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At least 1,783 records · Page 99

Abiotic ozone and oxygen in atmospheres similar to prebiotic Earth

The search for life on planets outside our solar system will use spectroscopic identification of atmospheric biosignatures. The most robust remotely detectable potential biosignature is considered to be the detection of oxygen (O{sub 2}) or ozone (O{sub 3}) simultaneous to methane (CH{sub 4}) at levels indicating fluxes from the planetary surface in excess of those that could be produced abiotically. Here we use an altitude-dependent photochemical model with the enhanced lower boundary conditions necessary to carefully explore abiotic O{sub 2} and O{sub 3} production on lifeless planets with a wide variety of volcanic gas fluxes and stellar energy distributions. On some of these worlds, we predict limited O{sub 2} and O{sub 3} buildup, caused by fast chemical production of these gases. This results in detectable abiotic O{sub 3} and CH{sub 4} features in the UV-visible, but no detectable abiotic O{sub 2} features. Thus, simultaneous detection of O{sub 3} and CH{sub 4} by a UV-visible mission is not a strong biosignature without proper contextual information. Discrimination between biological and abiotic sources of O{sub 2} and O{sub 3} is possible through analysis of the stellar and atmospheric context—particularly redox state and O atom inventory—of the planet in question. Specifically, understanding the spectral characteristics of the star and obtaining a broad wavelength range for planetary spectra should allow more robust identification of false positives for life. This highlights the importance of wide spectral coverage for future exoplanet characterization missions. Specifically, discrimination between true and false positives may require spectral observations that extend into infrared wavelengths and provide contextual information on the planet's atmospheric chemistry.

79 ASTRONOMY AND ASTROPHYSICS↗

A SECOND NEUTRON STAR IN M4?

We show that the optical counterpart of the X-ray source CX 1 in M4 is a {approx}20th magnitude star, located in the color-magnitude diagram on (or very close to) the main sequence of the cluster, and exhibiting sinusoidal variations of the flux. We find the X-ray flux to be also periodically variable, with X-ray and optical minima coinciding. Stability of the optical light curve, lack of UV-excess, and unrealistic mean density resulting from period-density relation for semidetached systems speak against the original identification of CX 1 as a cataclysmic variable. We argue that the X-ray active component of this system is a neutron star (probably a millisecond pulsar).

79 ASTRONOMY AND ASTROPHYSICS↗

A Bayesian approach to multi-messenger astronomy: identification of gravitational-wave host galaxies

We present a general framework for incorporating astrophysical information into Bayesian parameter estimation techniques used by gravitational wave data analysis to facilitate multi-messenger astronomy. Since the progenitors of transient gravitational wave events, such as compact binary coalescences, are likely to be associated with a host galaxy, improvements to the source sky location estimates through the use of host galaxy information are explored. To demonstrate how host galaxy properties can be included, we simulate a population of compact binary coalescences and show that for ∼8.5% of simulations within 200 Mpc, the top 10 most likely galaxies account for a ∼50% of the total probability of hosting a gravitational wave source. The true gravitational wave source host galaxy is in the top 10 galaxy candidates ∼10% of the time. Furthermore, we show that by including host galaxy information, a better estimate of the inclination angle of a compact binary gravitational wave source can be obtained. We also demonstrate the flexibility of our method by incorporating the use of either the B or K band into our analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

The identification of H3S(+) with the ion of mass per charge (m/q) 35 observed in the coma of Comet Halley

A sharp peak in the mass spectrum at 35 amu is observed by the heavy ion analyzer on board the Giotto spacecraft just inside the ionopause. This peak is identified with H3S(+) and it is argued that the dominant source of its likely parent molecule (H2S) is the observed distributed source of circumnuclear dust, rather than the central nucleus. In this case, the total production rate of H2S is more than about 0.5 percent that of the dominant cometary molecule H2O.

Marconi, M. L.↗

MILLIMETER AND SUBMILLIMETER REST FREQUENCIES FOR NaCN (X-tilde{sup 1}A'): A REMARKABLY ABUNDANT CIRCUMSTELLAR MOLECULE

The pure rotational spectrum of NaCN has been recorded in the millimeter/submillimeter region using direct absorption techniques, the first experimental study of this molecule at frequencies above 40 GHz. The species was produced in the gas phase in an AC discharge by the reaction of sodium vapor with cyanogen. Twelve rotational transitions of NaCN have been measured in the range of 180-530 GHz, extending the previous microwave data to millimeter/submillimeter frequencies. Multiple K{sub a} asymmetry components were recorded in each rotational transition up to K{sub a} = 5 or 6, a total of 131 individual lines. These data have been analyzed with a standard asymmetric top Hamiltonian, combined with prior microwave measurements. Higher-order centrifugal distortion terms were clearly needed to model the millimeter-wave transitions of this floppy molecule. From this revised set of spectroscopic constants, accurate frequency predictions can now be made up to 600 GHz for NaCN for the lower-value K{sub a} components (K{sub a} {<=} 4). Based on the new laboratory data and past spectral surveys, a revised abundance for NaCN in IRC+10216 has been estimated. For a 5'' source, the fractional abundance for this molecule was found to be f (NaCN/H{sub 2}) {approx} 1 x 10{sup -8}, comparable to that of c-C{sub 3}H{sub 2}. These new frequency measurements should aid in line identification in surveys in the 0.8 mm band and at shorter wavelengths.

79 ASTRONOMY AND ASTROPHYSICS↗

EVIDENCE THAT GAMMA-RAY BURST 130702A EXPLODED IN A DWARF SATELLITE OF A MASSIVE GALAXY

GRB 130702A is a nearby long-duration gamma-ray burst (LGRB) discovered by the Fermi satellite whose associated afterglow was detected by the Palomar Transient Factory. Subsequent photometric and spectroscopic monitoring has identified a coincident broad-lined Type Ic supernova (SN), and nebular emission detected near the explosion site is consistent with a redshift of z = 0.145. The SN-GRB exploded at an offset of {approx}7.''6 from the center of an inclined r = 18.1 mag red disk-dominated galaxy, and {approx}0.''6 from the center of a much fainter r = 23 mag object. We obtained Keck-II DEIMOS spectra of the two objects and find a 2{sigma} upper limit on their line-of-sight velocity offset of {approx}<60 km s{sup -1}. If we calculate the inclination angle of the massive red galaxy from its axis ratio and assume that its light is dominated by a very thin disk, the explosion would have a {approx}60 kpc central offset, or {approx}9 times the galaxy's half-light radius. A significant bulge or a thicker disk would imply a higher inclination angle and greater central offset. The substantial offset suggests that the faint source is a separate dwarf galaxy. The star-formation rate of the dwarf galaxy is {approx}0.05 M{sub Sun} yr{sup -1}, and we place an upper limit on its oxygen abundance of 12 + log(O/H) < 8.16 dex. The identification of an LGRB in a dwarf satellite of a massive, metal-rich primary galaxy suggests that recent detections of LGRBs spatially coincident with metal-rich galaxies may be, in some cases, superpositions.

79 ASTRONOMY AND ASTROPHYSICS↗

Collaborative Research Towards a tonne-scale bolometer-based neutrinoless double beta decay experiment (Final Report)

Cryogenic bolometers are an excellent technology for neutrinoless double beta decay searches owing to their very high energy resolution and potential for high radiopurity. The current most advanced large-scale experiment using these detectors is the Cryogenic Underground Observatory for Rare Events (CUORE). The largest source of background in CUORE is degraded alpha particles, emitted from shallow depths of the detector holders, which can deposit a thermal energy signature similar to neutrinoless double beta decay. To mitigate this background, the CUPID concept (CUORE Upgrade with Particle IDentification) proposes to use scintillating cryogenic detectors. Detecting both the scintillation light and the thermal signal allows discrimination between alpha particle events and beta/gamma events. We report on the design and execution of R&D tests to optimize the design of the single detector module, in particular the scintillation light collection efficiency at cryogenic temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On C4H versus vibrationally excited CO in IRC + 10216

The identification of the 114,221-MHz line in the spectrum of the evolved carbon star IRC +10216 with a blend of the rotational transition of C4H and the first rotational transition of vibrationally excited CO is investigated. A spectrum of the source was obtained using an 11-m telescope in the range covering the N = 12 to 11 and 11 to 10 spin-doublet rotational transitions of C4H. Two peaks of equal intensity and width are found in each band, suggesting a spin rotation constant of 1.06 for the 12 to 11 doublet and 1.09 for the 11 to 10 doublet, and excluding the possibility that vibrationally excited CO made any contribution to the 12 to 11 doublet. An additional survey of the regions from 103.8 to 107.5 and 113.3 to 117.0 GHz has revealed no new lines stronger than 0.1 K in the spectrum of IRC +10216.

Cummins, S. E.↗

Application of Machine Learning Algorithms to the Study of Noise Artifacts in Gravitational-Wave Data

The sensitivity of searches for astrophysical transients in data from the Laser Interferometer Gravitationalwave Observatory (LIGO) is generally limited by the presence of transient, non-Gaussian noise artifacts, which occur at a high-enough rate such that accidental coincidence across multiple detectors is non-negligible. Furthermore, non-Gaussian noise artifacts typically dominate over the background contributed from stationary noise. These "glitches" can easily be confused for transient gravitational-wave signals, and their robust identification and removal will help any search for astrophysical gravitational-waves. We apply Machine Learning Algorithms (MLAs) to the problem, using data from auxiliary channels within the LIGO detectors that monitor degrees of freedom unaffected by astrophysical signals. Terrestrial noise sources may manifest characteristic disturbances in these auxiliary channels, inducing non-trivial correlations with glitches in the gravitational-wave data. The number of auxiliary-channel parameters describing these disturbances may also be extremely large; high dimensionality is an area where MLAs are particularly well-suited. We demonstrate the feasibility and applicability of three very different MLAs: Artificial Neural Networks, Support Vector Machines, and Random Forests. These classifiers identify and remove a substantial fraction of the glitches present in two very different data sets: four weeks of LIGO's fourth science run and one week of LIGO's sixth science run. We observe that all three algorithms agree on which events are glitches to within 10% for the sixth science run data, and support this by showing that the different optimization criteria used by each classifier generate the same decision surface, based on a likelihood-ratio statistic. Furthermore, we find that all classifiers obtain similar limiting performance, suggesting that most of the useful information currently contained in the auxiliary channel parameters we extract is already being used. Future performance gains are thus likely to involve additional sources of information, rather than improvements in the MLAs themselves.

gravitational-wave data↗

Lucy L’Ralph In-Flight Calibration and Results at (152830) Dinkinesh

The L'Ralph instrument is a key component of NASA's Lucy mission, intended to provide spectral image data of multiple Jupiter Trojans. The instrument operates from ∼0.35 to 4 μm using two focal plane assemblies: a 350–950 nm multispectral imager, Multi-spectral Visible Imaging Camera (MVIC), and a 0.97–4 μm imaging spectrometer, Linear Etalon Imaging Spectral Array (LEISA). Instrument calibration was established through ground testing before launch and has been monitored during cruise utilizing internal calibration sources and stellar targets. In-flight data have shown that the instrument thermal performance is exceeding expectations, allowing for early updates to LEISA radiometric and pointing calibrations. MVIC radiometric performance remains stable more than 3 yr since launch. The serendipitous identification of a new flyby target, (152830) Dinkinesh, allowed testing of instrument performance and interleaved LEISA and MVIC acquisitions on an asteroid target. Both MVIC and LEISA obtained data of Dinkinesh and its moon, Selam, demonstrating that they show good spectral agreement with an S- or Sq-type asteroid, along with evidence of a 3 μm absorption feature.

Amy A Simon↗

Planetary Protection at Marshall Space Flight Center

Introduction: NASA Marshall Space Flight Center (MSFC) is historically known for its role in propulsion. While this is still the mainstay of MSFC’s expertise, many unique capabilities exist at MSFC which pertain to Planetary Protection (PP), including 1) identifying PP threats, and 2) developing novel methods to neutralize those threats. Furthermore, because these capabilities exist among diverse groups at MSFC, this work promotes collaboration both within and outside MSFC to expand and develop PP studies related to a full spectrum of NASA research, design, manufacture, and test interests. This abstract describes the PP research ongoing at MSFC and describes how it contributes to NASA’s overall PP objectives. Microbial Identification in Cleanrooms: One of the greatest threats to successful implementation of PP requirements is recontamination post bioburden reduction. One method to prevent recontamination is to keep the spacecraft in clean environments (i.e. cleanrooms) as much as possible during assembly and integration. However, cleanrooms are not without their own sources of contamination, which is why NASA is interested in monitoring the cleanliness of cleanrooms and characterizing the microbial species present. Such information allows a greater understanding of the resistance of these microbes to cleaning methods, as well as the risk of their contaminating the targeted planetary body of a given mission. MSFC has multiple cleanrooms of various ISO cleanliness levels onsite. We sampled the air and surfaces of three of these rooms, isolated microbes, and then sequenced the 16S rRNA gene or ITS region of the 18S rRNA gene for bacterial and fungal isolates, respectively. This has resulted in a microbial library which currently includes nearly 100 isolates. Microbial Enumeration of Spacecraft Materials: Currently, there are only a couple bioburden reduction methods approved by NASA, and often the harshness of these methods presents additional concerns or risks related to material properties. The goal of this research is to assess the microbial content of solid rocket motor (SRM) materials potentially used for lander missions. This work aims to more accurately define the risk of planetary contamination by providing empirical data associated with commonly used SRM raw materials. In this study, we pulverized nonmetallic SRM materials using a cryogenic grinder, then analyzed the resulting substrate for microbial colony forming units (CFU). We found that many SRM nonmetallic materials do not harbor detectable bioburden, though a range existed depending on the material. The results from this work provide quantitative data to potentially reduce concerns of contamination, while also providing a foundation for follow up studies into additional sterilization methods and molecular identification of contaminating microbes. Space Environmental Effects on Microbial Survival: One potential area of microbial reduction is the space environment. Understanding the survivability of hardy microbes in space-like conditions is a crucial first step in answering how space may reduce bioburden and if it can be relied upon for adherence to PP requirements. This work studied the effects of ultraviolet (UV) and ionizing radiation on survival of Bacillus atrophaeus spores. Microbes were dried on relevant polymeric materials then exposed to space environmental stressors. Coupons were submerged in water, diluted, and plated to determine survival compared with controls. We found that both UV and ionizing radiation were capable of reducing viability by nearly 99%, but there were still survivors, some with changed morphology indicating resistance mechanisms within certain cells. Manufacturing credit: Finally, given the above-mentioned limitations of the NASA-approved bioburden reduction methods, there is interest in understanding if manufacturing processes may provide enough bioburden reduction without additional PP-specific bakeouts. For instance, some material additives may be antimicrobial. Given this, we investigated the effects of several commonly used rubber additives on the growth of B. atrophaeus spores. We found that some of the materials inhibited growth of the spores, possibly supporting the use of these additives on missions with PP constraints. Future work into manufacturing credit for bioburden reduction includes inoculation of green insulation with B. atrophaeus spores, followed by a typical cure. Thermal profiles will be verified for appropriate temperature and durations to meet PP requirements, and cured samples will be analyzed using a cryogenic grinder to determine survivability of spores.

Chelsi D. Cassilly↗

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of changes subsurface electrical conductivity, in both the saturated and unsaturated zones, arising from water table changes and from river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev .

Environmental Molecular Sciences Laboratory↗

Demonstration of neutron identification in neutrino interactions in the MicroBooNE liquid argon time projection chamber

A significant challenge in measurements of neutrino oscillations is reconstructing the incoming neutrino energies. While modern fully-active tracking calorimeters such as liquid argon time projection chambers in principle allow the measurement of all final state particles above some detection threshold, undetected neutrons remain a considerable source of missing energy with little to no data constraining their production rates and kinematics. We present the first demonstration of tagging neutrino-induced neutrons in liquid argon time projection chambers using secondary protons emitted from neutron-argon interactions in the MicroBooNE detector. We describe the method developed to identify neutrino-induced neutrons and demonstrate its performance using neutrons produced in muon-neutrino charged current interactions. The method is validated using a small subset of MicroBooNE’s total dataset. The selection yields a sample with 60% of selected tracks corresponding to neutron-induced secondary protons. At this purity, the integrated efficiency is 8.4% for neutrons that produce a detectable proton.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Identification of PM{sub 10} characteristics involved in cellular responses in human bronchial epithelial cells (Beas-2B)

Notwithstanding evidence is present that physicochemical characteristics of ambient particles attribute to adverse health effects, there is still some lack of understanding in this complex relationship. At this moment it is not clear which properties (such as particle size, chemical composition) or sources of the particles are most relevant for health effects. This study investigates the in vitro toxicity of PM{sub 10} in relation to PM chemical composition, black carbon (BC), endotoxin content and oxidative potential (OP). In 2013–2014 PM{sub 10} was sampled (24 h sampling, 108 sampling days) in ambient air at three sites in Flanders (Belgium) with different pollution characteristics: an urban traffic site (Borgerhout), an industrial area (Zelzate) and a rural background location (Houtem). To characterize the toxic potential of PM{sub 10}, airway epithelial cells (Beas-2B cells) have been exposed to particles in vitro. Different endpoints were studied including cell damage and death (cell viability) using the Neutral red Uptake assay, the production of pro-inflammatory molecules by interleukin 8 (IL-8) induction and DNA-damaging activity using the FPG-modified Comet assay. The endotoxin levels in the collected samples were analysed and the capacity of PM{sub 10} particles to produce reactive oxygen species (OP) was evaluated by electron paramagnetic resonance (EPR) spectroscopy. Chemical characteristics of PM{sub 10} (BC, As, Cd, Cr, Cu, Mn, Ni, Pb, Zn) and meteorological conditions were recorded on the sampling days. PM{sub 10} particles exhibited dose-dependent cytotoxicity in Beas-2B cells and were found to significantly induce the release of IL-8 in samples from the three locations. Oxidatively damaged DNA was observed in exposed Beas-2B cells. Endotoxin levels above the detection limit were detected in half of the samples. OP was measurable in all samples. Associations between PM{sub 10} characteristics and biological effects of PM{sub 10} were assessed by single and multiple regression analyses. The reduction in cell viability was significantly correlated with BC, Cd and Pb. The induction of IL-8 in Beas-2B cells was significantly associated with Cu, Ni and Zn and endotoxin. Endotoxin levels explained 33% of the variance in IL-8 induction. A significant interaction between ambient temperature and endotoxin on the pro-inflammatory activity was seen. No association was found between OP and the cellular responses. This study supports the hypothesis that, on an equal mass basis, PM{sub 10} induced biological effects differ due to differences in PM{sub 10} characteristics. Metals (Cd, Cu, Ni and Zn), BC, and endotoxin were among the main determinants for the observed biological responses. - Highlights: • On an equal mass basis, PM{sub 10} sampled at an urban, rural and industrial site induced different cellular effects in Beas-2B. • Endotoxin levels and oxidative potential (OP) were analysed in the PM{sub 10} samples. • Black carbon, cadmium and lead were correlated with decreased cell viability. • Endotoxin levels explained the majority of the variance in il-8 induction. • Oxidatively damaged DNA was observed in all the samples.

54 ENVIRONMENTAL SCIENCES↗

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗

DISCOVERING THE MISSING 2.2 < z < 3 QUASARS BY COMBINING OPTICAL VARIABILITY AND OPTICAL/NEAR-INFRARED COLORS

The identification of quasars in the redshift range 2.2 < z < 3 is known to be very inefficient because the optical colors of such quasars are indistinguishable from those of stars. Recent studies have proposed using optical variability or near-infrared (near-IR) colors to improve the identification of the missing quasars in this redshift range. Here we present a case study combining both methods. We select a sample of 70 quasar candidates from variables in Sloan Digital Sky Survey (SDSS) Stripe 82, which are non-ultraviolet excess sources and have UKIDSS near-IR public data. They are clearly separated into two parts on the Y - K/g - z color-color diagram, and 59 of them meet or lie close to a newly proposed Y - K/g - z selection criterion for z < 4 quasars. Of these 59 sources, 44 were previously identified as quasars in SDSS DR7, and 35 of them are quasars at 2.2 < z < 3. We present spectroscopic observations of 14 of 15 remaining quasar candidates using the Bok 2.3 m telescope and the MMT 6.5 m telescope, and successfully identify all of them as new quasars at z = 2.36-2.88. We also apply this method to a sample of 643 variable quasar candidates with SDSS-UKIDSS nine-band photometric data selected from 1875 new quasar candidates in SDSS Stripe 82 given by Butler and Bloom based on the time-series selections, and find that 188 of them are probably new quasars with photometric redshifts at 2.2 < z < 3. Our results indicate that the combination of optical variability and optical/near-IR colors is probably the most efficient way to find 2.2 < z < 3 quasars and is very helpful for constructing a complete quasar sample. We discuss its implications for ongoing and upcoming large optical and near-IR sky surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

59 BASIC BIOLOGICAL SCIENCES↗