq km at nadir) and daily global coverage. OM1 will make a major contribution to our understanding of atmospheric chemistry and to climate research. OM1 will provide data continuity with the TOMS instruments. One of the pleasant surprises of the TOMS data record was its information on aerosol properties. First, only the absorbing aerosol index, which is sensitive to elevated lay- ers of aerosols such as desert dust and smoke aerosols, was derived. Recently these methods were further improved to yield aerosol optical thickness and single scattering albedo over land and ocean for 19 years of TOMS data (1979-1992,1997-2002), making it one of the longest and most valuable time series for aerosols presently available. Such long time series are essential to quantify the effect of aerosols on the Earth& climate. The OM1 instrument is better suited to measure aerosols than the TOMS instruments because of the smaller footprint, and better spectral coverage. The better capabilities of OMI will enable us to provide an improved aerosol product, but the knowledge will also be used for further analysis of the aerosol record from TOMS. The OM1 aerosol product that is currently being developed for OM1 combines the TOMS experience and the multi-spectral techniques that are used in the visible and near infrared. The challenge for this new product is to provide aerosol optical thickness and single scattering albedo from the near ultraviolet to the visible (330-500 nm) over land and ocean. In this presentation the methods for deriving the OM1 aerosol product will be presented. Part of these methods developed for OM1 can already be applied to TOMS data and results of such analysis will be shown.

Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer

NASA Astrophysics Data System (ADS)

Ruske, Simon; Topping, David O.; Foot, Virginia E.; Kaye, Paul H.; Stanley, Warren R.; Crawford, Ian; Morse, Andrew P.; Gallagher, Martin W.

2017-03-01

Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen.This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification.For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks).The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol.Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was

CRISPR-Cas9 Structures and Mechanisms.

PubMed

Jiang, Fuguo; Doudna, Jennifer A

2017-05-22

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems employ the dual RNA-guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific double-stranded breaks in target DNA. Target recognition strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target site, and subsequent R-loop formation and strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9-DNA interactions, and associated conformational changes. The use of CRISPR-Cas9 as an RNA-programmable DNA targeting and editing platform is simplified by a synthetic single-guide RNA (sgRNA) mimicking the natural dual trans-activating CRISPR RNA (tracrRNA)-CRISPR RNA (crRNA) structure. This review aims to provide an in-depth mechanistic and structural understanding of Cas9-mediated RNA-guided DNA targeting and cleavage. Molecular insights from biochemical and structural studies provide a framework for rational engineering aimed at altering catalytic function, guide RNA specificity, and PAM requirements and reducing off-target activity for the development of Cas9-based therapies against genetic diseases.

CRISPR-Cas: biology, mechanisms and relevance

PubMed Central

Hille, Frank

2016-01-01

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’. PMID:27672148

CRISPR-Cas: biology, mechanisms and relevance.

PubMed

Hille, Frank; Charpentier, Emmanuelle

2016-11-05

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes-termed spacers-into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent.This article is part of the themed issue 'The new bacteriology'. © 2016 The Authors.

Chemical composition and characteristics of ambient aerosols and rainwater residues during Indian summer monsoon: Insight from aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Chakraborty, Abhishek; Gupta, Tarun; Tripathi, Sachchida N.

2016-07-01

Real time composition of non-refractory submicron aerosol (NR-PM1) is measured via Aerosol mass spectrometer (AMS) for the first time during Indian summer monsoon at Kanpur, a polluted urban location located at the heart of Indo Gangetic Plain (IGP). Submicron aerosols are found to be dominated by organics followed by nitrate. Source apportionment of organic aerosols (OA) via positive matrix factorization (PMF) revealed several types of secondary/oxidized and primary organic aerosols. On average, OA are completely dominated by oxidized OA with a very little contribution from biomass burning OA. During rain events, PM1 concentration is decreased almost by 60%, but its composition remains nearly the same. Oxidized OA showed slightly more decrease than primary OAs, probably due to their higher hygroscopicity. The presence of organo nitrates (ON) is also detected in ambient aerosols. Apart from real-time sampling, collected fog and rainwater samples were also analyzed via AMS in offline mode and in the ICP-OES (Inductively coupled plasma - Optical emission spectrometry) for elements. The presence of sea salt, organo nitrates and sulfates has been observed. Rainwater residues are also dominated by organics but their O/C ratios are 15-20% lower than the observed values for ambient OA. Alkali metals such as Ca, Na, K are found to be most abundant in the rainwater followed by Zn. Rainwater residues are also found to be much less oxidized than the aerosols present inside the fog water, indicating presence of less oxidized organics. These findings indicate that rain can act as an effective scavenger of different types of pollutants even for submicron particle range. Rainwater residues also contain organo sulfates which indicate that some portion of the dissolved aerosols has undergone aqueous processing, possibly inside the cloud. Highly oxidized and possibly hygroscopic OA during monsoon period compared to other seasons (winter, post monsoon), indicates that they can act

Secondary organic aerosol formation from isoprene photooxidation

NASA Astrophysics Data System (ADS)

Kroll, J. H.; Ng, N. L.; Murphy, S. M.; Flagan, R. C.; Seinfeld, J. H.

2005-12-01

We report chamber studies of the formation of secondary organic aerosol (SOA) from the oxidation of isoprene (2-methyl-1,3-butadiene). Isoprene is the most abundant non-methane hydrocarbon emitted into the troposphere (source strength of ~500 Tg/year), so even small SOA yields may have a large impact on global SOA production. Reactions are carried out in Caltech's dual 28 m3 Teflon chambers, and aerosol growth is monitored by a differential mobility analyzer (DMA) and an Aerodyne time-of-flight aerosol mass spectrometer (AMS). Isoprene oxidation is initiated by the UV irradiation of isoprene in the presence of hydrogen peroxide, with NO added for high-NOx experiments. These conditions ensure that isoprene oxidation is initiated by reaction with the OH radical, with negligible interference from other oxidants (ozone, nitrate radicals, and O atoms). Aerosol growth is observed under both high-NOx and low-NOx conditions, at isoprene concentrations lower than measured in previous studies (down to 8 ppb). SOA yields are found to be in the range of 1-2%. Yields exhibit a complex dependence on NOx concentration, likely a result of changes in the chemistry of organic peroxy radicals. It is shown that condensable compounds are formed from further reactions of first-generation isoprene oxidation products; the rates and products of such gas-phase reactions are at present poorly understood. Additionally, measurements of SOA composition indicate that these products undergo reactions in the aerosol phase, leading to the formation of low-volatility oligomeric products.

Heavy Ion Formation in Titan's Ionosphere: Magnetospheric Introduction of Free Oxygen and Source of Titan's Aerosols?

NASA Technical Reports Server (NTRS)

Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Johnson, R. E.; Coates, A.; dePater, imke; Strom, Daphne; Simoes, F.; Steele, A.; Robb, F.

2007-01-01

With the recent discovery of heavy ions, positive and negative, by the Cassini Plasma Spectrometer (CAPS) instrument in Titan's ionosphere, it reveals new possibilities for aerosol formation at Titan and the introduction of free oxygen to the aerosol chemistry from Saturn's magnetosphere with Enceladus as the primary oxygen source. One can estimate whether the heavy ions in the ionosphere are of sufficient number to account for all the aerosols, under what conditions are favorable for heavy ion formation and how they are introduced as seed particles deeper in Titan's atmosphere where the aerosols form and eventually find themselves on Titan's surface where unknown chemical processes can take place. Finally, what are the possibilities with regard to their chemistry on the surface with some free oxygen present in their seed particles?

Rational Design of Mini-Cas9 for Transcriptional Activation.

PubMed

Ma, Dacheng; Peng, Shuguang; Huang, Weiren; Cai, Zhiming; Xie, Zhen

2018-04-20

Nuclease dead Cas9 (dCas9) has been widely used for modulating gene expression by fusing with different activation or repression domains. However, delivery of the CRISPR/Cas system fused with various effector domains in a single adeno-associated virus (AAV) remains challenging due to the payload limit. Here, we engineered a set of downsized variants of Cas9 including Staphylococcus aureus Cas9 (SaCas9) that retained DNA binding activity by deleting conserved functional domains. We demonstrated that fusing FokI nuclease domain to the N-terminal of the minimal SaCas9 (mini-SaCas9) or to the middle of the split mini-SaCas9 can trigger efficient DNA cleavage. In addition, we constructed a set of compact transactivation domains based on the tripartite VPR activation domain and self-assembled arrays of split SpyTag:SpyCatch peptides, which are suitable for fusing to the mini-SaCas9. Lastly, we produced a single AAV containing the mini-SaCas9 fused with a downsized transactivation domain along with an optimized gRNA expression cassette, which showed efficient transactivation activity. Our results highlighted a practical approach to generate down-sized CRISPR/Cas9 and gene activation systems for in vivo applications.

48 CFR 30.201-1 - CAS applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false CAS applicability. 30.201-1 Section 30.201-1 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS COST ACCOUNTING STANDARDS ADMINISTRATION CAS Program Requirements 30.201-1 CAS...

Fusion of SpCas9 to E. coli Rec A protein enhances CRISPR-Cas9 mediated gene knockout in mammalian cells.

PubMed

Lin, Lin; Petersen, Trine Skov; Jensen, Kristopher Torp; Bolund, Lars; Kühn, Ralf; Luo, Yonglun

2017-04-10

Mammalian cells repair double-strand DNA breaks (DSB) by a range of different pathways following DSB induction by the engineered clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein Cas9. While CRISPR-Cas9 thus enables predesigned modifications of the genome, applications of CRISPR-Cas9-mediated genome-editing are frequently hampered by the unpredictable and varying pathways for DSB repair in mammalian cells. Here we present a strategy of fusing Cas9 to recombinant proteins for fine-tuning of the DSB repair preferences in mammalian cells. By fusing Streptococcus Pyogenes Cas9 (SpCas9) to the recombinant protein A (Rec A, NP_417179.1) from Escherichia coli, we create a recombinant Cas9 protein (rSpCas9) which enhances the generation of indel mutations at DSB sites in mammalian cells, increases the frequency of DSB repair by homology-directed single-strand annealing (SSA), and represses homology-directed gene conversion by approximately 33%. Our study thus proves for the first time that fusing SpCas9 to recombinant proteins can influence the balance between DSB repair pathways in mammalian cells. This approach may form the basis for further investigations of the applications of recombinant Cas9 proteins to fine-tuning DSB repair pathways in eukaryotic cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of black carbon mixing state from traffic: Implications for aerosol optical properties

DOE PAGES

Willis, Megan D.; Healy, Robert M.; Riemer, Nicole; ...

2016-04-14

The climatic impacts of black carbon (BC) aerosol, an important absorber of solar radiation in the atmosphere, remain poorly constrained and are intimately related to its particle-scale physical and chemical properties. Using particle-resolved modelling informed by quantitative measurements from a soot-particle aerosol mass spectrometer, we confirm that the mixing state (the distribution of co-emitted aerosol amongst fresh BC-containing particles) at the time of emission significantly affects BC-aerosol optical properties even after a day of atmospheric processing. Both single particle and ensemble aerosol mass spectrometry observations indicate that BC near the point of emission co-exists with hydrocarbon-like organic aerosol (HOA) inmore » two distinct particle types: HOA-rich and BC-rich particles. The average mass fraction of black carbon in HOA-rich and BC-rich particle classes was < 0.1 and 0.8, respectively. Notably, approximately 90 % of BC mass resides in BC-rich particles. This new measurement capability provides quantitative insight into the physical and chemical nature of BC-containing particles and is used to drive a particle-resolved aerosol box model. Lastly, significant differences in calculated single scattering albedo (an increase of 0.1) arise from accurate treatment of initial particle mixing state as compared to the assumption of uniform aerosol composition at the point of BC injection into the atmosphere.« less

RNA Editing with CRISPR-Cas13

PubMed Central

Cox, David B.T.; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Franklin, Brian; Kellner, Max J.; Joung, Julia; Zhang, Feng

2017-01-01

Nucleic acid editing holds promise for treating genetic disease, particularly at the RNA level, where disease-relevant sequences can be rescued to yield functional protein products. Type VI CRISPR-Cas systems contain the programmable single-effector RNA-guided RNases Cas13. Here, we profile Type VI systems to engineer a Cas13 ortholog capable of robust knockdown and demonstrate RNA editing by using catalytically-inactive Cas13 (dCas13) to direct adenosine to inosine deaminase activity by ADAR2 to transcripts in mammalian cells. This system, referred to as RNA Editing for Programmable A to I Replacement (REPAIR), has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations. We further engineer this system to create a high specificity variant, REPAIRv2, that is 919 times more specific than REPAIRv1 as well as minimize the system to ease viral delivery. REPAIR presents a promising RNA editing platform with broad applicability for research, therapeutics, and biotechnology. PMID:29070703

The Reverse Transcriptases Associated with CRISPR-Cas Systems.

PubMed

Toro, Nicolás; Martínez-Abarca, Francisco; González-Delgado, Alejandro

2017-08-02

CRISPR (clustered regularly interspaced short palindromic repeats) and associated proteins (Cas) act as adaptive immune systems in bacteria and archaea. Some CRISPR-Cas systems have been found to be associated with putative reverse transcriptases (RT), and an RT-Cas1 fusion associated with a type III-B system has been shown to acquire RNA spacers in vivo. Nevertheless, the origin and evolutionary relationships of these RTs and associated CRISPR-Cas systems remain largely unknown. We performed a comprehensive phylogenetic analysis of these RTs and associated Cas1 proteins, and classified their CRISPR-Cas modules. These systems were found predominantly in bacteria, and their presence in archaea may be due to a horizontal gene transfer event. These RTs cluster into 12 major clades essentially restricted to particular phyla, suggesting host-dependent functioning. The RTs and associated Cas1 proteins may have largely coevolved. They are, therefore, subject to the same selection pressures, which may have led to coadaptation within particular protein complexes. Furthermore, our results indicate that the association of an RT with a CRISPR-Cas system has occurred on multiple occasions during evolution.

Biogenic influence on the composition and growth of summertime Arctic aerosol

NASA Astrophysics Data System (ADS)

Willis, M. D.; Burkart, J.; Thomas, J. L.; Koellner, F.; Schneider, J.; Bozem, H.; Hoor, P. M.; Aliabadi, A. A.; Schulz, H.; Herber, A. B.; Leaitch, R.; Abbatt, J.

2016-12-01

The summertime Arctic lower troposphere is a relatively pristine background aerosol environment dominated by nucleation and Aitken mode particles. Understanding the mechanisms that control the formation and growth of aerosol is crucial for our ability to predict cloud properties and therefore radiative balance and climate. We present aircraft-based observations of submicron aerosol composition from an aerosol mass spectrometer made during the NETCARE 2014 summertime arctic campaign, based in the Canadian High Arctic, at Resolute Bay, NU (74°N). Under stable and regionally influenced atmospheric conditions with low carbon monoxide and black carbon concentrations (< 100 ppbv and < 50 ng/m3, respectively), we observed organic aerosol (OA)-to-sulfate ratios ranging from 0.5 to > 6 with evidence for enhancement within the lower boundary layer. Methanesulfonic acid (MSA), a marker for the contribution of ocean-derived biogenic sulphur, was also observed in submicron aerosol. MSA-to-sulfate ratios ranged from near zero to 0.3 and tended to increase within the lower boundary layer, suggesting a contribution to aerosol loading from the ocean. In one notable case while flying in the lower boundary layer above open water in Lancaster Sound, we observed growth of small particles, <20 nm in diameter, into sizes above 50 nm. Aerosol growth was correlated with the presence of organic species, trimethylamine, and MSA in particles 80 nm and larger, where the organics were similar to those previously observed in marine settings. The organic-rich aerosol contributed significantly to particles active as cloud condensation nuclei (CCN, supersaturation = 0.6%). Our results highlight the potential importance of secondary organic aerosol formation and its role in growing nucleation mode aerosol into CCN-active sizes in this remote marine environment.

Aerosol-cloud interaction determined by satellite data over the Baltic Sea countries

NASA Astrophysics Data System (ADS)

Saponaro, Giulia; Kolmonen, Pekka; Sogacheva, Larisa; de Leeuw, Gerrit

2015-04-01

The present study investigates the use of long-term satellite data to assess the influence of aerosols upon cloud parameters over the Baltic Sea region. This particular area offers the contrast of a very clean environment (Fennoscandia) against a more polluted one (Germany, Poland). The datasets consists of Collection 6 Level 3 daily observations from 2002 to 2014 collected by the NASA's Moderate-Resolution Imaging Spectrometer (MODIS) instrument on-board the Aqua platform. The MODIS aerosol optical depth (AOD) product is used as a proxy for the number concentration of aerosol particles while the cloud effective radius (CER) and cloud optical thickness (COT) describe cloud microphysical and optical properties respectively. Satellite data have certain limitations, such as the restriction to summer season due to solar zenith angle restrictions and the known problem of the ambiguity of the aerosol-cloud interface, for instance. Through the analysis of a 12-years dataset, distribution maps provide information on a regional scale about the first aerosol indirect effect (AIE) by determining the aerosol-cloud interaction (ACI). The ACI is defined as the change in cloud optical depth or effective radius as a function of aerosol load for a fixed liquid water path (LWP). The focusing point of the current study is the evaluation of regional trends of ACI over the observed area of the Baltic Sea.

The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists.

PubMed

Wolter, Felix; Puchta, Holger

2018-06-01

Application of the bacterial CRISPR/Cas systems to eukaryotes is revolutionizing biology. Cas9 and Cas12 (previously called Cpf1) are widely used as DNA nucleases for inducing site-specific DNA breaks for different kinds of genome engineering applications, and in their mutated forms as DNA-binding proteins to modify gene expression. Moreover, histone modifications, as well as cytosine methylation or base editing, were achieved with these systems in plants. Recently, with the discovery of the nuclease Cas13a (previously called C2c2), molecular biologists have obtained a system that enables sequence-specific cleavage of single-stranded RNA molecules. The latest experiments with this and also the alternative Cas13b system demonstrate that these proteins can be used in a similar manner in eukaryotes for RNA manipulation as Cas9 and Cas12 for DNA manipulations. The first application of Cas13a for post-transcriptional regulation of gene expression in plants has been reported. Recent results show that the system is also applicable for combating viral infection in plants. As single-stranded RNA viruses are by far the most abundant class of viruses in plants, the application of this system is of special promise for crops. More interesting applications are imminent for plant biologists, with nuclease dead versions of Cas13 enabling the ability to visualize RNA molecules in vivo, as well as to edit different kinds of RNA molecules at specific bases by deamination or to modify them by conjugation. Moreover, by combining DNA- and RNA-directed systems, the most complex of changes in plant metabolism might be achievable. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Aerosol composition and the contribution of SOA formation over Mediterranean forests

NASA Astrophysics Data System (ADS)

Freney, Evelyn; Sellegri, Karine; Chrit, Mounir; Adachi, Kouji; Brito, Joel; Waked, Antoine; Borbon, Agnès; Colomb, Aurélie; Dupuy, Régis; Pichon, Jean-Marc; Bouvier, Laetitia; Delon, Claire; Jambert, Corinne; Durand, Pierre; Bourianne, Thierry; Gaimoz, Cécile; Triquet, Sylvain; Féron, Anaïs; Beekmann, Matthias; Dulac, François; Sartelet, Karine

2018-05-01

As part of the Chemistry-Aerosol Mediterranean Experiment (ChArMEx), a series of aerosol and gas-phase measurements were deployed aboard the SAFIRE ATR42 research aircraft in summer 2014. The present study focuses on the four flights performed in late June early July over two forested regions in the south of France. We combine in situ observations and model simulations to aid in the understanding of secondary organic aerosol (SOA) formation over these forested areas in the Mediterranean and to highlight the role of different gas-phase precursors. The non-refractory particulate species measured by a compact aerosol time-of-flight mass spectrometer (cToF-AMS) were dominated by organics (60 to 72 %) followed by a combined contribution of 25 % by ammonia and sulfate aerosols. The contribution from nitrate and black carbon (BC) particles was less than 5 % of the total PM1 mass concentration. Measurements of non-refractory species from off-line transmission electron microscopy (TEM) showed that particles have different mixing states and that large fractions (35 %) of the measured particles were organic aerosol containing C, O, and S but without inclusions of crystalline sulfate particles. The organic aerosol measured using the cToF-AMS contained only evidence of oxidized organic aerosol (OOA), without a contribution of fresh primary organic aerosol. Positive matrix factorization (PMF) on the combined organic-inorganic matrices separated the oxidized organic aerosol into a more-oxidized organic aerosol (MOOA), and a less-oxidized organic aerosol (LOOA). The MOOA component is associated with inorganic species and had higher contributions of m/z 44 than the LOOA factor. The LOOA factor is not associated with inorganic species and correlates well with biogenic volatile organic species measured with a proton-transfer-reaction mass spectrometer, such as isoprene and its oxidation products (methyl vinyl ketone, MVK; methacroleine, MACR; and isoprene hydroxyhydroperoxides

Spectroscopic studies of three Cepheids with high positive pulsation period increments: SZ Cas, BY Cas, and RU Sct

NASA Astrophysics Data System (ADS)

Usenko, I. A.; Klochkova, V. G.

2015-07-01

Three high-resolution spectra have been taken at different times with the 6-m SAO RAS telescope (LYNX and PFES spectrographs) for three Cepheids exhibiting high positive period increments: the small-amplitude (DCEPS) SZ Cas and BY Cas and the classical (DCEP) RU Sct. SZ Cas and RU Sct are members of the Galactic open clusters χ and h Per and Trump 35, respectively. Analysis of the spectra has shown that the interstellar Na I D1 and D2 lines in all objects are considerably stronger than the atmospheric ones and are redshifted in SZ Cas and BY Cas and blushifted in RU Sct. The core of the H α absorption line in BY Cas has an asymmetric knifelike shape, while RU Sct exhibits an intense emission in the blue wing of this line. Such phenomena are observed in long-period Cepheids and bright hypergiants with an extended envelope. In this case, the strong Mg Ib 5183.62 Å and Ba II 5853.67, 6141.713, and 6496.90 Å lines with low χlow in SZ Cas and RU Sct also show characteristic knifelike profiles with an asymmetry in the red region, while the Ba II 4934.095 Å line shows similar profiles in the blue one. The absorption lines of neutral atoms and singly ionized metals with different lowerlevel excitation potentials exhibit different degrees of asymmetry: from a pronounced one with secondary components in BY Cas (similar to those in the small-amplitude Cepheid BG Cru pulsating in the first overtone and having an envelope) to its insignificance or virtual absence in SZ Cas and RU Sct. Analysis of the secular changes in mean T eff determined from photometric color indices and spectra over the last 55 years for these stars has revealed periodic fluctuations of 200 K for SZ Cas and BY Cas and 500 K for RU Sct. For SZ Cas and RU Sct, T eff determined in some years from some color indices show much lower values, which together with the temperature fluctuations can be associated with mass loss and dust formation. Based on these facts, we hypothesize the existence of

Aerosol and CCN in southwest Saudi Arabia

NASA Astrophysics Data System (ADS)

Collins, Don; Li, Runjun; Axisa, Duncan; Kucera, Paul; Burger, Roelof

2010-05-01

As part of an ongoing study of the microphysical and dynamical controls on precipitation in southwest Saudi Arabia, a number of surface and aircraft-based instruments were used in summer / fall 2009 to measure the size distribution, hygroscopic properties, and cloud droplet nucleation efficiency of the local aerosol. Submicron size distributions were measured using differential mobility analyzers both on the ground and on board the aircraft, while an aerodynamic particle sizer and a forward scattering spectrometer probe were used to measure the supermicron size distributions on the ground and from on board the aircraft, respectively. Identical continuous flow cloud condensation nuclei counters were used to measure CCN spectra at the surface and aloft and a humidified tandem differential mobility analyzer was operated on the ground to measure size-resolved hygroscopicity. The aerosol in this arid environment is characterized by a persistent accumulation mode having hygroscopic and CCN efficiency properties consistent with a sulfate-rich aged aerosol. The particles in that background aerosol are generally sufficiently large and hygroscopic to activate at those supersaturations expected in the convective clouds responsible for most of the regional precipitation, which consequently acts as a lower bound on the resulting cloud droplet concentrations. Though the concentration, size distribution, and properties of the submicron aerosol generally changed very slowly over periods of several hours, abrupt ~doubling in concentration almost always accompanied the arrival of the sea breeze front that began along the Red Sea. Interestingly, the hygroscopicity and the shape of the size distribution differed little in the pre- and post-sea breeze air masses. The dust-dominated coarse mode typically contributed significantly more to the aerosol mass concentration than did the submicron mode and likely controlled the ice nuclei concentration, though no direct measurements were made

Vertical distribution of Martian aerosols from SPICAM/Mars-Express limb observations

NASA Astrophysics Data System (ADS)

Fedorova, A.; Korablev, O.; Bertaux, J.-L.; Rodin, A.; Perrier, S.; Moroz, V. I.

Limb spectroscopic observations provide invaluable information about vertical distribution of main atmospheric components in the Martian atmosphere, in particular vertical distribution and structure of aerosols, which play an important role in the heat balance of the planet. Only limited set of successful limb spectroscopic observations have been carried out on Mars so far, including those by MGS/TES spectrometer and Thermoscan and Auguste experiments of Phobos mission. Currently SPICAM instrument onboard Mars-Express spacecraft has accomplished several sequences of limb observations. First analysis of limb sounding data received by SPICAM IR and UV channels, which imply the presence of fine, deep, optically thin aerosol fraction extended over broad range of altitudes, is presented.

X-ray Vision for Aerosol Scientists: LCLS Snapshots of Soot (Narrated)

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2012-10-22

This short conceptual animation depicts how scientists can now simultaneously capture fractal morphology (structure), chemical composition and nanoscale imagery of individual aerosol particles in flight. These particles, known as "PM2.5" because they are smaller than 2.5 microns in diameter, affect climate by interacting with sunlight and impact human health by entering the lungs. The single LCLS laser pulses travel to the Atomic, Molecular and Optical Sciences (AMO) laboratory in the Near Experimental Hall. As we zoom in, we see deep inside a simplified aerosol inlet, where the complex fractal structure of the soot particles, each one completely unique, is shown.more » Individual soot particles are then delivered into the pulses of the LCLS beam, which destroys them. X-rays are scattered to the detector before the particle is destroyed, giving information about the morphology of the particle. Ion fragments released in the explosion are sent into a mass spectrometer, which measures their mass-to-charge ratio -- giving scientists information about the chemical composition of the particle. Many different particles are analyzed in this manner, allowing scientists to probe variations in the particles due to changes in their environment before being sent through the aerosol inlet. The final visual of aerosols emitted from a factory is representative of the goal that such LCLS aerosol dynamics experiments can provide critical feedback into modeling and understanding combustion, aerosol processes in manufacturing or aerosol effects on climate change.« less

X-ray Vision for Aerosol Scientists: LCLS Snapshots of Soot (Narrated)

ScienceCinema

None

2018-01-26

This short conceptual animation depicts how scientists can now simultaneously capture fractal morphology (structure), chemical composition and nanoscale imagery of individual aerosol particles in flight. These particles, known as "PM2.5" because they are smaller than 2.5 microns in diameter, affect climate by interacting with sunlight and impact human health by entering the lungs. The single LCLS laser pulses travel to the Atomic, Molecular and Optical Sciences (AMO) laboratory in the Near Experimental Hall. As we zoom in, we see deep inside a simplified aerosol inlet, where the complex fractal structure of the soot particles, each one completely unique, is shown. Individual soot particles are then delivered into the pulses of the LCLS beam, which destroys them. X-rays are scattered to the detector before the particle is destroyed, giving information about the morphology of the particle. Ion fragments released in the explosion are sent into a mass spectrometer, which measures their mass-to-charge ratio -- giving scientists information about the chemical composition of the particle. Many different particles are analyzed in this manner, allowing scientists to probe variations in the particles due to changes in their environment before being sent through the aerosol inlet. The final visual of aerosols emitted from a factory is representative of the goal that such LCLS aerosol dynamics experiments can provide critical feedback into modeling and understanding combustion, aerosol processes in manufacturing or aerosol effects on climate change.

Particle size distribution of the stratospheric aerosol from SCIAMACHY limb measurements

NASA Astrophysics Data System (ADS)

Rozanov, Alexei; Malinina, Elizaveta; Bovensmann, Heinrich; Burrows, John

2017-04-01

A crucial role of the stratospheric aerosols for the radiative budget of the Earth's atmosphere and the consequences for the climate change are widely recognized. A reliable knowledge on physical and optical properties of the stratospheric aerosols as well as on their vertical and spatial distributing is a key issue to assure a proper initialization and running conditions for climate models. On a global scale this information can only be gained from space borne measurements. While a series of past, present and future instruments provide extensive date sets of such aerosol characteristics as extinction coefficient or backscattering ratio, information on a size distribution of the stratospheric aerosols is sparse. One of the important sources on vertically and spatially resolved information on the particle size distribution of stratospheric aerosols is provided by space borne measurements of the scattered solar light in limb viewing geometry performed in visible, near-infrared and short-wave infrared spectral ranges. SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) instrument operated on the European satellite Envisat from 2002 to 2102 was capable of providing spectral information needed to retrieve parameters of aerosol particle size distributions. In this presentation we discuss the retrieval method, present first validation results with SAGE II data and analyze first data sets of stratospheric aerosol particle size distribution parameters obtained from SCIAMACHY limb measurements. The research work was performed in the framework of ROMIC (Role of the middle atmosphere in climate) project.

Comparisons of Spectral Aerosol Single Scattering Albedo in Seoul, South Korea

NASA Technical Reports Server (NTRS)

Mok, Jungbin; Krotkov, Nickolay A.; Torres, Omar; Jethva, Hiren; Loughman, Robert P.; Spinei, Elena; Campanelli, Monica; Li, Zhanqing; Go, Sujung; Labow, Gordon;

Non-linear photochemical pathways in laser-induced atmospheric aerosol formation

PubMed Central

Mongin, Denis; Slowik, Jay G.; Schubert, Elise; Brisset, Jean-Gabriel; Berti, Nicolas; Moret, Michel; Prévôt, André S. H.; Baltensperger, Urs; Kasparian, Jérôme; Wolf, Jean-Pierre

2015-01-01

We measured the chemical composition and the size distribution of aerosols generated by femtosecond-Terawatt laser pulses in the atmosphere using an aerosol mass spectrometer (AMS). We show that nitric acid condenses in the form of ammonium nitrate, and that oxidized volatile organics also contribute to particle growth. These two components account for two thirds and one third, respectively, of the dry laser-condensed mass. They appear in two different modes centred at 380 nm and 150 nm. The number concentration of particles between 25 and 300 nm increases by a factor of 15. Pre-existing water droplets strongly increase the oxidative properties of the laser-activated atmosphere, substantially enhancing the condensation of organics under laser illumination. PMID:26450172

Lidar sprectroscopy instrument (LISSI): An infrastructure facility for chemical aerosol profiling at the University of Hertfordshire

NASA Astrophysics Data System (ADS)

Tesche, Matthias; Tatarov, Boyan; Noh, Youngmin; Müller, Detlef

2018-04-01

The lidar development at the University of Hertfordshire explores the feasibility of using Raman backscattering for chemical aerosol profiling. This paper provides an overview of the new facility. A high-power Nd:YAG/OPO setup is used to excite Raman backscattering at a wide range of wavelengths. The receiver combines a spectrometer with a 32-channel detector or an ICCD camera to resolve Raman signals of various chemical compounds. The new facility will open new avenues for chemical profiling of aerosol pollution from measurements of Raman scattering by selected chemical compounds, provide data that allow to close the gap between optical and microphysical aerosol profiling with lidar and enables connecting lidar measurements to parameters used in atmospheric modelling.

The statistical distribution of aerosol properties in sourthern West Africa

NASA Astrophysics Data System (ADS)

Haslett, Sophie; Taylor, Jonathan; Flynn, Michael; Bower, Keith; Dorsey, James; Crawford, Ian; Brito, Joel; Denjean, Cyrielle; Bourrianne, Thierry; Burnet, Frederic; Batenburg, Anneke; Schulz, Christiane; Schneider, Johannes; Borrmann, Stephan; Sauer, Daniel; Duplissy, Jonathan; Lee, James; Vaughan, Adam; Coe, Hugh

2017-04-01

The population and economy in southern West Africa have been growing at an exceptional rate in recent years and this trend is expected to continue, with the population projected to more than double to 800 million by 2050. This will result in a dramatic increase in anthropogenic pollutants, already estimated to have tripled between 1950 and 2000 (Lamarque et al., 2010). It is known that aerosols can modify the radiative properties of clouds. As such, the entrainment of anthropogenic aerosol into the large banks of clouds forming during the onset of the West African Monsoon could have a substantial impact on the region's response to climate change. Such projections, however, are greatly limited by the scarcity of observations in this part of the world. As part of the Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa (DACCIWA) project, three research aircraft were deployed, each carrying equipment capable of measuring aerosol properties in-situ. Instrumentation included Aerosol Mass Spectrometers (AMS), Single Particle Soot Photometers (SP2), Condensation Particle Counters (CPC) and Scanning Mobility Particle Sizers (SMPS). Throughout the intensive aircraft campaign, 155 hours of scientific flights covered an area including large parts of Benin, Togo, Ghana and parts of Côte D'Ivoire. Approximately 70 hours were dedicated to the measurement of cloud-aerosol interactions, with many other flights producing data contributing towards this objective. Using datasets collected during this campaign period, it is possible to build a robust statistical understanding of aerosol properties in this region for the first time, including size distributions and optical and chemical properties. Here, we describe preliminary results from aerosol measurements on board the three aircraft. These have been used to describe aerosol properties throughout the region and time period encompassed by the DACCIWA aircraft campaign. Such statistics will be invaluable for improving future

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation.

PubMed

Kieper, Sebastian N; Almendros, Cristóbal; Behler, Juliane; McKenzie, Rebecca E; Nobrega, Franklin L; Haagsma, Anna C; Vink, Jochem N A; Hess, Wolfgang R; Brouns, Stan J J

2018-03-27

CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Disabling Cas9 by an anti-CRISPR DNA mimic.

PubMed

Shin, Jiyung; Jiang, Fuguo; Liu, Jun-Jie; Bray, Nicolas L; Rauch, Benjamin J; Baik, Seung Hyun; Nogales, Eva; Bondy-Denomy, Joseph; Corn, Jacob E; Doudna, Jennifer A

2017-07-01

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established. We show that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9-single-guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo-electron microscopy structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with a 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif. Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on preformed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.

Transformation of OODT CAS to Perform Larger Tasks

NASA Technical Reports Server (NTRS)

Mattmann, Chris; Freeborn, Dana; Crichton, Daniel; Hughes, John; Ramirez, Paul; Hardman, Sean; Woollard, David; Kelly, Sean

2008-01-01

A computer program denoted OODT CAS has been transformed to enable performance of larger tasks that involve greatly increased data volumes and increasingly intensive processing of data on heterogeneous, geographically dispersed computers. Prior to the transformation, OODT CAS (also alternatively denoted, simply, 'CAS') [wherein 'OODT' signifies 'Object-Oriented Data Technology' and 'CAS' signifies 'Catalog and Archive Service'] was a proven software component used to manage scientific data from spaceflight missions. In the transformation, CAS was split into two separate components representing its canonical capabilities: file management and workflow management. In addition, CAS was augmented by addition of a resource-management component. This third component enables CAS to manage heterogeneous computing by use of diverse resources, including high-performance clusters of computers, commodity computing hardware, and grid computing infrastructures. CAS is now more easily maintainable, evolvable, and reusable. These components can be used separately or, taking advantage of synergies, can be used together. Other elements of the transformation included addition of a separate Web presentation layer that supports distribution of data products via Really Simple Syndication (RSS) feeds, and provision for full Resource Description Framework (RDF) exports of metadata.

Chronic arsenic intoxication diagnostic score (CAsIDS).

PubMed

Dani, Sergio Ulhoa; Walter, Gerhard Franz

2018-01-01

Arsenic and its compounds are well-established, potent, environmentally widespread and persistent toxicants with metabolic, genotoxic, mutagenic, teratogenic, epigenetic and carcinogenic effects. Arsenic occurs naturally in the Earth's crust, but anthropogenic arsenic emissions have surmounted the emissions from important natural sources such as volcanism. Inorganic arsenicals exhibit acute and chronic toxicities in virtually all cell types and tissues, and hence arsenic intoxication affects multiple systems. Whereas acute arsenic intoxication is rare and relatively easy to diagnose, chronic arsenic intoxication (CAsI) is common but goes often misdiagnosed. Based on a review of the literature as well as our own clinical experience, we propose a chronic arsenic intoxication diagnostic score (CAsIDS). A distinctive feature of CAsIDS is the use of bone arsenic load as an essential criterion for the individual risk assessment of chronic arsenic intoxication, combined with a systemic clinical assessment. We present clinical examples where CAsIDS is applied for the diagnosis of CAsI, review the main topics of the toxicity of arsenic in different cell and organ systems and discuss the therapy and prevention of disease caused or aggravated by chronic arsenic intoxication. CAsIDS can help physicians establish the diagnosis of CAsI and associated conditions. Copyright © 2017 John Wiley & Sons, Ltd.

Sulfonamide inhibition studies of two β-carbonic anhydrases from the ascomycete fungus Sordaria macrospora, CAS1 and CAS2.

PubMed

Vullo, Daniela; Lehneck, Ronny; Pöggeler, Stefanie; Supuran, Claudiu T

2018-12-01

The two β-carbonic anhydrases (CAs, EC 4.2.1.1) recently cloned and purified from the ascomycete fungus Sordaria macrospora, CAS1 and CAS2, were investigated for their inhibition with a panel of 39 aromatic, heterocyclic, and aliphatic sulfonamides and one sulfamate, many of which are clinically used agents. CAS1 was efficiently inhibited by tosylamide, 3-fluorosulfanilamide, and 3-chlorosulfanilamide (K I s in the range of 43.2-79.6 nM), whereas acetazolamide, methazolamide, topiramate, ethoxzolamide, dorzolamide, and brinzolamide were medium potency inhibitors (K I s in the range of 360-445 nM). CAS2 was less sensitive to sulfonamide inhibitors. The best CAS2 inhibitors were 5-amino-1,3,4-thiadiazole-2-sulfonamide (the deacetylated acetazolamide precursor) and 4-hydroxymethyl-benzenesulfonamide, with K I s in the range of 48.1-92.5 nM. Acetazolamide, dorzolamide, ethoxzolamide, topiramate, sulpiride, indisulam, celecoxib, and sulthiame were medium potency CAS2 inhibitors (K I s of 143-857 nM). Many other sulfonamides showed affinities in the high micromolar range or were ineffective as CAS1/2 inhibitors. Small changes in the structure of the inhibitor led to important differences of the activity. As these enzymes may show applications for the removal of anthropically generated polluting gases, finding modulators of their activity may be crucial for designing environmental-friendly CO 2 capture processes.

Urban organic aerosols measured by single particle mass spectrometry in the megacity of London

NASA Astrophysics Data System (ADS)

Dall'Osto, M.; Harrison, R. M.

2011-02-01

During the month of October 2006, as part of the REPARTEE-I experiment (Regent's Park and Tower Environmental Experiment) an Aerosol Time-Of-Flight Mass Spectrometer (ATOFMS) was deployed at an urban background location in the city of London, UK. Fifteen particle types were classified, some of which were accompanied by Aerosol Mass Spectrometer (AMS) quantitative aerosol mass loading measurements (Dall'Osto et al., 2009a, b). In this manuscript the origins and properties of four particle types associated with locally generated aerosols, independent of the air mass type advected into London, are examined. One particle type, originating from lubricating oil (referred to as Ca-EC), was associated with morning rush hour traffic emissions. A second particle type, composed of both inorganic and organic species (called Na-EC-OC), was found enhanced in particle number concentration during evening time periods, and is likely to originate from a source operating at this time of day, or more probably from condensation of semi-volatile species, and contains both primary and secondary components. A third class, internally mixed with organic carbon and sulphate (called OC), was found to spike both in the morning and evenings. The fourth class (SOA-PAH) exhibited maximum frequency during the warmest part of the day, and a number of factors point towards secondary production from traffic-related volatile aromatic compounds. Single particle mass spectra of this particle type showed an oxidized polycyclic aromatic compound signature. Finally, a comparison of ATOFMS particle class data is made with factors obtained by Positive Matrix Factorization from AMS data.. Both the Ca-EC and OC particle types correlate with the AMS HOA primary organic fraction (R2 = 0.65 and 0.50 respectively), and Na-EC-OC, but not SOA-PAH, which correlates weakly with the AMS OOA secondary organic aerosol factor (R2 = 0.35). A detailed analysis was conducted to identify ATOFMS particle type(s) representative

Simultaneous measurement of sulfur and lead isotopes in sulfides using nanosecond laser ablation coupled with two multi-collector inductively coupled plasma mass spectrometers

NASA Astrophysics Data System (ADS)

Yuan, Honglin; Liu, Xu; Chen, Lu; Bao, Zhian; Chen, Kaiyun; Zong, Chunlei; Li, Xiao-Chun; Qiu, Johnson Wenhong

2018-04-01

We herein report the coupling of a nanosecond laser ablation system with a large-scale multi-collector inductively coupled plasma mass spectrometer (Nu1700 MC-ICPMS, NP-1700) and a conventional Nu Plasma II MC-ICPMS (NP-II) for the simultaneous laser ablation and determination of in situ S and Pb isotopic compositions of sulfide minerals. We found that the required aerosol distribution between the two spectrometers depended on the Pb content of the sample. For example, for a sulfide containing 100-3000 ppm Pb, the aerosol was distributed between the NP-1700 and the NP-II spectrometers in a 1:1 ratio, while for lead contents >3000 and <100 ppm, these ratios were 5:1 and 1:3, respectively. In addition, S isotopic analysis showed a pronounced matrix effect, so a matrix-matched external standard was used for standard-sample bracketing correction. The NIST NBS 977 (NBS, National Bureau of Standards; NIST, National Institute of Standards & Technology) Tl (thallium) dry aerosol internal standard and the NIST SRM 610 (SRM, standard reference material) external standard were employed to obtain accurate results for the analysis of Pb isotopes. In tandem experiments where airflow conditions were similar to those employed during stand-alone analyses, small changes in the aerosol carrier gas flow did not significantly influence the accurate determination of S and Pb isotope ratios. In addition, careful optimization of the flow ratio of the aerosol carrier (He) and makeup (Ar) gases to match stand-alone analytical conditions allowed comparable S and Pb isotope ratios to be obtained within an error of 2 s analytical uncertainties. Furthermore, the results of tandem analyses obtained using our method were consistent with those of previously reported stand-alone techniques for the S and Pb isotopes of chalcopyrite, pyrite, galena, and sphalerite, thus indicating that this method is suitable for the simultaneous analysis of S and Pb isotopes of natural sulfide minerals, and provides

Evolution of Asian aerosols during transpacific transport in INTEX-B

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunlea, E. J.; DeCarlo, Peter; Aiken, Allison

2009-10-01

Measurements of aerosol composition were made with an Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) on board the NSF/NCAR C-130 aircraft as part of the Intercontinental Chemical Transport Experiment Phase B 5 (INTEX-B) field campaign over the Eastern Pacific Ocean. The HR-ToF-AMS measurements of non-refractory submicron aerosol mass are shown to compare well with other aerosol instrumentation in the INTEX-B field study. Two case studies are described for pollution layers transported across the Pacific from the Asian continent, intercepted 3–4 days and 7–10 days downwind of Asia, respectively. Aerosol chemistry is shown to 10 be a robust tracer formore » air masses originating in Asia, specifically the presence of sulfate dominated aerosol is a distinguishing feature of Asian pollution layers that have been transported to the Eastern Pacific. We examine the time scales of processing for sulfate and organic aerosol in the atmosphere and show that our observations confirm a conceptual model for transpacific transport from Asia proposed by Brock et al. (2004). 15 Our observations of both sulfate and organic aerosol in aged Asian pollution layers are consistent with fast formation near the Asian continent, followed by washout during lofting and subsequent transformation during transport across the Pacific. Our observations are the first atmospheric measurements to indicate that although secondary organic aerosol (SOA) formation from pollution happens on the timescale of one day, 20 the oxidation of organic aerosol continues at longer timescales in the atmosphere. Comparisons with chemical transport models of data from the entire campaign reveal an under-prediction of SOA mass in the MOZART model, but much smaller discrepancies with the GEOS-Chem model than found in previous studies over the Western Pacific. No evidence is found to support a previous hypothesis for significant secondary 25 organic aerosol formation in the free

Ambient measurement of fluorescent aerosol particles with a WIBS in the Yangtze River Delta of China: potential impacts of combustion-related aerosol particles

NASA Astrophysics Data System (ADS)

Yu, Xiawei; Wang, Zhibin; Zhang, Minghui; Kuhn, Uwe; Xie, Zhouqing; Cheng, Yafang; Pöschl, Ulrich; Su, Hang

2016-09-01

Fluorescence characteristics of aerosol particles in a polluted atmosphere were studied using a wideband integrated bioaerosol spectrometer (WIBS-4A) in Nanjing, Yangtze River Delta area of China. We observed strong diurnal and day-to-day variations of fluorescent aerosol particles (FAPs). The average number concentrations of FAPs (1-15 µm) detected in the three WIBS measurement channels (FL1: 0.6 cm-3, FL2: 3.4 cm-3, FL3: 2.1 cm-3) were much higher than those observed in forests and rural areas, suggesting that FAPs other than bioaerosols were detected. We found that the number fractions of FAPs were positively correlated with the black carbon mass fraction, especially for the FL1 channel, indicating a large contribution of combustion-related aerosols. To distinguish bioaerosols from combustion-related FAPs, we investigated two classification schemes for use with WIBS data. Our analysis suggests a strong size dependence for the fractional contributions of different types of FAPs. In the FL3 channel, combustion-related particles seem to dominate the 1-2 µm size range while bioaerosols dominate the 2-5 µm range. The number fractions of combustion-related particles and non-combustion-related particles to total aerosol particles were ˜ 11 and ˜ 5 %, respectively.

RNA editing with CRISPR-Cas13.

PubMed

Cox, David B T; Gootenberg, Jonathan S; Abudayyeh, Omar O; Franklin, Brian; Kellner, Max J; Joung, Julia; Zhang, Feng

2017-11-24

Nucleic acid editing holds promise for treating genetic disease, particularly at the RNA level, where disease-relevant sequences can be rescued to yield functional protein products. Type VI CRISPR-Cas systems contain the programmable single-effector RNA-guided ribonuclease Cas13. We profiled type VI systems in order to engineer a Cas13 ortholog capable of robust knockdown and demonstrated RNA editing by using catalytically inactive Cas13 (dCas13) to direct adenosine-to-inosine deaminase activity by ADAR2 (adenosine deaminase acting on RNA type 2) to transcripts in mammalian cells. This system, referred to as RNA Editing for Programmable A to I Replacement (REPAIR), which has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations. We further engineered this system to create a high-specificity variant and minimized the system to facilitate viral delivery. REPAIR presents a promising RNA-editing platform with broad applicability for research, therapeutics, and biotechnology. Copyright © 2017, American Association for the Advancement of Science.

Effects of Using a Computer Algebra System (CAS) on Junior College Students' Attitudes towards CAS and Achievement in Mathematics

ERIC Educational Resources Information Center

Leng, Ng Wee; Choo, Kwee Tiow; Soon, Lau Hock; Yi-Huak, Koh; Sun, Yap Yew

2005-01-01

This study examines the effects of using Texas Instruments' Voyage 200 calculator (V200), a graphing calculator with a built-in computer algebra system (CAS), on attitudes towards CAS and achievement in mathematics of junior college students (17 year olds). Students' attitudes towards CAS were examined using a 40-item Likert-type instrument…

Photochemical processing of organic aerosol at nearby continental sites: contrast between urban plumes and regional aerosol

NASA Astrophysics Data System (ADS)

Slowik, J. G.; Brook, J.; Chang, R. Y.-W.; Evans, G. J.; Hayden, K.; Jeong, C.-H.; Li, S.-M.; Liggio, J.; Liu, P. S. K.; McGuire, M.; Mihele, C.; Sjostedt, S.; Vlasenko, A.; Abbatt, J. P. D.

2010-10-01

As part of the BAQS-Met 2007 field campaign, Aerodyne time-of-flight aerosol mass spectrometers (ToF-AMS) were deployed at two sites in southwestern Ontario from 17 June to 11 July, 2007. One instrument was located at Harrow, ON, a rural, agriculture-dominated area approximately 40 km southeast of the Detroit/Windsor/Windsor urban area and 5 km north of Lake Erie. The second instrument was located at Bear Creek, ON, a rural site approximately 70 km northeast of the Harrow site and 50 km east of Detroit/Windsor. Positive matrix factorization analysis of the combined organic mass spectral dataset yields factors related to secondary organic aerosol (SOA), direct emissions, and uptake processes. This is the first application of PMF to simultaneous AMS measurements at different sites, an approach which allows for self-consistent, direct comparison of the datasets. Case studies are utilized to investigate processing of SOA from (1) fresh emissions from Detroit/Windsor and (2) regional aerosol during periods of inter-site flow. A strong correlation is observed between SOA/excess CO and photochemical age as represented by the NOx/NOy ratio for Detroit/Windsor outflow. Although this correlation is not evident for more aged air, measurements at the two sites during inter-site transport nevertheless show evidence of continued atmospheric processing by SOA production.

Chemical composition of Titan's aerosols analogues characterized with a systematic pyrolysis-gas chromatography-mass spectrometry characterization

NASA Astrophysics Data System (ADS)

Szopa, Cyril; Raulin, Francois; Coll, Patrice; Cabane, Michel; GCMS Team

2014-05-01

The in situ chemical characterization of Titan's atmosphere was achieved in 2005 with two instruments present onboard the Huygens atmospheric probe : the Aerosol Collector and Pyrolyzer (ACP) devoted to collect and pyrolyse Titan's aerosols ; the Gas Chromatograph-Mass Spectrometer (GCMS) experiment devoted to analyze gases collected in the atmosphere or coming from the aerosols pyrolysis. The GCMS was developed by Hasso Niemann in the filiation of the quadrupole mass spectrometers he built for several former space missions. The main objectives were to : determine the concentration profile of the most abundant chemical species; seek for minor atmospheric organic species not detected with remote observations ; give a first view of the organic aerosols structure; characterize the condensed volatiles present at the surface (e.g. lakes) in case of survival of the probe to the landing impact. Taking into account for the potential complexity of the gaseous samples to be analyzed, it was decided to couple to the MS analyzer a gas chromatograph capable to separate volatile species from light inorganic molecules and noble gases, to organic compounds including aromatics. This was the first GCMS analyzer that worked in an extraterrestrial environment since the Viking missions on Mars. Even if the GCMS coupling mode did not provide any result of interest, it has been demonstrated to be functional during the Huygens descent. But, the direct MS analysis of the atmosphere, and the pyrolysis-MS analysis of aerosols allowed to make great discoveries which are still of primary importance to describe the Titan's lower atmosphere composition. This contribution aims at presenting this instrument that worked in the Titan's atmosphere, and summarizing the most important discoveries it allowed.

Airborne single particle mass spectrometers (SPLAT II & miniSPLAT) and new software for data visualization and analysis in a geo-spatial context.

PubMed

Zelenyuk, Alla; Imre, Dan; Wilson, Jacqueline; Zhang, Zhiyuan; Wang, Jun; Mueller, Klaus

2015-02-01

Understanding the effect of aerosols on climate requires knowledge of the size and chemical composition of individual aerosol particles-two fundamental properties that determine an aerosol's optical properties and ability to serve as cloud condensation or ice nuclei. Here we present our aircraft-compatible single particle mass spectrometers, SPLAT II and its new, miniaturized version, miniSPLAT that measure in-situ and in real-time the size and chemical composition of individual aerosol particles with extremely high sensitivity, temporal resolution, and sizing precision on the order of a monolayer. Although miniSPLAT's size, weight, and power consumption are significantly smaller, its performance is on par with SPLAT II. Both instruments operate in dual data acquisition mode to measure, in addition to single particle size and composition, particle number concentrations, size distributions, density, and asphericity with high temporal resolution. We also present ND-Scope, our newly developed interactive visual analytics software package. ND-Scope is designed to explore and visualize the vast amount of complex, multidimensional data acquired by our single particle mass spectrometers, along with other aerosol and cloud characterization instruments on-board aircraft. We demonstrate that ND-Scope makes it possible to visualize the relationships between different observables and to view the data in a geo-spatial context, using the interactive and fully coupled Google Earth and Parallel Coordinates displays. Here we illustrate the utility of ND-Scope to visualize the spatial distribution of atmospheric particles of different compositions, and explore the relationship between individual particle compositions and their activity as cloud condensation nuclei.

[CRISPR/CAS9, the King of Genome Editing Tools].

PubMed

Bannikov, A V; Lavrov, A V

2017-01-01

The discovery of CRISPR/Cas9 brought a hope for having an efficient, reliable, and readily available tool for genome editing. CRISPR/Cas9 is certainly easy to use, while its efficiency and reliability remain the focus of studies. The review describes the general principles of the organization and function of Cas nucleases and a number of important issues to be considered while planning genome editing experiments with CRISPR/Cas9. The issues include evaluation of the efficiency and specificity for Cas9, sgRNA selection, Cas9 variants designed artificially, and use of homologous recombination and nonhomologous end joining in DNA editing.

Chemical Characteristics of Particulate Matter from Vehicle emission using High Resolution Time of Flight Aerosol Mass Spectrometer (HR-ToF-AMS)

NASA Astrophysics Data System (ADS)

Park, T.; Lee, T.; Kang, S.; Lee, J.; Kim, J.; Son, J.; Yoo, H. M.; Kim, K.; Park, G.

2015-12-01

Car emissions are major contributors of particulate matter (PM) in the urban environment and effects of air pollution, climate change, and human activities. By increasing of interest in research of car emission for assessment of the PM control, it became require to understand the chemical composition and characteristics of the car exhaust gases and particulate matter. To understand car emission characteristics of PM, we will study PM of car emissions for five driving modes (National Institute Environmental Research (NIER)-5, NIER-9, NIER-12, NIER-14) and three fixed speed driving modes (30km/h, 70km/h, 110km/h) using different fuel types (gasoline, diesel, and LPG) at Transportation Pollution Research Center (TPRC) of NIER in Incheon, South Korea. PM chemical composition of car emission was measured for concentrations of organics, sulfate, nitrate, ammonium, PAHs, oxidation states and size distribution using an Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and engine exhaust particle sizer (EEPS) on real-time. In the study, organics concentration was dominated for all cases of driving modes and the concentration of organics was increased in 110km/h fixed speed mode for gasoline and diesel. The presentation will provide an overview of the chemical composition of PM in the car emissions.

Effect of secondary organic aerosol coating thickness on the real-time detection and characterization of biomass-burning soot by two particle mass spectrometers

DOE PAGES

Ahern, Adam T.; Subramanian, Ramachandran; Saliba, Georges; ...

2016-12-22

Biomass burning is a large source of light-absorbing refractory black carbon (rBC) particles with a wide range of morphologies and sizes. The net radiative forcing from these particles is strongly dependent on the amount and composition of non-light-absorbing material internally mixed with the rBC and on the morphology of the mixed particles. Understanding how the mixing state and morphology of biomass-burning aerosol evolves in the atmosphere is critical for constraining the influence of these particles on radiative forcing and climate. We investigated the response of two commercial laser-based particle mass spectrometers, the vacuum ultraviolet (VUV) ablation LAAPTOF and the IRmore » vaporization SP-AMS, to monodisperse biomass-burning particles as we sequentially coated the particles with secondary organic aerosol (SOA) from α-pinene ozonolysis. We studied three mobility-selected soot core sizes, each with a number of successively thicker coatings of SOA applied. Using IR laser vaporization, the SP-AMS had different changes in sensitivity to rBC compared to potassium as a function of applied SOA coatings. We show that this is due to different effective beam widths for the IR laser vaporization region of potassium versus black carbon. The SP-AMS's sensitivity to black carbon (BC) mass was not observed to plateau following successive SOA coatings, despite achieving high OA : BC mass ratios greater than 9. We also measured the ion fragmentation pattern of biomass-burning rBC and found it changed only slightly with increasing SOA mass. The average organic matter ion signal measured by the LAAPTOF demonstrated a positive correlation with the condensed SOA mass on individual particles, despite the inhomogeneity of the particle core compositions. This demonstrates that the LAAPTOF can obtain quantitative mass measurements of aged soot-particle composition from realistic biomass-burning particles with complex morphologies and composition.« less

Effect of secondary organic aerosol coating thickness on the real-time detection and characterization of biomass-burning soot by two particle mass spectrometers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahern, Adam T.; Subramanian, Ramachandran; Saliba, Georges

Biomass burning is a large source of light-absorbing refractory black carbon (rBC) particles with a wide range of morphologies and sizes. The net radiative forcing from these particles is strongly dependent on the amount and composition of non-light-absorbing material internally mixed with the rBC and on the morphology of the mixed particles. Understanding how the mixing state and morphology of biomass-burning aerosol evolves in the atmosphere is critical for constraining the influence of these particles on radiative forcing and climate. We investigated the response of two commercial laser-based particle mass spectrometers, the vacuum ultraviolet (VUV) ablation LAAPTOF and the IRmore » vaporization SP-AMS, to monodisperse biomass-burning particles as we sequentially coated the particles with secondary organic aerosol (SOA) from α-pinene ozonolysis. We studied three mobility-selected soot core sizes, each with a number of successively thicker coatings of SOA applied. Using IR laser vaporization, the SP-AMS had different changes in sensitivity to rBC compared to potassium as a function of applied SOA coatings. We show that this is due to different effective beam widths for the IR laser vaporization region of potassium versus black carbon. The SP-AMS's sensitivity to black carbon (BC) mass was not observed to plateau following successive SOA coatings, despite achieving high OA : BC mass ratios greater than 9. We also measured the ion fragmentation pattern of biomass-burning rBC and found it changed only slightly with increasing SOA mass. The average organic matter ion signal measured by the LAAPTOF demonstrated a positive correlation with the condensed SOA mass on individual particles, despite the inhomogeneity of the particle core compositions. This demonstrates that the LAAPTOF can obtain quantitative mass measurements of aged soot-particle composition from realistic biomass-burning particles with complex morphologies and composition.« less

Measurement of aerosol optical properties by integrating cavity ring-down spectroscopy and nephelometery

NASA Astrophysics Data System (ADS)

Tedela, Getachew; Singh, Sujeeta; Fiddler, Marc; Bililign, Solomon

2013-03-01

Accurate measurement of optical properties of aerosols is crucial for quantifying the influence of aerosols on climate. Aerosols that scatter and absorb radiation can have a cooling or warming effect depending on the magnitude of the respective scattering and absorption terms. One example is black carbon known for its strong absorption. The reported refractive indices for black carbon particles range from 1.2 +0i to 2.75 +1.44i. Our work attempts to measure extinction coefficient, and scattering coefficient of black carbon particles at different incident beam wavelengths using a cavity ring-down spectrometer and a Nephelometer and compare to Mie theory predictions. We report calibration results using polystyrene latex spheres and preliminary results on using commercial black carbon particles. The work is supported by the Department of Defense grant W911NF-11-1-0188.

CRISM Limb Observations of Aerosols and Water Vapor

NASA Technical Reports Server (NTRS)

Smith, Michael D.; Wolff, M.J.; Clancy, R.T.; Seelos, F.; Murchie, S.L.

2009-01-01

Near-infrared spectra taken in a limb-viewing geometry by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) on-board the Mars Reconnaissance Orbiter (MRO) provide a useful tool for probing atmospheric structure. Here we describe preliminary work on the retrieval of vertical profiles of aerosols and water vapor from the CRISM limb observations. The first full set of CRISM limb observations was taken in July 2009, with subsequent limb observations planned once every two months. Each set of limb observations contains about four dozen scans across the limb giving pole-to-pole coverage for two orbits at roughly 100 and 290 W longitude. Radiative transfer modeling taking account of aerosol scattering in the limb-viewing geometry is used to model the observations. The retrievals show the height to which dust and water vapor extend and the location and height of water ice clouds. Results from the First set of CRISM limb observations (July 2009, Ls=300) show dust aerosol well-mixed to about three scale heights above the surface with thin water ice clouds above the dust near the equator and at mid-northern latitudes. Water vapor is concentrated at high southern latitudes.

Pseudoslit Spectrometer

NASA Technical Reports Server (NTRS)

Reuter, Dennis C.; McCabe, George H.

2004-01-01

The pseudoslit spectrometer is a conceptual optoelectronic instrument that would offer some of the advantages, without the disadvantages, of prior linear-variable etalon (LVE) spectrometers and prior slit spectrometers. The pseudoslit spectrometer is so named because it would not include a slit, but the combined effects of its optical components would include a spatial filtering effect approximately equivalent to that of a slit. Like a prior LVE spectrometer, the pseudoslit spectrometer would include an LVE (essentially, a wedge-like narrowband- pass filter, the pass wavelength of which varies linearly with position in one dimension) in a focal plane covering an imaging planar array of photodetectors. However, the pseudoslit spectrometer would be more efficient because unlike a prior LVE spectrometer, the pseudoslit spectrometer would not have to be scanned across an entire field of view to obtain the spectrum of an object of interest that may occupy only a small portion of the field of view. Like a prior slit spectrometer, the pseudoslit spectrometer could acquire the entire spectrum of such a small object without need for scanning. However, the pseudoslit spectrometer would be optically and mechanically simpler: it would have fewer components and, hence, would pose less of a problem of alignment of components and would be less vulnerable to misalignment.

Analysis of Marine Aerosol Polysaccharides by Pyrolysis Time-of-Flight Mass Spectrometry

NASA Astrophysics Data System (ADS)

Lawler, M. J.; Grieman, M. M.; Sengur, I.; Saltzman, E. S.

2017-12-01

The relationship between surface ocean biological productivity and marine cloud formation and properties has been explored for decades, but the impacts of marine biogenic emissions on cloudiness and climate remain highly uncertain. This is in part due to the challenge of directly linking biogenic materials in the surface ocean with cloud-forming aerosol. It has been shown that polysaccharide gel-forming materials, also known as transparent exopolymers, may be mechanically ejected from the sea surface during air bubble bursting (Leck and Bigg, 2005). Existing analysis methods for such aerosols require considerable sample mass and sample preparation. As part of the multi-year seasonal North Atlantic Aerosols and Marine Ecosystems Study (NAAMES), ambient submicron marine aerosol was collected in November 2015 and May 2016 from the R/V Atlantis at using a Particle into Liquid Sampler (PILS). These samples of roughly 15 minute time resolution were frozen and returned to UC Irvine for analysis. A new technique has been developed to attempt to quantify polysaccharide material in these ambient samples. A small subsample (1- 5 µL) is taken from the PILS vial samples and allowed to dry on a Pt ribbon filament in the chemical ionization source region of a time-of-flight mass spectrometer. The sample then undergoes a two-step heating process, in which volatilizable molecules are first desorbed and then non-volatilizable large molecules such as polysaccharides are pyrolyzed. These desorbed molecules and decomposition products are ionized using either O2- or H3O+ reagent ion and are directly sampled into the mass spectrometer. The resulting spectra can then be compared to standards of known polysaccharide materials for quantification and potentially structural and/or compositional information.

CRISPR/Cas9 for cancer research and therapy.

PubMed

Zhan, Tianzuo; Rindtorff, Niklas; Betge, Johannes; Ebert, Matthias P; Boutros, Michael

2018-04-16

CRISPR/Cas9 has become a powerful method for making changes to the genome of many organisms. First discovered in bacteria as part of an adaptive immune system, CRISPR/Cas9 and modified versions have found a widespread use to engineer genomes and to activate or to repress the expression of genes. As such, CRISPR/Cas9 promises to accelerate cancer research by providing an efficient technology to dissect mechanisms of tumorigenesis, identify targets for drug development, and possibly arm cells for cell-based therapies. Here, we review current applications of the CRISPR/Cas9 technology for cancer research and therapy. We describe novel Cas9 variants and how they are used in functional genomics to discover novel cancer-specific vulnerabilities. Furthermore, we highlight the impact of CRISPR/Cas9 in generating organoid and mouse models of cancer. Finally, we provide an overview of the first clinical trials that apply CRISPR/Cas9 as a therapeutic approach against cancer. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Development of a Qcl-Based Spectrometer for Spectroscopic Analysis of Biogenic Volatile Organic Compounds

NASA Astrophysics Data System (ADS)

Iranpour, Michael Cyrus; Tran, Minh Nhat; Stewart, Jacob

2017-06-01

Biogenic volatile organic compounds (BVOCs) are naturally occurring molecules that are emitted into the atmosphere by plants. BVOCs have an important role in atmospheric chemistry as they react readily with ozone, hydroxyl radicals, and nitric oxides to form aerosols and pollutants such as ozone in the troposphere. We are developing an IR spectrometer with the aim of measuring spectra of atmospheric samples of BVOCs to determine their concentrations. Using an external cavity quantum cascade laser (EC-QCL), we have acquired IR spectra of isoprene (C_{5}H_{8}) near 993 cm^{-1}. Isoprene represents an ideal target, as it is the simplest and most abundant BVOC. IR spectra of standard samples of isoprene were acquired in order to determine the detection limit of the spectrometer. We have also been working to improve the capabilities of the spectrometer by implementing wavelength modulation spectroscopy and increasing the path length through our samples by using a multipass cell. In this talk, we will present data from our initial measurements of the standard isoprene samples using a simple direct absorption setup as well as measurements using the improved spectrometer.

Physico-chemical properties of aerosols in Sao Paulo, Brazil and mechanisms of secondary organic aerosol formation.

NASA Astrophysics Data System (ADS)

Artaxo, Paulo; Ferreira de Brito, Joel; Varanda Rizzo, Luciana; Luiza Godoy, Maria; Godoy, Jose Marcus

2013-04-01

Megacities emissions are increasingly becoming a global issue, where emissions from the transportation sector play an increasingly important role. Sao Paulo is a megacity with a population of about 18 million people, 7 million cars and large-scale industrial emissions. As a result of the vehicular and industrial emissions, the air quality in Sao Paulo is bellow WMO standards for aerosol particles and ozone. Many uncertainties are found on gas- and particulate matter vehicular emission factors and their following atmospheric processes, e.g. secondary organic aerosol formation. Due to the uniqueness of the vehicular fuel in Brazil, largely based on ethanol use, such characterization currently holds further uncertainties. To improve the understanding of the role of this unique emission characteristics, we are running a source apportionment study in Sao Paulo focused on the mechanisms of organic aerosol formation. One of the goals of this study is a quantitative aerosol source apportionment focused on vehicular emissions, including ethanol and gasohol (both fuels used by light-duty vehicles). This study comprises four sampling sites with continuous measurements for one year, where trace elements and organic aerosol are being measured for PM2.5 and PM10 along with real-time NOx, O3, PM10 and CO measurements. Aerosol optical properties and size distribution are being measured on a rotation basis between sampling stations. Furthermore, a Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) and an Aerosol Chemical Speciation Monitor (ACSM) are used to measure in real time VOCs and aerosol composition, respectively. Trace elements were measured using XRF and OC/EC analysis was determined with a Sunset OC/EC instrument. A TSI Nephelometer with 3 wavelengths measure light scattering and a MAAP measure black carbon. Results show aerosol number concentrations ranging between 10,000 and 35,000 cm-3, mostly concentrated in the nucleation and Aitken modes, with a peak in size at 80

Aerosol Optical Properties of Smoke from the Las Conchas Wildfire, Los Alamos, NM

NASA Astrophysics Data System (ADS)

Gorkowski, K.; Dubey, M. K.; Flowers, B. A.; Aiken, A. C.; Klein, B. Z.; Mazzoleni, C.; Sharma, N.; China`, S.

2011-12-01

The Las Conchas wildfire in Northern New Mexico started on June, 26 2011 and spread rapidly, eventually burning an area of 634 km2 (245 mi2). Due to the close proximity to the fire, the Los Alamos National Laboratory (LANL) was shut down and the town evacuated for several days. Immediately after LANL reopened (7/6/2011) the Earth and Environmental Sciences Division (EES-14) attained unique measurements of the smoke by sampling the ambient air. Three Integrated Photoacoustic/Nephelometer Spectrometers (DMT Inc.) were set up to measure aerosol light absorption and scattering coefficients. A University of Northwest Switzerland thermodenuder was used to remove compounds that are volatile at temperatures up to 200C. The aerosol's optical properties were measured before and after denuding the sample at 405nm (blue), 532nm (green), 781nm (red), and for non-denuded particles also at 375nm (ultraviolet). The aerosol size distributions were measured after the denuder with a Laser Aerosol Spectrometer (LAS, TSI Inc.) and black carbon was measured with a Single Particle Soot Photometer (SP2, DMT Inc.). Additionally, ambient measurements of Total Particulate Matter (PM2.5 and PM10) were collected continuously at the LANL air monitoring stations. These measurements are used in conjunction with numerical simulations to determine the bulk optical properties of the aerosol. Aerosols in wildfire smoke are composed of organic and black carbon (soot) particles that are formed during wood combustion and pyrolysis. The optical properties of the smoke particles are complex and lead to large uncertainties in assessing the global climate. During the measurement period, the Las Conchas fire provided very high particle concentrations (up to 200 μg/m3) that were exploited to investigate their optical properties. By heating the particles to temperatures ranging from 75 to 200C in the denuder, volatile organics were removed and the optical properties of the remaining particles were measured

Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity.

PubMed

Lee, Ciaran M; Davis, Timothy H; Bao, Gang

2018-04-01

What is the topic of this review? In this review, we analyse the performance of recently described tools for CRISPR/Cas9 guide RNA design, in particular, design tools that predict CRISPR/Cas9 activity. What advances does it highlight? Recently, many tools designed to predict CRISPR/Cas9 activity have been reported. However, the majority of these tools lack experimental validation. Our analyses indicate that these tools have poor predictive power. Our preliminary results suggest that target site accessibility should be considered in order to develop better guide RNA design tools with improved predictive power. The recent adaptation of the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system for targeted genome engineering has led to its widespread application in many fields worldwide. In order to gain a better understanding of the design rules of CRISPR/Cas9 systems, several groups have carried out large library-based screens leading to some insight into sequence preferences among highly active target sites. To facilitate CRISPR/Cas9 design, these studies have spawned a plethora of guide RNA (gRNA) design tools with algorithms based solely on direct or indirect sequence features. Here, we demonstrate that the predictive power of these tools is poor, suggesting that sequence features alone cannot accurately inform the cutting efficiency of a particular CRISPR/Cas9 gRNA design. Furthermore, we demonstrate that DNA target site accessibility influences the activity of CRISPR/Cas9. With further optimization, we hypothesize that it will be possible to increase the predictive power of gRNA design tools by including both sequence and target site accessibility metrics. © 2017 The Authors. Experimental Physiology © 2017 The Physiological Society.

Aerosol detection efficiency in inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Hubbard, Joshua A.; Zigmond, Joseph A.

2016-05-01

An electrostatic size classification technique was used to segregate particles of known composition prior to being injected into an inductively coupled plasma mass spectrometer (ICP-MS). Size-segregated particles were counted with a condensation nuclei counter as well as sampled with an ICP-MS. By injecting particles of known size, composition, and aerosol concentration into the ICP-MS, efficiencies of the order of magnitude aerosol detection were calculated, and the particle size dependencies for volatile and refractory species were quantified. Similar to laser ablation ICP-MS, aerosol detection efficiency was defined as the rate at which atoms were detected in the ICP-MS normalized by the rate at which atoms were injected in the form of particles. This method adds valuable insight into the development of technologies like laser ablation ICP-MS where aerosol particles (of relatively unknown size and gas concentration) are generated during ablation and then transported into the plasma of an ICP-MS. In this study, we characterized aerosol detection efficiencies of volatile species gold and silver along with refractory species aluminum oxide, cerium oxide, and yttrium oxide. Aerosols were generated with electrical mobility diameters ranging from 100 to 1000 nm. In general, it was observed that refractory species had lower aerosol detection efficiencies than volatile species, and there were strong dependencies on particle size and plasma torch residence time. Volatile species showed a distinct transition point at which aerosol detection efficiency began decreasing with increasing particle size. This critical diameter indicated the largest particle size for which complete particle detection should be expected and agreed with theories published in other works. Aerosol detection efficiencies also displayed power law dependencies on particle size. Aerosol detection efficiencies ranged from 10- 5 to 10- 11. Free molecular heat and mass transfer theory was applied, but

Aerosol detection efficiency in inductively coupled plasma mass spectrometry

DOE PAGES

Hubbard, Joshua A.; Zigmond, Joseph A.

2016-03-02

We used an electrostatic size classification technique to segregate particles of known composition prior to being injected into an inductively coupled plasma mass spectrometer (ICP-MS). Moreover, we counted size-segregated particles with a condensation nuclei counter as well as sampled with an ICP-MS. By injecting particles of known size, composition, and aerosol concentration into the ICP-MS, efficiencies of the order of magnitude aerosol detection were calculated, and the particle size dependencies for volatile and refractory species were quantified. Similar to laser ablation ICP-MS, aerosol detection efficiency was defined as the rate at which atoms were detected in the ICP-MS normalized bymore » the rate at which atoms were injected in the form of particles. This method adds valuable insight into the development of technologies like laser ablation ICP-MS where aerosol particles (of relatively unknown size and gas concentration) are generated during ablation and then transported into the plasma of an ICP-MS. In this study, we characterized aerosol detection efficiencies of volatile species gold and silver along with refractory species aluminum oxide, cerium oxide, and yttrium oxide. Aerosols were generated with electrical mobility diameters ranging from 100 to 1000 nm. In general, it was observed that refractory species had lower aerosol detection efficiencies than volatile species, and there were strong dependencies on particle size and plasma torch residence time. Volatile species showed a distinct transition point at which aerosol detection efficiency began decreasing with increasing particle size. This critical diameter indicated the largest particle size for which complete particle detection should be expected and agreed with theories published in other works. Aerosol detection efficiencies also displayed power law dependencies on particle size. Aerosol detection efficiencies ranged from 10 -5 to 10 -11. Free molecular heat and mass transfer theory was

Biological Particle Emissions From a South-East Asian Tropical Rainforest Using a Real- Time Dual Channel UV Fluorescence Bio-Aerosol Spectrometer

NASA Astrophysics Data System (ADS)

Gabey, A.; Coe, H.; Gallagher, M.; McFiggans, G.; Kaye, P.; Stanley, W.; Foot, V.

2008-12-01

and net emission for all fungal spores is ~1 μ g m-3 and ~50 Tg yr-1. These calculations demonstrate the potential importance of PBA, and in particular fungal spores, for global budgets of organic aerosols, particularly in tropical regions, however uncertainties are extremely large, ranging from 50 - 1000 Tg yr- 1. In this study we use the WIBS-3: a low-cost portable single-particle dual-channel UV fluorescence spectrometer (Kaye et al., 2008) to investigate the dynamics of PBA in real-time within and above a tropical forest of 50 m height in Borneo, Malaysia, to estimate net PBA emissions. Different circadian cycles were observed for bio and non-bio aerosol sources and the factors controlling bioaerosol emissions will be discussed in detail.

Cloud condensation nuclei closure study on summer arctic aerosol

NASA Astrophysics Data System (ADS)

Martin, M.; Chang, R. Y.-W.; Sierau, B.; Sjogren, S.; Swietlicki, E.; Abbatt, J. P. D.; Leck, C.; Lohmann, U.

2011-03-01

We present an aerosol - cloud condensation nuclei CCN) closure study on summer high Arctic aerosol based on measurements that were carried out in summer 2008 during the Arctic Summer Cloud Ocean Study (ASCOS) on board the Swedish ice breaker Oden. The data presented here were collected during a three-week time period in the pack ice (>85° N) when the icebreaker Oden was moored to an ice floe and drifted passively during the most biological active period into autumn freeze up conditions. CCN number concentrations were obtained using two CCN counters measuring at different supersaturations. The directly measured CCN number concentration is then compared with a CCN number concentration calculated using both bulk aerosol mass composition data from an aerosol mass spectrometer and aerosol number size distributions obtained from a differential mobility particle sizer, assuming κ-Köhler theory and an internally mixed aerosol. For the two highest measured supersaturations, 0.73 and 0.41%, closure could not be achieved with the investigated settings concerning hygroscopicity and density. The calculated CCN number concentration was always higher than the measured one. One possible explanation is that the smaller particles that activate at these supersaturations have a relative larger insoluble organic mass fraction and thus are less good CCN than the larger particles. At 0.20, 0.15 and 0.10% supersaturation, the measured CCN number can be represented with different parameters for the hygroscopicity and density of the particles. For the best agreement of the calculated CCNnumber concentration with the measured one the organic fraction of the aerosol needs to be nearly insoluble (қorg=0.02). However, this is not unambigious and қorg=0.2 is found as an upper limit at 0.1% supersaturation.

Broadband measurements of aerosol extinction in the ultraviolet spectral region

NASA Astrophysics Data System (ADS)

Washenfelder, R. A.; Flores, J. M.; Brock, C. A.; Brown, S. S.; Rudich, Y.

2013-04-01

Aerosols influence the Earth's radiative budget by scattering and absorbing incoming solar radiation. The optical properties of aerosols vary as a function of wavelength, but few measurements have reported the wavelength dependence of aerosol extinction cross sections and complex refractive indices. We describe a new laboratory instrument to measure aerosol optical extinction as a function of wavelength, using cavity enhanced spectroscopy with a broadband light source. The instrument consists of two broadband channels which span the 360-390 and 385-420 nm spectral regions using two light emitting diodes (LED) and a grating spectrometer with charge-coupled device (CCD) detector. We determined aerosol extinction cross sections and directly observed Mie scattering resonances for aerosols that are purely scattering (polystyrene latex spheres and ammonium sulfate), slightly absorbing (Suwannee River fulvic acid), and strongly absorbing (nigrosin dye). We describe an approach for retrieving refractive indices as a function of wavelength from the measured extinction cross sections over the 360-420 nm wavelength region. The retrieved refractive indices for PSL and ammonium sulfate agree within uncertainty with the literature values for this spectral region. The refractive index determined for nigrosin is 1.78 (± 0.03) + 0.19 (± 0.08)i at 360 nm and 1.63 (± 0.03) + 0.21 (± 0.05)i at 420 nm. The refractive index determined for Suwannee River fulvic acid is 1.71 (± 0.02) + 0.07 (± 0.06)i at 360 nm and 1.66 (± 0.02) + 0.06 (± 0.04)i at 420 nm. These laboratory results support the potential for a field instrument capable of determining ambient aerosol optical extinction, average aerosol extinction cross section, and complex refractive index as a function of wavelength.

Broadband measurements of aerosol extinction in the ultraviolet spectral region

NASA Astrophysics Data System (ADS)

Washenfelder, R. A.; Flores, J. M.; Brock, C. A.; Brown, S. S.; Rudich, Y.

2013-01-01

Aerosols influence the Earth's radiative budget by scattering and absorbing incoming solar radiation. The optical properties of aerosols vary as a function of wavelength, but few measurements have reported the wavelength dependence of aerosol extinction cross-sections and complex refractive indices. We describe a new laboratory instrument to measure aerosol optical extinction as a function of wavelength, using cavity enhanced spectroscopy with a broadband light source. The instrument consists of two broadband channels which span the 360-390 and 385-420 nm spectral regions using two light emitting diodes (LED) and a grating spectrometer with charge-coupled device (CCD) detector. We determined aerosol extinction cross-sections and directly observed Mie scattering resonances for aerosols that are purely scattering (polystyrene latex spheres and ammonium sulfate), slightly absorbing (Suwannee River fulvic acid), and strongly absorbing (nigrosin dye). We describe an approach for retrieving refractive indices as a function of wavelength from the measured extinction cross-sections over the 360-420 nm wavelength region. The retrieved refractive indices for PSL and ammonium sulfate agree within uncertainty with literature values for this spectral region. The refractive index determined for nigrosin is 1.78 (±0.03) + 0.19 (±0.08) i at 360 nm and 1.53 (±0.03) + 0.21 (±0.05) i at 420 nm. The refractive index determined for Suwannee River fulvic acid is 1.71 (±0.02) + 0.07 (±0.06) i at 360 nm and 1.66 (±0.02) + 0.06 (±0.04) i at 420 nm. These laboratory results support the potential for a field instrument capable of determining ambient aerosol optical extinction, average aerosol extinction cross-section, and complex refractive index as a function of wavelength.

Investigating biomass burning aerosol morphology using a laser imaging nephelometer

NASA Astrophysics Data System (ADS)

Manfred, Katherine M.; Washenfelder, Rebecca A.; Wagner, Nicholas L.; Adler, Gabriela; Erdesz, Frank; Womack, Caroline C.; Lamb, Kara D.; Schwarz, Joshua P.; Franchin, Alessandro; Selimovic, Vanessa; Yokelson, Robert J.; Murphy, Daniel M.

2018-02-01

Particle morphology is an important parameter affecting aerosol optical properties that are relevant to climate and air quality, yet it is poorly constrained due to sparse in situ measurements. Biomass burning is a large source of aerosol that generates particles with different morphologies. Quantifying the optical contributions of non-spherical aerosol populations is critical for accurate radiative transfer models, and for correctly interpreting remote sensing data. We deployed a laser imaging nephelometer at the Missoula Fire Sciences Laboratory to sample biomass burning aerosol from controlled fires during the FIREX intensive laboratory study. The laser imaging nephelometer measures the unpolarized scattering phase function of an aerosol ensemble using diode lasers at 375 and 405 nm. Scattered light from the bulk aerosol in the instrument is imaged onto a charge-coupled device (CCD) using a wide-angle field-of-view lens, which allows for measurements at 4-175° scattering angle with ˜ 0.5° angular resolution. Along with a suite of other instruments, the laser imaging nephelometer sampled fresh smoke emissions both directly and after removal of volatile components with a thermodenuder at 250 °C. The total integrated aerosol scattering signal agreed with both a cavity ring-down photoacoustic spectrometer system and a traditional integrating nephelometer within instrumental uncertainties. We compare the measured scattering phase functions at 405 nm to theoretical models for spherical (Mie) and fractal (Rayleigh-Debye-Gans) particle morphologies based on the size distribution reported by an optical particle counter. Results from representative fires demonstrate that particle morphology can vary dramatically for different fuel types. In some cases, the measured phase function cannot be described using Mie theory. This study demonstrates the capabilities of the laser imaging nephelometer instrument to provide realtime, in situ information about dominant particle

Satellite Detection of Smoke Aerosols Over a Snow/Ice Surface by TOMS

NASA Technical Reports Server (NTRS)

Hsu, N. Christina; Herman, Jay R.; Gleason, J. F.; Torres, O.; Seftor, C. J.

1998-01-01

The use of TOMS (Total Ozone Mapping Spectrometer) satellite data demonstrates the recently developed technique of using satellite UV radiance measurements to detect absorbing tropospheric aerosols is effective over snow/ice surfaces. Instead of the traditional single wavelength (visible or infrared) method of measuring tropospheric aerosols, this method takes advantage of the wavelength dependent reduction in the backscattered radiance due to the presence of absorbing aerosols over snow/ice surfaces. An example of the resulting aerosol distribution derived from TOMS data is shown for an August 1998 event in which smoke generated by Canadian forest fires drifts over and across Greenland. As the smoke plume moved over Greenland, the TOMS observed 380 nm reflectivity over the snow/ice surface dropped drastically from 90-100% down to 30-40%. To study the effects of this smoke plume in both the UV and visible regions of the spectrum, we compared a smoke-laden spectrum taken over Greenland by the high spectral resolution (300 to 800 nm) GOME instrument with one that is aerosol-free. We also discuss the results of modeling the darkening effects of various types of absorbing aerosols over snow/ice surfaces using a radiative transfer code. Finally, we investigated the history of such events by looking at the nearly twenty year record of TOMS aerosol index measurements and found that there is a large interannual variability in the amount of smoke aerosols observed over Greenland. This information will be available for studies of radiation and transport properties in the Arctic.

Biomass Burning Aerosol Absorption Measurements with MODIS Using the Critical Reflectance Method

NASA Technical Reports Server (NTRS)

Zhu, Li; Martins, Vanderlei J.; Remer, Lorraine A.

2010-01-01

This research uses the critical reflectance technique, a space-based remote sensing method, to measure the spatial distribution of aerosol absorption properties over land. Choosing two regions dominated by biomass burning aerosols, a series of sensitivity studies were undertaken to analyze the potential limitations of this method for the type of aerosol to be encountered in the selected study areas, and to show that the retrieved results are relatively insensitive to uncertainties in the assumptions used in the retrieval of smoke aerosol. The critical reflectance technique is then applied to Moderate Resolution Imaging Spectrometer (MODIS) data to retrieve the spectral aerosol single scattering albedo (SSA) in South African and South American 35 biomass burning events. The retrieved results were validated with collocated Aerosol Robotic Network (AERONET) retrievals. One standard deviation of mean MODIS retrievals match AERONET products to within 0.03, the magnitude of the AERONET uncertainty. The overlap of the two retrievals increases to 88%, allowing for measurement variance in the MODIS retrievals as well. The ensemble average of MODIS-derived SSA for the Amazon forest station is 0.92 at 670 nm, and 0.84-0.89 for the southern African savanna stations. The critical reflectance technique allows evaluation of the spatial variability of SSA, and shows that SSA in South America exhibits higher spatial variation than in South Africa. The accuracy of the retrieved aerosol SSA from MODIS data indicates that this product can help to better understand 44 how aerosols affect the regional and global climate.

Miniature Dual-Corona Ionizer for Bipolar Charging of Aerosol

PubMed Central

Qi, Chaolong; Kulkarni, Pramod

2015-01-01

A corona-based bipolar charger has been developed for use in compact, field-portable mobility size spectrometers. The charger employs an aerosol flow cavity exposed to two corona ionizers producing ions of opposite polarity. Each corona ionizer houses two electrodes in parallel needle-mesh configuration and is operated at the same magnitude of corona current. Experimental measurement of detailed charge distribution of near-monodisperse particles of different diameter in the submicrometer size range showed that the charger is capable of producing well-defined, consistent bipolar charge distributions for flow rates up to 1.5 L/min and aerosol concentration up to 107 per cm3. For particles with preexisting charge of +1, 0, and −1, the measured charge distributions agreed well with the theoretical distributions within the range of experimental and theoretical uncertainties. The transmission efficiency of the charger was measured to be 80% for 10 nm particles (at 0.3 L/min and 5 μA corona current) and increased with increasing diameter beyond this size. Measurement of uncharged fractions at various combinations of positive and negative corona currents showed the charger performance to be insensitive to fluctuations in corona current. Ion concentrations under positive and negative unipolar operation were estimated to be 8.2 × 107 and 3.37 × 108 cm−3 for positive and negative ions; the n·t product value under positive corona operation was independently estimated to be 8.5 × 105 s/cm3. The ion concentration estimates indicate the charger to be capable of “neutralizing” typical atmospheric and industrial aerosols in most measurement applications. The miniature size, simple and robust operation makes the charger suitable for portable mobility spectrometers. PMID:26512158

Miniature Dual-Corona Ionizer for Bipolar Charging of Aerosol.

PubMed

Qi, Chaolong; Kulkarni, Pramod

2013-01-01

A corona-based bipolar charger has been developed for use in compact, field-portable mobility size spectrometers. The charger employs an aerosol flow cavity exposed to two corona ionizers producing ions of opposite polarity. Each corona ionizer houses two electrodes in parallel needle-mesh configuration and is operated at the same magnitude of corona current. Experimental measurement of detailed charge distribution of near-monodisperse particles of different diameter in the submicrometer size range showed that the charger is capable of producing well-defined, consistent bipolar charge distributions for flow rates up to 1.5 L/min and aerosol concentration up to 10 7 per cm 3 . For particles with preexisting charge of +1, 0, and -1, the measured charge distributions agreed well with the theoretical distributions within the range of experimental and theoretical uncertainties. The transmission efficiency of the charger was measured to be 80% for 10 nm particles (at 0.3 L/min and 5 μ A corona current) and increased with increasing diameter beyond this size. Measurement of uncharged fractions at various combinations of positive and negative corona currents showed the charger performance to be insensitive to fluctuations in corona current. Ion concentrations under positive and negative unipolar operation were estimated to be 8.2 × 10 7 and 3.37 × 10 8 cm -3 for positive and negative ions; the n · t product value under positive corona operation was independently estimated to be 8.5 × 10 5 s/cm 3 . The ion concentration estimates indicate the charger to be capable of "neutralizing" typical atmospheric and industrial aerosols in most measurement applications. The miniature size, simple and robust operation makes the charger suitable for portable mobility spectrometers.

Advances in therapeutic CRISPR/Cas9 genome editing.

PubMed

Savić, Nataša; Schwank, Gerald

2016-02-01

Targeted nucleases are widely used as tools for genome editing. Two years ago the clustered regularly interspaced short palindromic repeat (CRISPR)-associated Cas9 nuclease was used for the first time, and since then has largely revolutionized the field. The tremendous success of the CRISPR/Cas9 genome editing tool is powered by the ease design principle of the guide RNA that targets Cas9 to the desired DNA locus, and by the high specificity and efficiency of CRISPR/Cas9-generated DNA breaks. Several studies recently used CRISPR/Cas9 to successfully modulate disease-causing alleles in vivo in animal models and ex vivo in somatic and induced pluripotent stem cells, raising hope for therapeutic genome editing in the clinics. In this review, we will summarize and discuss such preclinical CRISPR/Cas9 gene therapy reports. Copyright © 2016 Elsevier Inc. All rights reserved.

Recent Advances in Genome Editing Using CRISPR/Cas9.

PubMed

Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

2016-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding.

Recent Advances in Genome Editing Using CRISPR/Cas9

PubMed Central

Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

2016-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding. PMID:27252719

Characterization of aerosol composition and sources in the greater Atlanta area by aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Ng, N. L.; Xu, L.; Suresh, S.; Weber, R. J. J.; Baumann, K.; Edgerton, E. S.

2014-12-01

An important and uncertain aspect of biogenic secondary organic aerosol (SOA) formation is that it is often associated with anthropogenic pollution tracers. Prior studies in Atlanta suggested that 70-80% of the carbon in water-soluble organic carbon (WSOC) is modern, yet it is well-correlated with the anthropogenic CO. In this study, we deployed a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and an Aerosol Chemical Speciation Monitor (ACSM) at multiple sites in different seasons (May 2012-February 2013) to characterize the sources and chemical composition of aerosols in the greater Atlanta area. This area in the SE US is ideal to investigate anthropogenic-biogenic interactions due to high natural and anthropogenic emissions. These extensive field studies are part of the Southeastern Center for Air Pollution and Epidemiology study (SCAPE). The HR-ToF-AMS is deployed at four sites (~ 3 weeks each) in rotation: Jefferson Street (urban), Yorkville (rural), roadside site (near Highway 75/85), and Georgia Tech site (campus), with the urban and rural sites being part of the SEARCH network. We obtained seven HR-ToF-AMS datasets in total. During the entire measurement period, the ACSM is stationary at the GIT site and samples continuously. We perform positive matrix factorization (PMF) analysis on the HR-ToF-AMS and ACSM data to deconvolve the OA into different components. While the diurnal cycle of the total OA is flat as what have been previously observed, the OA factors resolved by PMF analysis show distinctively different diurnal trends. We find that the "more-oxidized oxygenated OA" (MO-OOA) constitutes a major fraction of OA at all sites. In summer, OA is dominated by SOA, e.g., isoprene-OA and OOA with different degrees of oxidation. In contrary, biomass burning OA is more prominent in winter data. By comparing HR-ToF-AMS and ACSM data during the same sampling periods, we find that the aerosol time series are highly correlated, indicating the

Aerosol Size and Chemical Composition in the Canadian High Arctic

NASA Astrophysics Data System (ADS)

Chang, R. Y. W.; Hayes, P. L.; Leaitch, W. R.; Croft, B.; O'Neill, N. T.; Fogal, P.; Drummond, J. R.; Sloan, J. J.

2015-12-01

Arctic aerosol have a strong annual cycle, with winter months dominated by long range transport from lower latitudes resulting in high mass loadings. Conversely, local emissions are more prominent in the summer months because of the decreased influence of transported aerosol, allowing us to regularly observe both transported and local aerosol. This study will present observations of aerosol chemical composition and particle number size distribution collected at the Polar Environment Artic Research Laboratory and the Alert Global Atmospheric Watch Observatory at Eureka (80N, 86W) and Alert (82N, 62W), Nunavut, respectively. Summer time observations of the number size distribution reveal a persistent mode of particles centered between 30-50 nm, with occasional bursts of smaller particles. The non-refractory aerosol chemical composition, measured by the Canadian Network for the Detection of Atmospheric Change quadrupole aerosol mass spectrometer, is primarily organic, with contributions from both aged and fresher organic aerosol. Factor analysis will be conducted to better understand these sources. The site at Eureka is more susceptible to long range transport since it is at the top of a mountain ridge (610 m above sea level) and will be compared to the site at Alert on an elevated plain (200 m above sea level). This will allow us to determine the relative contributions from processes and sources at the sites at different elevations. Comparisons with aerosol optical depth and GEOS-Chem model output will also be presented to put these surface measurements into context with the overlying and regional atmosphere. Results from this study contribute to our knowledge of aerosol in the high Arctic.

Potential source identification for aerosol concentrations over a site in Northwestern India

NASA Astrophysics Data System (ADS)

Payra, Swagata; Kumar, Pramod; Verma, Sunita; Prakash, Divya; Soni, Manish

2016-03-01

The collocated measurements of aerosols size distribution (ASD) and aerosol optical thickness (AOT) are analyzed simultaneously using Grimm aerosol spectrometer and MICROTOP II Sunphotometer over Jaipur, capital of Rajasthan in India. The contrast temperature characteristics during winter and summer seasons of year 2011 are investigated in the present study. The total aerosol number concentration (TANC, 0.3-20 μm) during winter season was observed higher than in summer time and it was dominated by fine aerosol number concentration (FANC < 2 μm). Particles smaller than 0.8 μm (at aerodynamic size) constitute ~ 99% of all particles in winter and ~ 90% of particles in summer season. However, particles greater than 2 μm contribute ~ 3% and ~ 0.2% in summer and winter seasons respectively. The aerosols optical thickness shows nearly similar AOT values during summer and winter but corresponding low Angstrom Exponent (AE) values during summer than winter, respectively. In this work, Potential Source Contribution Function (PSCF) analysis is applied to identify locations of sources that influenced concentrations of aerosols over study area in two different seasons. PSCF analysis shows that the dust particles from Thar Desert contribute significantly to the coarse aerosol number concentration (CANC). Higher values of the PSCF in north from Jaipur showed the industrial areas in northern India to be the likely sources of fine particles. The variation in size distribution of aerosols during two seasons is clearly reflected in the log normal size distribution curves. The log normal size distribution curves reveals that the particle size less than 0.8 μm is the key contributor in winter for higher ANC.

Season-dependent size distribution of aerosols over the tropical coastal environment of south-west India

NASA Astrophysics Data System (ADS)

Aryasree, S.; Nair, Prabha R.

2018-01-01

This paper presents the results of a detailed study on the size characteristics of aerosols at the tropical coastal site Thiruvananthapuram based on the in-situ measurements of size resolved aerosol number density using an aerosol spectrometer, covering a period of 28 months from September 2011 to December 2013. The diurnal pattern of aerosol number density is characterized by day time low and a two-fold increase during nighttime and these changes are closely associated with the strong mesoscale features namely the sea breeze and land breeze prevailing at the site. Aerosol Number Size Distribution (NSD) depicts a multi-modal nature with two prominent modes, one ≤0.1 μm and other ∼1 μm. Two other less pronounced modes are also observed in the NSD, one ∼0.3-0.5 μm and other ∼5-8 μm. The NSDs also exhibited strong seasonal changes linked with the synoptic meteorological feature of this region namely the South Asian monsoon. The seasonal NSDs were parameterized and analyzed. In addition to this, the effects of meteorological parameters temperature, relative humidity, and wind speed and airflow patterns on aerosol number density as revealed by partial correlation analysis were found to be aerosol size dependent.

Assisting Students' Cognitive Strategies with the Use of CAS

ERIC Educational Resources Information Center

Sarvari, Csaba; Lavicza, Zsolt; Klincsik, Mihaly

2010-01-01

This paper examines various cognitive strategies applied while CAS (Computer Algebra System) are used in undergraduate-level engineering mathematics teaching and learning. We posed some questions in relation to such CAS use: What kind of tools can CAS offer to enhance different cognitive strategies of students? How can the use of CAS widen the…

Urban organic aerosols measured by single particle mass spectrometry in the megacity of London

NASA Astrophysics Data System (ADS)

Dall'Osto, M.; Harrison, R. M.

2012-05-01

During the month of October 2006, as part of the REPARTEE-I experiment (Regent's Park and Tower Environmental Experiment) an Aerosol Time-Of-Flight Mass Spectrometer (ATOFMS) was deployed at an urban background location in the city of London, UK. Fifteen particle types were classified, some of which were already discussed (Dall'Osto et al., 2009a,b; Harrison et al., 2012). In this manuscript the origins and properties of four unreported particle types postulated to be due to locally generated aerosols, independent of the air mass type advected into London, are examined. One particle type, originating from lubricating oil (referred to as Ca-EC), was associated with morning rush hour traffic emissions. A second particle type, composed of both inorganic and organic species (called Na-EC-OC), was found enhanced in particle number concentration during evening time periods, and is likely to originate from a source operating at this time of day, or more probably from condensation of semi-volatile species. A third class, internally mixed with organic carbon and sulphate (called OC), was found to spike both in the morning and evenings although it could not unambiguously associated with a specific source or atmospheric process. The fourth class (Secondary Organic Aerosols - Polycyclic Aromatic Hydrocarbon; SOA-PAH) exhibited maximum frequency during the warmest part of the day, and a number of factors point towards secondary aerosol production from traffic-related volatile aromatic compounds. Single particle mass spectra of this particle type showed an oxidized polycyclic aromatic compound signature. A comparison of ATOFMS particle class data is then made with factors obtained by Positive Matrix Factorization and PAH signatures obtained from Aerosol Mass Spectrometer (AMS) data (Allan et al., 2010). Both the Ca-EC and OC particle types correlate with primary Hydrocarbon-like Organic Aerosol (HOA, R2 = 0.65 and 0.50 respectively), and Na-EC-OC correlates weakly with the AMS

Production of Purified CasRNPs for Efficacious Genome Editing.

PubMed

Lingeman, Emily; Jeans, Chris; Corn, Jacob E

2017-10-02

CRISPR-Cas systems have been harnessed as modular genome editing reagents for functional genomics and show promise to cure genetic diseases. Directed by a guide RNA, a Cas effector introduces a double stranded break in DNA and host cell DNA repair leads to the introduction of errors (e.g., to knockout a gene) or a programmed change. Introduction of a Cas effector and guide RNA as a purified Cas ribonucleoprotein complex (CasRNP) has recently emerged as a powerful approach to alter cell types and organisms. Not only does CasRNP editing exhibit increased efficacy and specificity, it avoids optimization and iteration of species-specific factors such as codon usage, promoters, and terminators. CasRNP editing has been rapidly adopted for research use in many contexts and is quickly becoming a popular method to edit primary cells for therapeutic application. This article describes how to make a Cas9 RNP and outlines its use for gene editing in human cells. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Complementary online aerosol mass spectrometry and offline FT-IR spectroscopy measurements: Prospects and challenges for the analysis of anthropogenic aerosol particle emissions

NASA Astrophysics Data System (ADS)

Faber, Peter; Drewnick, Frank; Bierl, Reinhard; Borrmann, Stephan

2017-10-01

The aerosol mass spectrometer (AMS) is well established in investigating highly time-resolved dynamics of submicron aerosol chemical composition including organic aerosol (OA). However, interpretation of mass spectra on molecular level is limited due to strong fragmentation of organic substances and potential reactions inside the AMS ion chamber. Results from complementary filter-based FT-IR absorption measurements were used to explain features in high-resolution AMS mass spectra of different types of OA (e.g. cooking OA, cigarette smoking OA, wood burning OA). Using this approach some AMS fragment ions were validated in this study as appropriate and rather specific markers for a certain class of organic compounds for all particle types under investigation. These markers can therefore be used to get deeper insights in the chemical composition of OA based on AMS mass spectra in upcoming studies. However, the specificity of other fragment ions such as C2H4O2+ (m/z 60.02114) remains ambiguous. In such cases, complementary FT-IR measurements allow the interpretation of highly time-resolved AMS mass spectra at the level of molecular functional groups. Furthermore, this study discusses the challenges in reducing inorganic interferences (e.g. from water and ammonium salts) in FT-IR spectra of atmospheric aerosols to decrease spectral uncertainties for better comparisons and, thus, to get more robust results.

The role of cloud contamination, aerosol layer height and aerosol model in the assessment of the OMI near-UV retrievals over the ocean

NASA Astrophysics Data System (ADS)

Gassó, Santiago; Torres, Omar

2016-07-01

Retrievals of aerosol optical depth (AOD) at 388 nm over the ocean from the Ozone Monitoring Instrument (OMI) two-channel near-UV algorithm (OMAERUV) have been compared with independent AOD measurements. The analysis was carried out over the open ocean (OMI and MODerate-resolution Imaging Spectrometer (MODIS) AOD comparisons) and over coastal and island sites (OMI and AERONET, the AErosol RObotic NETwork). Additionally, a research version of the retrieval algorithm (using MODIS and CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) information as constraints) was utilized to evaluate the sensitivity of the retrieval to different assumed aerosol properties. Overall, the comparison resulted in differences (OMI minus independent measurements) within the expected levels of uncertainty for the OMI AOD retrievals (0.1 for AOD < 0.3, 30 % for AOD > 0.3). Using examples from case studies with outliers, the reasons that led to the observed differences were examined with specific purpose to determine whether they are related to instrument limitations (i.e., pixel size, calibration) or algorithm assumptions (such as aerosol shape, aerosol height). The analysis confirms that OMAERUV does an adequate job at rejecting cloudy scenes within the instrument's capabilities. There is a residual cloud contamination in OMI pixels with quality flag 0 (the best conditions for aerosol retrieval according to the algorithm), resulting in a bias towards high AODs in OMAERUV. This bias is more pronounced at low concentrations of absorbing aerosols (AOD 388 nm ˜ < 0.5). For higher aerosol loadings, the bias remains within OMI's AOD uncertainties. In pixels where OMAERUV assigned a dust aerosol model, a fraction of them (< 20 %) had retrieved AODs significantly lower than AERONET and MODIS AODs. In a case study, a detailed examination of the aerosol height from CALIOP and the AODs from MODIS, along with sensitivity tests, was carried out by varying the different assumed parameters in the

The Role of Cloud Contamination, Aerosol Layer Height and Aerosol Model in the Assessment of the OMI Near-UV Retrievals Over the Ocean

NASA Technical Reports Server (NTRS)

Gasso, Santiago; Torres, Omar

2016-01-01

Retrievals of aerosol optical depth (AOD) at 388 nm over the ocean from the Ozone Monitoring Instrument (OMI) two-channel near-UV algorithm (OMAERUV) have been compared with independent AOD measurements. The analysis was carried out over the open ocean (OMI and MODerate-resolution Imaging Spectrometer (MODIS) AOD comparisons) and over coastal and island sites (OMI and AERONET, the AErosol RObotic NETwork). Additionally, a research version of the retrieval algorithm (using MODIS and CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) information as constraints) was utilized to evaluate the sensitivity of the retrieval to different assumed aerosol properties. Overall, the comparison resulted in differences (OMI minus independent measurements) within the expected levels of uncertainty for the OMI AOD retrievals (0.1 for AOD less than 0.3, 30% for AOD greater than 0.3). Using examples from case studies with outliers, the reasons that led to the observed differences were examined with specific purpose to determine whether they are related to instrument limitations (i.e., pixel size, calibration) or algorithm assumptions (such as aerosol shape, aerosol height). The analysis confirms that OMAERUV does an adequate job at rejecting cloudy scenes within the instrument's capabilities. There is a residual cloud contamination in OMI pixels with quality flag 0 (the best conditions for aerosol retrieval according to the algorithm), resulting in a bias towards high AODs in OMAERUV. This bias is more pronounced at low concentrations of absorbing aerosols (AOD 388 nm approximately less than 0.5). For higher aerosol loadings, the bias remains within OMI's AOD uncertainties. In pixels where OMAERUV assigned a dust aerosol model, a fraction of them (less than 20 %) had retrieved AODs significantly lower than AERONET and MODIS AODs. In a case study, a detailed examination of the aerosol height from CALIOP and the AODs from MODIS, along with sensitivity tests, was carried out by

Aerosol number size distributions in the lower troposphere over a background region and megalopolis (Novosibirsk) on result of airborne sounding in 2011-2013

NASA Astrophysics Data System (ADS)

Belan, Boris D.; Kozlov, Artem V.; Simonenkov, Denis V.; Tolmachev, Gennadii N.; Tsaruk, Victoria V.

2014-11-01

In this paper we present a comparison of the data on aerosol number size distribution measured with GRIMM 1.109 aerosol spectrometer in the lower troposphere over Novosibirsk and background area 150 km south-west of it during research flights of Optik TU-134 aircraft laboratory carried out along the route Novosibirsk - Ordynskoye - Novosibirsk in 2011-2013. Aerosol number size distributions averaged over 3 years as together so for warm and cold seasons separately are considered here. It is shown that the accumulation of anthropogenic aerosol within the BL over the city is typical for the cold period, which is most likely caused by inversions those are rapidly destroyed by vertical mixing during warm season and anthropogenic aerosols from the city are transported into the free troposphere.

A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.

PubMed

Qian, Pengge; Wang, Xu; Yang, Zhenke; Li, Zhenkui; Gao, Han; Su, Xin-Zhuan; Cui, Huiting; Yuan, Jing

2018-06-01

The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P. yoelii. The resulted PyCas9ki parasite displays normal progression during the whole life cycle and possesses the Cas9 protein expression in asexual blood stage. By introducing the plasmid (pYCs) containing only sgRNA and homologous template elements, we successfully achieved both deletion and tagging modifications for different endogenous genes in the genome of PyCas9ki parasite. This cas9-knockin PyCas9ki parasite provides a new platform facilitating gene functions study in the rodent malaria parasite P. yoelii. Copyright © 2018 Elsevier B.V. All rights reserved.

CRISPR/Cas9 in Genome Editing and Beyond.

PubMed

Wang, Haifeng; La Russa, Marie; Qi, Lei S

2016-06-02

The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.

Overview of TANGENT (Tandem Aerosol Nucleation and Growth ENvironment Tube) 2017 IOP Study

NASA Astrophysics Data System (ADS)

Tiszenkel, L.

2017-12-01

New particle formation consists of two steps: nucleation and growth of nucleated particles. However, most laboratory studies have been conducted under conditions where these two processes are convoluted together, thereby hampering the detailed understanding of the effect of chemical species and atmospheric conditions on two processes. The objective of the Tandem Aerosol Nucleation and Growth ENvironment Tube (TANGENT) laboratory study is to investigate aerosol nucleation and growth properties independently by separating these two processes in two different flow tubes. This research is a collaboration between the University of Alabama in Huntsville and the University of Delaware. In this poster we will present the experimental setup of TANGENT and summarize the key results from the first IOP (intense observation period) experiments undertaken during Summer 2017. Nucleation takes place in a temperature- and RH-controlled fast flow reactor (FT-1) where sulfuric acid forms from OH radicals and sulfur dioxide. Sulfuric acid and impurity base compounds are detected with chemical ionization mass spectrometers (CIMS). Particle sizes and number concentrations of newly nucleated particles are measured with a scanning mobility particle sizer (SMPS) and particle size magnifier (PSM), providing concentrations of particles between 1-100 nm. The nucleation particles are transferred directly to the growth tube (FT-2) where oxidants and biogenic organic precursors are added to grow nucleated nanoparticles. Sizes of particles after growth are analyzed with an additional SMPS and elemental chemical composition of 50 nm and above particles detected with a nano-aerosol mass spectrometer (NAMS). TANGENT provides the unique ability to conduct experiments that can monitor and control reactant concentrations, aerosol size and aerosol chemical composition during nucleation and growth. Experiments during this first IOP study have elucidated the effects of sulfur dioxide, particle size

Structural and functional insights into the interaction between the Cas family scaffolding protein p130Cas and the focal adhesion-associated protein paxillin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chi; Miller, Darcie J.; Guibao, Cristina D.

The Cas family scaffolding protein p130Cas is a Src substrate localized in focal adhesions (FAs) and functions in integrin signaling to promote cell motility, invasion, proliferation, and survival. p130Cas targeting to FAs is essential for its tyrosine phosphorylation and downstream signaling. Although the N-terminal SH3 domain is important for p130Cas localization, it has also been reported that the C-terminal region is involved in p130Cas FA targeting. The C-terminal region of p130Cas or Cas family homology domain (CCHD) has been reported to adopt a structure similar to that of the focal adhesion kinase C-terminal focal adhesion-targeting domain. The mechanism by whichmore » the CCHD promotes FA targeting of p130Cas, however, remains unclear. In this study, using a calorimetry approach, we identified the first LD motif (LD1) of the FA-associated protein paxillin as the binding partner of the p130Cas CCHD (in a 1:1 stoichiometry with a Kd ~4.2 μM) and elucidated the structure of the p130Cas CCHD in complex with the paxillin LD1 motif by X-ray crystallography. Of note, a comparison of the CCHD/LD1 complex with a previously solved structure of CCHD in complex with the SH2-containing protein NSP3 revealed that LD1 had almost identical positioning of key hydrophobic and acidic residues relative to NSP3. Because paxillin is one of the key scaffold molecules in FAs, we propose that the interaction between the p130Cas CCHD and the LD1 motif of paxillin plays an important role in p130Cas FA targeting.« less

RNA-dependent RNA targeting by CRISPR-Cas9

PubMed Central

Strutt, Steven C; Torrez, Rachel M; Kaya, Emine; Negrete, Oscar A

2018-01-01

Double-stranded DNA (dsDNA) binding and cleavage by Cas9 is a hallmark of type II CRISPR-Cas bacterial adaptive immunity. All known Cas9 enzymes are thought to recognize DNA exclusively as a natural substrate, providing protection against DNA phage and plasmids. Here, we show that Cas9 enzymes from both subtypes II-A and II-C can recognize and cleave single-stranded RNA (ssRNA) by an RNA-guided mechanism that is independent of a protospacer-adjacent motif (PAM) sequence in the target RNA. RNA-guided RNA cleavage is programmable and site-specific, and we find that this activity can be exploited to reduce infection by single-stranded RNA phage in vivo. We also demonstrate that Cas9 can direct PAM-independent repression of gene expression in bacteria. These results indicate that a subset of Cas9 enzymes have the ability to act on both DNA and RNA target sequences, and suggest the potential for use in programmable RNA targeting applications. PMID:29303478

Lung Toxicity of Condensed Aerosol from E-CIG Liquids: Influence of the Flavor and the In Vitro Model Used

PubMed Central

Bengalli, Rossella; Ferri, Emanuele; Labra, Massimo; Mantecca, Paride

2017-01-01

The diffusion of e-cigarette (e-CIG) opens a great scientific and regulatory debate about its safety. The huge number of commercialized devices, e-liquids with almost infinite chemical formulations and the growing market demand for a rapid and efficient toxicity screen system that is able to test all of these references and related aerosols. A consensus on the best protocols for the e-CIG safety assessment is still far to be achieved, since the huge number of variables characterizing these products (e.g., flavoring type and concentration, nicotine concentration, type of the device, including the battery and the atomizer). This suggests that more experimental evidences are needed to support the regulatory frameworks. The present study aims to contribute in this field by testing the effects of condensed aerosols (CAs) from three main e-liquid categories (tobacco, mint, and cinnamon as food-related flavor), with (18 mg/mL) or without nicotine. Two in vitro models, represented by a monoculture of human epithelial alveolar cells and a three-dimensional (3D) co-culture of alveolar and lung microvascular endothelial cells were used. Cell viability, pro-inflammatory cytokines release and alveolar-blood barrier (ABB) integrity were investigated as inhalation toxicity endpoints. Results showed that nicotine itself had almost no influence on the modulation of the toxicity response, while flavor composition did have. The cell viability was significantly decreased in monoculture and ABB after exposure to the mints and cinnamon CAs. The barrier integrity was significantly affected in the ABB after exposure to cytotoxic CAs. With the exception of the significant IL-8 release in the monoculture after Cinnamon exposure, no increase of inflammatory cytokines (IL-8 and MCP-1) release was observed. These findings point out that multiple assays with different in vitro models are able to discriminate the acute inhalation toxicity of CAs from liquids with different flavors, providing the

Lung Toxicity of Condensed Aerosol from E-CIG Liquids: Influence of the Flavor and the In Vitro Model Used.

PubMed

Bengalli, Rossella; Ferri, Emanuele; Labra, Massimo; Mantecca, Paride

2017-10-20

The diffusion of e-cigarette (e-CIG) opens a great scientific and regulatory debate about its safety. The huge number of commercialized devices, e-liquids with almost infinite chemical formulations and the growing market demand for a rapid and efficient toxicity screen system that is able to test all of these references and related aerosols. A consensus on the best protocols for the e-CIG safety assessment is still far to be achieved, since the huge number of variables characterizing these products (e.g., flavoring type and concentration, nicotine concentration, type of the device, including the battery and the atomizer). This suggests that more experimental evidences are needed to support the regulatory frameworks. The present study aims to contribute in this field by testing the effects of condensed aerosols (CAs) from three main e-liquid categories (tobacco, mint, and cinnamon as food-related flavor), with (18 mg/mL) or without nicotine. Two in vitro models, represented by a monoculture of human epithelial alveolar cells and a three-dimensional (3D) co-culture of alveolar and lung microvascular endothelial cells were used. Cell viability, pro-inflammatory cytokines release and alveolar-blood barrier (ABB) integrity were investigated as inhalation toxicity endpoints. Results showed that nicotine itself had almost no influence on the modulation of the toxicity response, while flavor composition did have. The cell viability was significantly decreased in monoculture and ABB after exposure to the mints and cinnamon CAs. The barrier integrity was significantly affected in the ABB after exposure to cytotoxic CAs. With the exception of the significant IL-8 release in the monoculture after Cinnamon exposure, no increase of inflammatory cytokines (IL-8 and MCP-1) release was observed. These findings point out that multiple assays with different in vitro models are able to discriminate the acute inhalation toxicity of CAs from liquids with different flavors, providing the

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit.

PubMed

Murugan, Karthik; Babu, Kesavan; Sundaresan, Ramya; Rajan, Rakhi; Sashital, Dipali G

2017-10-05

CRISPR-Cas systems defend prokaryotes against bacteriophages and mobile genetic elements and serve as the basis for revolutionary tools for genetic engineering. Class 2 CRISPR-Cas systems use single Cas endonucleases paired with guide RNAs to cleave complementary nucleic acid targets, enabling programmable sequence-specific targeting with minimal machinery. Recent discoveries of previously unidentified CRISPR-Cas systems have uncovered a deep reservoir of potential biotechnological tools beyond the well-characterized Type II Cas9 systems. Here we review the current mechanistic understanding of newly discovered single-protein Cas endonucleases. Comparison of these Cas effectors reveals substantial mechanistic diversity, underscoring the phylogenetic divergence of related CRISPR-Cas systems. This diversity has enabled further expansion of CRISPR-Cas biotechnological toolkits, with wide-ranging applications from genome editing to diagnostic tools based on various Cas endonuclease activities. These advances highlight the exciting prospects for future tools based on the continually expanding set of CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Cluster Analysis of the Organic Peaks in Bulk Mass Spectra Obtained During the 2002 New England Air Quality Study with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M.; Bertman, S. B.; Middlebrook, A. M.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel R. H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Vertical distribution of aerosol number concentration in the troposphere over Siberia derived from airborne in-situ measurements

NASA Astrophysics Data System (ADS)

Arshinov, Mikhail Yu.; Belan, Boris D.; Paris, Jean-Daniel; Machida, Toshinobu; Kozlov, Alexandr; Malyskin, Sergei; Simonenkov, Denis; Davydov, Denis; Fofonov, Alexandr

2016-04-01

Knowledge of the vertical distribution of aerosols particles is very important when estimating aerosol radiative effects. To date there are a lot of research programs aimed to study aerosol vertical distribution, but only a few ones exist in such insufficiently explored region as Siberia. Monthly research flights and several extensive airborne campaigns carried out in recent years in Siberian troposphere allowed the vertical distribution of aerosol number concentration to be summarized. In-situ aerosol measurements were performed in a wide range of particle sizes by means of improved version of the Novosibirsk-type diffusional particle sizer and GRIMM aerosol spectrometer Model 1.109. The data on aerosol vertical distribution enabled input parameters for the empirical equation of Jaenicke (1993) to be derived for Siberian troposphere up to 7 km. Vertical distributions of aerosol number concentration in different size ranges averaged for the main seasons of the year will be presented. This work was supported by Interdisciplinary integration projects of the Siberian Branch of the Russian Academy of Science No. 35, No. 70 and No. 131; the Branch of Geology, Geophysics and Mining Sciences of RAS (Program No. 5); and Russian Foundation for Basic Research (grant No. 14-05-00526). Jaenicke R. Tropospheric aerosols, in Aerosol-Cloud-Climate Interactions, edited by P.V. Hobs. -Academic Press, San Diego, CA, 1993.- P. 1-31.

Fluxes of Submicron Organic Aerosol above London Measured by Eddy Covariance using the Aerodyne HR-ToF-AMS

NASA Astrophysics Data System (ADS)

Phillips, G. J.; di Marco, C. F.; Farmer, D.; Kimmel, J. R.; Jimenez, J. L.; Nemitz, E.

2009-12-01

Urban centres are large sources of sub-micron particles. The myriad of emission sources combined with the complex interaction between regional aerosol and the particulate and gaseous photochemistry make for a complex system. It is evident that particulate emissions from cities will affect the regional atmosphere as well as the environment within the urban area. Aerosol particles have been associated with respiratory and cardio-vascular disease and are also linked with the climate through scattering of radiation and indirect effects such as cloud formation. The Aerodyne Aerosol Mass Spectrometer (AMS) provides a powerful tool to elucidate the sources and processing of organic aerosol in the urban atmosphere. Normally this is done through concentration measurements, by statistical analysis of the organic mass spectra, e.g. using Positive Matrix Factorization (PMF). Recently the quadrupole based AMS (Q-AMS) has been used for the micrometeorological measurement of organic aerosol fluxes above several cities, based on high frequency measurements of individual masses (m/z) representative of different organic mass fractions. While providing a major step forward towards quantification of urban organic aerosol emissions and processing, the interpretation of Q-AMS flux data requires assumptions to scale up signals on individual m/z to total organic mass fluxes. In this paper we present chemically-speciated and size-segregated number aerosol fluxes measured using the next generation eddy covariance flux system based on the Aerodyne HR-ToF-AMS, now capable of recording fast-response eddy-covariance time-series of all m/z simultaneously. This allows organic mass fluxes to be calculated more quantitatively and provides 'flux mass spectra' in addition to concentration mass spectra, which produces novel information on the local emission and processing of organic aerosols in the urban environment, while concentration analysis includes the regional background. The measurements were

Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays.

PubMed

Lee, Hayun; Zhou, Yi; Taylor, David W; Sashital, Dipali G

2018-04-05

CRISPR-Cas immune systems integrate short segments of foreign DNA as spacers into the host CRISPR locus to provide molecular memory of infection. Cas4 proteins are widespread in CRISPR-Cas systems and are thought to participate in spacer acquisition, although their exact function remains unknown. Here we show that Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4 interacts tightly with the Cas1 integrase, forming a heterohexameric complex containing two Cas1 dimers and two Cas4 subunits. In the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Our results reveal the critical role of Cas4 in maintaining fidelity during CRISPR adaptation, providing a structural and mechanistic model for prespacer processing and integration. Copyright © 2018 Elsevier Inc. All rights reserved.

Aerosol Absorption Measurements in MILAGRO.

NASA Astrophysics Data System (ADS)

Gaffney, J. S.; Marley, N. A.; Arnott, W. P.; Paredes-Miranda, L.; Barnard, J. C.

2007-12-01

During the month of March 2006, a number of instruments were used to determine the absorption characteristics of aerosols found in the Mexico City Megacity and nearby Valley of Mexico. These measurements were taken as part of the Department of Energy's Megacity Aerosol Experiment - Mexico City (MAX-Mex) that was carried out in collaboration with the Megacity Interactions: Local and Global Research Observations (MILAGRO) campaign. MILAGRO was a joint effort between the DOE, NSF, NASA, and Mexican agencies aimed at understanding the impacts of a megacity on the urban and regional scale. A super-site was operated at the Instituto Mexicano de Petroleo in Mexico City (designated T-0) and at the Universidad Technologica de Tecamac (designated T-1) that was located about 35 km to the north east of the T-0 site in the State of Mexico. A third site was located at a private rancho in the State of Hidalgo approximately another 35 km to the northeast (designated T-2). Aerosol absorption measurements were taken in real time using a number of instruments at the T-0 and T-1 sites. These included a seven wavelength aethalometer, a multi-angle absorption photometer (MAAP), and a photo-acoustic spectrometer. Aerosol absorption was also derived from spectral radiometers including a multi-filter rotating band spectral radiometer (MFRSR). The results clearly indicate that there is significant aerosol absorption by the aerosols in the Mexico City megacity region. The absorption can lead to single scattering albedo reduction leading to values below 0.5 under some circumstances. The absorption is also found to deviate from that expected for a "well-behaved" soot anticipated from diesel engine emissions, i.e. from a simple 1/lambda wavelength dependence for absorption. Indeed, enhanced absorption is seen in the region of 300-450 nm in many cases, particularly in the afternoon periods indicating that secondary organic aerosols are contributing to the aerosol absorption. This is likely due

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

PubMed Central

Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, Ricardo

2016-01-01

The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo. DOI: http://dx.doi.org/10.7554/eLife.13450.001 PMID:27130520

CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum.

PubMed

Pohl, C; Kiel, J A K W; Driessen, A J M; Bovenberg, R A L; Nygård, Y

2016-07-15

CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.

Two-Column Aerosol Project (TCAP) Field Campaign Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berg, Larry K

This study included the deployment of the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Mobile Facility (AMF), ARM Mobile Aerosol Observing System (MAOS) and the ARM Aerial Facility (AAF). The study was a collaborative effort involving scientists from DOE national laboratories, NOAA, NASA, and universities. The AAF and MAOS were deployed for two approximately month-long Intensive Operational Periods (IOPs) conducted in June 2012 and February 2013. Seasonal differences in the aerosol chemical and optical properties observed using the AMF, AAF, and MAOS are presented in this report. The total mass loading of aerosol is found tomore » be much greater in the summer than in the winter, with the difference associated with greater amounts of organic aerosol. The mass fraction of organic aerosol is much reduced in the winter, when sulfate is the dominant aerosol type. Surprisingly, very little sea-salt aerosol was observed in the summer. In contrast, much more sea salt aerosol was observed in the winter. The mass loading of black carbon is nearly the same in both seasons. These differences lead to a relative increase in the aerosol light absorption in the winter and an associated decrease in observed single-scattering albedo. Measurements of aerosol mixing state were made using a single-particle mass spectrometer, which showed that the majority of the summertime aerosol consisted of organic compounds mixed with various amounts of sulfate. A number of other findings are also summarized in the report, including: impact of aerosol layers aloft on the column aerosol optical depth; documentation of the aerosol properties at the AMF; differences in the aerosol properties associated with both columns, which are not systematic but reflect the complicated meteorological and chemical processes that impact aerosol as it is advected away from North America; and new instruments and data-processing techniques for measuring both

Characterizing LEDAPS surface reflectance products by comparisons with AERONET, field spectrometer, and MODIS data

USGS Publications Warehouse

Maiersperger, Tom; Scaramuzza, Pat; Leigh, Larry; Shrestha, S.; Gallo, Kevin; Jenkerson, Calli B.; Dwyer, John L.

2013-01-01

This study provides a baseline quality check on provisional Landsat Surface Reflectance (SR) products as generated by the U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center using Landsat Ecosystem Disturbance Adaptive Processing System (LEDAPS) software. Characterization of the Landsat SR products leveraged comparisons between aerosol optical thickness derived from LEDAPS and measured by Aerosol Robotic Network (AERONET), as well as reflectance correlations with field spectrometer and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Results consistently indicated similarity between LEDAPS and alternative data products in longer wavelengths over vegetated areas with no adjacent water, while less reliable performance was observed in shorter wavelengths and sparsely vegetated areas. This study demonstrates the strengths and weaknesses of the atmospheric correction methodology used in LEDAPS, confirming its successful implementation to generate Landsat SR products.

Aerosol fluxes and dynamics within and above a tropical rainforest in South-East Asia

NASA Astrophysics Data System (ADS)

Whitehead, J. D.; Gallagher, M. W.; Dorsey, J. R.; Robinson, N.; Gabey, A. M.; Coe, H.; McFiggans, G.; Flynn, M. J.; Ryder, J.; Nemitz, E.; Davies, F.

2010-10-01

Atmospheric aerosol measurements were conducted near Danum Valley, in the Malaysian state of Sabah, North-East Borneo, as part of the OP3 and ACES projects, in April and June/July 2008. Here, aerosol fluxes and diurnal variability in and above the rainforest canopy were examined in order to gain an understanding of their behaviour in the surface layer of the South-East Asian rainforest. Aerosol fluxes were calculated by eddy covariance from measurements above the rainforest canopy on the Global Atmosphere Watch (GAW) tower. Upward fluxes were seen on most mornings between 09:00 and 11:00 local time and this could be attributed to venting of the nocturnal boundary layer as it broke up in the morning. Measurements were also conducted within the canopy and trunk space at a nearby site. Profiles in aerosol number concentrations were investigated using GRIMM Optical Particle Counters (OPCs) at various levels within the rainforest canopy and trunk space, as well as a single OPC on a vertically moving platform. These showed an overnight increase in larger particles (1-20 μm) at all levels, but much more prominently near the top of the canopy, which could be attributed to fog formation. At ground level, number concentrations in this size range correlated with enhancements in biological aerosol concentrations, measured using a Wide Issue Bioaerosol Spectrometer (WIBS) located near the forest floor, suggesting that coarse particle number concentrations were dominated by biological aerosols. A comparison of particle number concentrations (in the size range 0.5-1.0 μm) between above canopy and the trunk space showed correlations, despite turbulence data suggesting persistent decoupling between the two measurement sites. These correlations often relied on a shift of the particle time-series against each other, implying a time delay in observations between the sites, which varied according to time of day. This lag time was shortest during the middle of the day by a significant

Spatio-temporal variability in cloud microphysical properties over the South East Atlantic

NASA Astrophysics Data System (ADS)

Gupta, S.; McFarquhar, G. M.; Poellot, M.; O'Brien, J.; Delene, D. J.

2016-12-01

The ObseRvations of Aerosols above Clouds and their intEractionS (ORACLES) project will provide in-situ measurements and remotely sensed retrievals of aerosol and cloud properties over the South East Atlantic off the coast of Namibia during August-September 2016. Biomass burning aerosol from Southern Africa is advected toward the South East Atlantic at elevated altitudes and overlies the ubiquitous stratocumulus cloud deck over the ocean. The aerosols subside farther from the coast so that the vertical displacement between the clouds and aerosols varies, and whose effect on aerosol-cloud interaction is poorly known. A NASA P-3 aircraft will be equipped with a Cloud Droplet Probe CDP sizing particles between 2 and 50μm, a Cloud and Aerosol Spectrometer CAS sizing between 0.51 and 50μm, a 2D-stereo probe 2DS, nominally sizing between 10 and 1280μm, a Cloud Imaging Probe CIP, from 25 to 1600μm, and a High Volume Precipitation Sampler HVPS-3, from 150μm to 1.92cm for measuring number distribution functions (n(D)) along with a King probe and hot wire probe for measuring the total liquid water content, LWC. A Passive Cavity Aerosol Spectrometer Probe PCASP will measure aerosol particles between 0.1 to 3μm. By examining consistency between n(D) measured by probes in the overlap ranges and by conducting closure tests whereby the bulk LWC is compared against that derived from n(D), a probe-independent product will be generated to provide the best estimate of the following cloud parameters: total concentration, extinction, n(D), effective radius and LWC. The resulting database will be used to determine how cloud properties vary with distance away from the coast of Africa and with aerosol concentrations measured in the accumulation mode by the PCASP above and below cloud. The impact of the changing separation between the cloud and aerosol layers will be examined and potential impacts of the variation of cloud microphysical properties with aerosol concentrations on

Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

PubMed Central

Ma, Enbo; Harrington, Lucas B.; O’Connell, Mitchell R.; Zhou, Kaihong; Doudna, Jennifer A.

2015-01-01

Summary Double-stranded DNA (dsDNA) cleavage by Cas9 is a hallmark of type II CRISPR-Cas immune systems. Cas9–guide RNA complexes recognize 20-base-pair sequences in DNA and generate a site-specific double-strand break, a robust activity harnessed for genome editing. DNA recognition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site. We show that Cas9 enzymes from evolutionarily divergent bacteria can recognize and cleave single-stranded DNA (ssDNA) by an RNA-guided, PAM-independent recognition mechanism. Comparative analysis shows that in contrast to the type II-A S. pyogenes Cas9 that is widely used for genome engineering, the smaller type II-C Cas9 proteins have limited dsDNA binding and unwinding activity and promiscuous guide-RNA specificity. These results indicate that inefficiency of type II-C Cas9 enzymes for genome editing results from a limited ability to cleave dsDNA, and suggest that ssDNA cleavage was an ancestral function of the Cas9 enzyme family. PMID:26545076

Primary and secondary organic aerosols in Fresno, California during wintertime: Results from high resolution aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Ge, Xinlei; Setyan, Ari; Sun, Yele; Zhang, Qi

2012-10-01

Organic aerosols (OA) were studied in Fresno, California, in winter 2010 with an Aerodyne High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS). OA dominated the submicron aerosol mass (average = 67%) with an average concentration of 7.9μg m-3 and a nominal formula of C1H1.59N0.014O0.27S0.00008, which corresponds to an average organic mass-to-carbon ratio of 1.50. Three primary OA (POA) factors and one oxygenated OA factor (OOA) representative of secondary OA (SOA) were identified via Positive Matrix Factorization of the high-resolution mass spectra. The three POA factors, which include a traffic-related hydrocarbon-like OA (HOA), a cooking OA (COA), and a biomass burning OA (BBOA) released from residential heating, accounted for an average 57% of the OA mass and up to 80% between 6 - 9 P.M., during which enhanced emissions from evening rush hour traffic, dinner cooking, and residential wood burning were exacerbated by low mixed layer height. The mass-based size distributions of the OA factors were estimated based on multilinear analysis of the size-resolved mass spectra of organics. Both HOA and BBOA peaked at ˜140 nm in vacuum aerodynamic diameter (Dva) while OOA peaked at an accumulation mode of ˜460 nm. COA exhibited a unique size distribution with two size modes centering at ˜200 nm and 450 nm respectively. This study highlights the leading roles played by anthropogenic POA emissions, primarily from traffic, cooking and residential heating, in aerosol pollution in Fresno in wintertime.

Geostationary Environment Monitoring Spectrometer (gems) Over the Korea Peninsula and Asia-Pacific Region

NASA Astrophysics Data System (ADS)

Lasnik, J.; Stephens, M.; Baker, B.; Randall, C.; Ko, D. H.; Kim, S.; Kim, Y.; Lee, E. S.; Chang, S.; Park, J. M.; SEO, S. B.; Youk, Y.; Kong, J. P.; Lee, D.; Lee, S. H.; Kim, J.

2014-12-01

Introduction: The Geostationary Environment Monitoring Spectrometer (GEMS) is one of two instruments manifested aboard the South Korean Geostationary Earth Orbit KOrea Multi-Purpose SATellite-2B (GEO-KOMPSAT-2B or GK2B), which is scheduled to launch in 2018. Jointly developed/built by KARI and Ball Aerospace, GEMS is a geostationary UV-Vis hyperspectral imager designed to monitor trans-boundary tropospheric pollution events over the Korean peninsula and Asia-Pacific region. The spectrometer provides high temporal and spatial resolution (3.5 km N/S by 7.2 km E/W) measurements of ozone, its precursors, and aerosols. Over the short-term, hourly measurements by GEMS will improve early warnings for potentially dangerous pollution events and monitor population exposure. Over the 10-year mission-life, GEMS will serve to enhance our understanding of long-term climate change and broader air quality issues on both a regional and global scale. The GEMS sensor design and performance are discussed, which includes an overview of measurement capabilities and the on-orbit concept of operations. GEMS Sensor Overview: The GEMS hyperspectral imaging system consists of a telescope and Offner grating spectrometer that feeds a single CCD detector array. A spectral range of 300-500 nm and sampling of 0.2 nm enables NO2, SO2, HCHO, O3, and aerosol retrieval. The GEMS field of regard (FOR), which extends from 5°S to 45°N in latitude and 75°E to 145°E in longitude, is operationally achieved using an onboard two-axis scan mirror. On-orbit, the radiometric calibration is maintained using solar measurements, which are performed using two onboard diffusers: a working diffuser that is deployed routinely for the purpose of solar calibration, and a reference diffuser that is deployed sparingly for the purpose of monitoring working diffuser performance degradation.

Vertical Profiles of Aerosol Volume from High Spectral Resolution Infrared Transmission Measurements: Results

NASA Technical Reports Server (NTRS)

Eldering, Annmarie; Kahn, Brian H.; Mills, Franklin P.; Irion, Fredrick W.; Steele, Helen M.; Gunson, Michael R.

2004-01-01

The high-resolution infrared absorption spectra of the Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment are utilized to derive vertical profiles of sulfate aerosol volume density and extinction coefficient. Following the eruption of Mt. Pinatubo in June 1991, the ATMOS spectra obtained on three Space Shuttle missions (1992, 1993, and 1994) provide a unique opportunity to study the global stratospheric sulfate aerosol layer shortly after a major volcanic eruption and periodically during the decay phase. Synthetic sulfate aerosol spectra are fit to the observed spectra, and a global fitting inversion routine is used to derive vertical profiles of sulfate aerosol volume density. Vertical profiles of sulfate aerosol volume density for the three missions over portions of the globe are presented, with the peak in aerosol volume density occurring from as low as 10 km (polar latitudes) to as high as 20 km (subtropical latitudes). Derived aerosol volume density is as high as 2-3.5 (mu)m(exp 3) per cubic centimeter +/-10% in 1992, decreasing to 0.2-0.5 (mu)m(exp 3) per cubic centimeter +/-20% in 1994, in agreement with other experiments. Vertical extinction profiles derived from ATMOS are compared with profiles from Improved Stratospheric And Mesospheric Sounder (ISAMS) and Cryogenic Limb Array Etalon Spectrometer (CLAES) that coincide in space and time and show good general agreement. The uncertainty of the ATMOS vertical profiles is similar to CLAES and consistently smaller than ISAMS at similar altitudes.

Sources, Composition, and Properties of Newly Formed and Regional Organic Aerosol in a Boreal Forest during the Biogenic Aerosol: Effects on Clouds and Climate Field Campaign Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thornton, Joel

2016-05-01

The Thornton Laboratory participated in the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Biogenic Aerosol Effects on Clouds and Climate (BAECC) campaign in Finland by deploying our mass spectrometer. We then participated in environmental simulation chamber studies at Pacific Northwest National Laboratory (PNNL). Thereafter, we analyzed the results as demonstrated in the several presentations and publications. The field campaign and initial environmental chamber studies are described below.

Ultra-Low Background Measurements Of Decayed Aerosol Filters

NASA Astrophysics Data System (ADS)

Miley, H.

2009-04-01

To experimentally evaluate the opportunity to apply ultra-low background measurement methods to samples collected, for instance, by the Comprehensive Test Ban Treaty International Monitoring System (IMS), aerosol samples collected on filter media were measured using HPGe spectrometers of varying low-background technology approaches. In this way, realistic estimates of the impact of low-background methodology can be assessed on the Minimum Detectable Activities obtained in systems such as the IMS. The current measurement requirement of stations in the IMS is 30 microBq per cubic meter of air for 140Ba, or about 106 fissions per daily sample. Importantly, this is for a fresh aerosol filter. Decay varying form 3 days to one week reduce the intrinsic background from radon daughters in the sample. Computational estimates of the improvement factor for these decayed filters for underground-based HPGe in clean shielding materials are orders of magnitude less, even when the decay of the isotopes of interest is included.

Application of CRISPR/Cas9 in plant biology.

PubMed

Liu, Xuan; Wu, Surui; Xu, Jiao; Sui, Chun; Wei, Jianhe

2017-05-01

The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) system was first identified in bacteria and archaea and can degrade exogenous substrates. It was developed as a gene editing technology in 2013. Over the subsequent years, it has received extensive attention owing to its easy manipulation, high efficiency, and wide application in gene mutation and transcriptional regulation in mammals and plants. The process of CRISPR/Cas is optimized constantly and its application has also expanded dramatically. Therefore, CRISPR/Cas is considered a revolutionary technology in plant biology. Here, we introduce the mechanism of the type II CRISPR/Cas called CRISPR/Cas9, update its recent advances in various applications in plants, and discuss its future prospects to provide an argument for its use in the study of medicinal plants.

Light-Absorbing Brown Carbon Aerosol Constituents from Combustion of Indonesian Peat and Biomass.

PubMed

Budisulistiorini, Sri Hapsari; Riva, Matthieu; Williams, Michael; Chen, Jing; Itoh, Masayuki; Surratt, Jason D; Kuwata, Mikinori

2017-04-18

Light-absorbing brown carbon (BrC) constituents of organic aerosol (OA) have been shown to significantly absorb ultraviolet (UV) and visible light and thus impact radiative forcing. However, molecular identification of the BrC constituents is still limited. In this study, we characterize BrC constituents at the molecular level in (i) aerosols emitted by combustion of peat, fern/leaf, and charcoal from Indonesia and (ii) ambient aerosols collected in Singapore during the 2015 haze episode. Aerosols were analyzed using ultra performance liquid chromatography instrument interfaced to a diode array detector and electrospray ionization high-resolution quadrupole time-of-flight mass spectrometer operated in the negative ion mode. In the laboratory-generated aerosols, we identified 41 compounds that can potentially absorb near-UV and visible wavelengths, such as oxygenated-conjugated compounds, nitroaromatics, and S-containing compounds. The sum of BrC constituents in peat, fern/leaf, and charcoal burning aerosols are 16%, 35%, and 28% of the OA mass, respectively, giving an average contribution of 24%. On average, the BrC constituents account for 0.4% of the ambient OA mass; however, large uncertainties in mass closure remain because of the lack of authentic standards. This study highlights the potential of light-absorbing BrC OA constituents from peat, fern/leaf, and charcoal burning and their importance in the atmosphere.

Reactive Heterogeneous Chemistry on Organic Aerosols: Two Case Studies

NASA Astrophysics Data System (ADS)

Abbatt, J.; Braban, C.; Broekhuizen, K.; Thornberry, T.; Thornton, J.

2003-12-01

Two sets of laboratory studies will be discussed to illustrate the impact that heterogeneous chemistry involving tropospheric organic aerosols may have on both the gas-phase composition of the atmosphere and the chemical nature of the particles themselves. In the first case, the reactive uptake coefficient for the hydrolysis of dinitrogen pentoxide (N2O5) on organic aerosols has been measured in an entrained aerosol flow tube coupled to a Chemical-Ionization Mass Spectrometer (CIMS). The general observation is that the reaction on aqueous malonic acid aerosols behaves in an analogous manner to that on aqueous inorganic salts, i.e. the uptake coefficient shows a linear dependence on the particle water content up to 50% relative humidity (RH), at which point the effect saturates. In addition, there is evidence for the kinetics being dependent on both the size of the particles and the levels of dissolved nitrate. By contrast, the N2O5 hydrolysis kinetics on solid azelaic acid particles are too slow to be atmospherically significant, even at 85% RH. In the second case, the kinetics and product yields from the oxidation of liquid oleic acid by ozone have been studied in considerable detail, with emphasis on the quantification of gas-phase products (nonanal) by CIMS and water-soluble species by HPLC/Electrospray-Ionization Mass Spectrometry (azelaic acid, nonanoic acid). The atmospheric importance of these results will be discussed, in particular with respect to the role of organic aerosol oxidation as a source of cloud condensation nuclei.

Spatial and temporal distributions of ice nucleating particles during the Atmospheric Radiation Measurement (ARM) Cloud Aerosol Precipitation Experiment (ACAPEX)

NASA Astrophysics Data System (ADS)

Levin, E. J.; DeMott, P. J.; Suski, K. J.; Boose, Y.; Hill, T. C. J.; McCluskey, C. S.; Schill, G. P.; Duncan, D.; Al-Mashat, H.; Prather, K. A.; Sedlacek, A. J., III; Tomlinson, J. M.; Mei, F.; Hubbe, J. M.; Pekour, M. S.; Leung, L. R.; Kreidenweis, S. M.

2016-12-01

California is currently under drought conditions and changes in precipitation due to future climate change scenarios are uncertain. Thus, understanding the controlling factors for precipitation in this region, and having the capability to accurately model these scenarios, is important. A crucial area in understanding precipitation is in the interplay between atmospheric moisture and aerosols. Specifically, ice nucleation in clouds is an important process controlling precipitation formation. A major component of CA's yearly precipitation comes from wintertime atmospheric river (AR) events which were the focus of the 2015 Atmospheric Radiation Measurement (ARM) Cloud Aerosol Precipitation Experiment (ACAPEX) and CalWater 2 campaigns. These two campaigns provided sampling platforms on four aircraft, including the ARM Aerial Facility G-1, as well as the NOAA Ron Brown research vessel and at a ground station at Bodega Bay, CA. Measurements of ice nucleating particles (INPs) were made with the Colorado State University (CSU) Continuous Flow Diffusion Chamber (CFDC) aboard the G-1 and at Bodega Bay, and using aerosol filter collections on these platforms as well as the Ron Brown for post-processing via immersion freezing in the CSU Ice Spectrometer. Aerosol composition was measured aboard the G-1 with the Aerosol Time-of-Flight Mass Spectrometer (ATOFMS). Both the CFDC and ATOFMS sampled off of an isokinetic inlet when flying in clear air and a counter-flow virtual impactor in clouds to capture ice crystal and cloud droplet residuals. In this presentation we present ice nucleating particle concentrations before, during and after an AR event from air, ground and ocean-based measurements. We also examine INP concentration variability in orographic clouds and in clear air at altitude along the Sierra Nevada range, in the marine boundary layer and through the Central Valley, and relate these INP measurements to other aerosol physical and chemical properties.