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Methods and apparatus for rapid, culture free pathogen detection. The methods utilize optical spectroscopy techniques to identify and/or characterize pathogens in a sample via the detection of unique properties and/or analytes that are specific to particular pathogens.
In the Central Plateau at the U.S. Department of Energy Hanford Site, a large inventory of contaminants resides in unsaturated sediments within the approximately 100-meter-thick vadose zone, posing a potential continuing risk to groundwater. Vadose zone remedies used to address these contaminants will require performance monitoring to provide feedback during implementation and for long-term verification that remedial action objectives have been met. Passive approaches may also need long-term monitoring to demonstrate that the flux of contaminants from the vadose zone to the groundwater are below thresholds established to meet groundwater protection goals. Collection of physical (e.g., groundwater or sediment) samples is a common method for identifying contaminant concentration distributions, but this approach is limited by the number of locations and the frequency with which data can be collected. In situ vadose zone measurements have evolved over the past few years to include key measurements of water content, soil water pressure, temperature, and chemical concentration. However, the current generation of sensors is designed for relatively short-term use in near-surface soils or sediments. Geophysical methods have been evolving but are also limited in that they have not been designed for the specific long-term vadose zone monitoring needs at the Hanford Site. Overall, monitoring under unsaturated conditions can be difficult due to the need to install and maintain instrumentation over a large area and depth and the need to identify preferential flow pathways due to geologic and chemical heterogeneities over long periods. Thus, a vadose zone monitoring test bed was initiated to address these challenges and identify cost-effective approaches for implementation and postclosure monitoring of the deep vadose zone. The monitoring test bed is expected to provide valuable field-scale information for the design of vadose zone monitoring systems. (authors)
Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.
1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is an insensitive high explosive synthesized in two steps; 1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB) is the only intermediate. Due to solubility limitations, TATB is often dissolved in dimethylsulfoxide (DMSO) for liquid chromatography-mass spectrometry (LC–MS) analyses; however, DMSO is capable of participating in a wide variety of reactions. Intending to use it as an impurity standard, TCTNB was dissolved in DMSO. A stark color change from colorless to yellow accompanied by wavelength and ion chromatogram changes occurred over 24 hours. Three compounds were identified as causing the color change. All three were present in both acetone and DMSO solutions, but, overtime the absorbance spectra of the DMSO solution changed indicating an underlying reaction occurs between these compounds and DMSO. The chemical formulas of impurities present in the TCTNB sample as well as reaction products are identified via quadrupole time of flight mass spectrometry. The chemical structures are also proposed. The combination of the solvent system, ionization technique, and halogenated/nitrated aromatic ring structures resulted in substitutions of both the chlorine and nitro groups to hydroxyl groups. Furthermore, three proposed structures were closely related to TCTNB, but only one was detected at a consistent mass and absorbance wavelength in both acetone and DMSO. This compound had undergone a chlorine to hydroxyl substitution and should be utilized for TCTNB detection.
Here, we present the results of our search through the early data release (EDR) of the Dark Energy Spectroscopic Instrument (DESI) for extreme coronal line emitters (ECLEs) – a rare classification of galaxies displaying strong, high-ionization iron coronal emission lines within their spectra. With the requirement of a strong X-ray continuum to generate the coronal emission, ECLEs have been linked to both active galactic nuclei (AGNs) and tidal disruption events (TDEs). We focus our search on identifying TDE-linked ECLEs. We identify three such objects within the EDR sample, highlighting DESI’s effectiveness for discovering new nuclear transients, and determine a galaxy-normalized TDE-linked ECLE rate of RG=5 −3+5×10−6 galaxy−1 yr−1 at a median redshift of z=0.2 – broadly consistent with previous work. Additionally, we identify more than 200 AGNs displaying coronal emission lines, which serve as the primary astrophysical contaminants in searches for TDE-related events. We also include an outline of the custom python code developed for this search.
This study used suspect and nontarget screening with high-resolution mass spectrometry to characterize the occurrence of contaminants of emerging concern (CECs) in the nearshore marine environment of Puget Sound (WA). In total, 87 non-polymeric CECs were identified; those confirmed with reference standards (45) included pharmaceuticals, herbicides, vehicle-related compounds, plasticizers, and flame retardants. Eight polyfluoroalkyl substances were detected; perfluorooctanesulfonic acid (PFOS) concentrations were as high as 72-140 ng/L at one location. Low levels of methamphetamine were detected in 41% of the samples. Transformation products of pesticides were tentatively identified, including two novel transformation products of tebuthiuron. While a hydrodynamic simulation, analytical results, and dilution calculations demonstrated the prevalence of wastewater effluent to nearshore marine environments, the identity and abundance of selected CECs revealed the additional contributions from stormwater and localized urban and industrial sources. For the confirmed CECs, risk quotients were calculated based on concentrations and predicted toxicities, and eight CECs had risk quotients >1. Dilution in the marine estuarine environment lowered the risks of most wastewater-derived CECs, but dilution alone is insufficient to mitigate risks of localized inputs. These findings highlighted the necessity of suspect and nontarget screening and revealed the importance of localized contamination sources in urban marine environments.
Marine energy devices are installed in highly dynamic environments and have the potential to affect benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats. Selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years, as well as national and international guidelines for surveying habitats around offshore activities. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Sampling designs varied considerably among the reviewed studies but transect was the predominant design for surveying seafloor, epifauna, and pelagic habitats. The most common data analyses were univariate and multivariate statistical analyses aimed at calculating and comparing biodiversity indices, characterizing faunal assemblages or sediment classes, or modeling the distribution of animals related to abiotic parameters. Technologies and sampling methods adaptable and designed to work efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.
Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.
We present a pipeline to identify photometric variability within strong gravitationally lensing candidates, in the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys. In our first paper, we laid out our pipeline and presented seven new gravitationally lensed supernovae candidates in a retrospective search. In this companion paper, we apply a modified version of that pipeline to search for gravitationally lensed quasars. From a sample of 5807 strong lenses, we have identified 13 new gravitationally lensed quasar candidates (three of them quadruply lensed). We note that our methodology differs from most lensed quasar search algorithms that solely rely on the morphology, location, and color of the candidate systems. By also accounting for the temporal photometric variability of the posited lensed images in our search via difference imaging, we have discovered new lensed quasar candidates. While variability searches using difference imaging algorithms have been done in the past, they are typically performed over vast swathes of the sky, whereas we specifically target strong gravitationally lensed candidates. We also have applied our pipeline to 655 known gravitationally lensed quasar candidates from past lensed quasar searches, of which we identified 13 that display significant variability (one of them quadruply lensed). This pipeline demonstrates a promising search strategy to discover gravitationally lensed quasars in other existing and upcoming surveys.
Additively manufactured scattered beam collimators are increasingly being employed to boost the sample to cell peak signal ratio in high pressure neutron diffraction studies because of manufacturing versatility and performance improvements. We study how the measured diffraction pattern is affected by the presence of a collimator downstream of the sample, and develop a novel protocol that provides more effective background rejection. This protocol takes into account critical performance-determinants that were identified in this study, namely: (i) effectively identifying the collimator pattern on the detector; (ii) understanding the dependence of this pattern on sample and cell composition; and (iii) accurately identifying and differentiating the different regions of the pattern on the detector based on the dependency of the cell or sample and finally (iv) resolving the intensities at regions of the detector where neutrons scattered from the sample are preferentially represented, in order to boost the sample to cell peak signal ratio. Application of this novel analysis protocol is shown to increase the collimator performance over the traditional method.
Clay mineral cementation is one of the most important controls on sandstone reservoir properties. Here, in this paper, the diagenetic history of the Mt. Simon reservoir complex is studied to reveal the origin, timing, and controls of illitization. Samples of sandstone and shale from Mt. Simon reservoir complex were acquired from the Illinois Basin–Decatur Project (IBDP), a CO 2 storage demonstration project in the central Illinois Basin. Petrographic, SEM, TEM, XRD analyses and K/Ar age dating were completed to identify the major detrital and diagenetic components of the samples and reveal illite to be the major clay component in all samples. Illitic clay coatings in the lower Mt. Simon reservoir are identified as a major control on reservoir properties by inhibiting major precipitation of authigenic quartz during illitization, resulting in highly permeable sandstone, essential for CO 2 storage. The coating box-work morphology and mineralogy are indicative of a detrital smectite origin with subsequent illite growth associated with feldspar dissolution and kaolinite alteration. The mineralogy of bulk material and separate grain size fractions (2–0.6 μm; 0.6–0.2 μm; < 0.2 μm) with illite polytypes 2M 1 , 1M, and 1M d were quantified and age dated via 40 K- 40 Ar methods. The shales or reservoir seals contain the highest proportions of detrital illite with illite in the lower Mt. Simon Sandstone reservoir identified as solely diagenetic. Two major events of illitization are identified throughout the Mt. Simon with more porous reservoir rock exhibiting the older event from approximately 360 to 315 Ma and tighter sandstone units with reservoir properties too low to be considered reservoir exhibiting illite dates from 250 to 220 Ma. This partitioning of illitization is attributed to varied mineralogy controlled by depositional changes and evolution of the greater basin.
Abstract The most dynamically relaxed clusters of galaxies play a special role in cosmological studies as well as astrophysical studies of the intracluster medium (ICM) and active galactic nucleus feedback. While high-spatial-resolution imaging of the morphology of the ICM has long been the gold standard for establishing a cluster’s dynamical state, such data are not available from current or planned surveys, and thus require separate, pointed follow-up observations. With optical and/or near-IR photometric imaging, and red-sequence cluster finding results from those data, expected to be ubiquitously available for clusters discovered in upcoming optical and millimeter-wavelength surveys, it is worth asking how effectively photometric data alone can identify relaxed cluster candidates, before investing in, e.g., high-resolution X-ray observations. Here we assess the ability of several simple photometric measurements, based on the redMaPPer cluster finder run on Sloan Digital Sky Survey data, to reproduce X-ray classifications of dynamical state for an X-ray selected sample of massive clusters. We find that two simple metrics contrasting the bright central galaxy (BCG) to other cluster members can identify a complete sample of relaxed clusters with a purity of ∼40% in our data set. Including minimal ICM information in the form of a center position increases the purity to ∼60%. However, all three metrics depend critically on correctly identifying the BCG, which is presently a challenge for optical red-sequence cluster finders.
Because of the importance of surfaces and interfaces in many scientific and technological areas, the use of x-ray photoelectron spectroscopy (XPS) has been growing exponentially. Although XPS is being used to obtain useful information about the surface composition of samples, much more information about materials and their properties can be extracted from XPS data than commonly obtained. This paper describes some of the areas where alternative analysis methods or experimental design can obtain information about the near-surface region of a sample, often information not available in other ways. Experienced XPS analysts are familiar with many of these methods, but they may not be known to new or casual XPS users, and sometimes, they have not been used because of an inappropriately assumed complexity. The information available includes optical, electronic, and electrical properties; nanostructure; expanded chemical information; and enhanced analysis of biological materials and solid/liquid interfaces. Many of these analyses can be conducted on standard laboratory XPS systems, with either no or relatively minor system alterations. Topics discussed include (1) considerations beyond the “traditional” uniform surface layer composition calculation, (2) using the Auger parameter to determine a sample property, (3) use of the D parameter to identify sp 2 and sp 3 carbon information, (4) information from the XPS valence band, (5) using cryocooling to expand range of samples that can be analyzed and minimize damage, and (6) using electrical potential effects on XPS signals to extract chemically resolved electrical measurements including band alignment and electrical property information.
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.
High-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge spectroscopy (XANES) is a spectroscopic method that allows for increased spectral feature resolution, and greater selectivity to decrease complex matrix effects compared with conventional XANES. XANES is an ideal tool for speciation of elements in solid-phase environmental samples. Accurate speciation of As in mine waste materials is important for understanding the mobility and toxicity of As in near-surface environments. In this study, linear combination fitting (LCF) was performed on synthetic spectra generated from mixtures of eight measured reference compounds for both HERFD-XANES and transmission-detected XANES to evaluate the improvement in quantitative speciation with HERFD-XANES spectra. The reference compounds arsenolite (As 2 O 3 ), orpiment (As 2 S 3 ), getchellite (AsSbS 3 ), arsenopyrite (FeAsS), kaňkite (FeAsO 4 ·3.5H 2 O), scorodite (FeAsO 4 ·2H 2 O), sodium arsenate (Na 3 AsO 4 ), and realgar (As 4 S 4 ) were selected for their importance in mine waste systems. Statistical methods of principal component analysis and target transformation were employed to determine whether HERFD improves identification of the components in a dataset of mixtures of reference compounds. LCF was performed on HERFD- and total fluorescence yield (TFY)-XANES spectra collected from mine waste samples. Arsenopyrite, arsenolite, orpiment, and sodium arsenate were more accurately identified in the synthetic HERFD-XANES spectra compared with the transmission-XANES spectra. In mine waste samples containing arsenopyrite and either scorodite or kaňkite, LCF with HERFD-XANES measurements resulted in fits with smaller R -factors than concurrently collected TFY measurements. The improved accuracy of HERFD-XANES analysis may provide enhanced delineation of As phases controlling biogeochemical reactions in mine wastes, contaminated soils, and remediation systems.
Marine energy devices are installed in highly dynamic environments and have the potential to affect the benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats, and selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Technologies and sampling methods that are designed for working efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.
This dataset is associated with the publication “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream” published in Water Research X (Leonard et al. 2022; https://doi.org/10.1016/j.wroa.2022.100144). The associated study analyzed temporal trends from the Town of Crested Butte water treatment facility and synoptic sampling at Coal Creek in Crested Butte, Colorado, US. This work demonstrates how drinking water quality archives combined with synoptic sampling and targeted analyses can be used to identify and understand export control points for dissolved organic matter. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) metadata and international geo-sample number (IGSN) mapping file; (4) dissolved organic carbon (DOC), ultraviolet absorbance at 254 nanometers (UV254), total nitrogen (TN), and specific ultraviolet absorbance (SUVA) data; (5) disinfection bioproduct formation potential (DBP-FP) data; (6) readme; (7) methods codes; (8) water collection protocol; (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory); and (10) folder of excitation emissions matrix (EEM) spectra. The FTICR folder contains a file of DOC (measured as non-purgeable organic carbon; NPOC) used for FTICR sample preparation. The FTICR folder also contains three subfolders: one subfolder containing the raw .xml data files, one containing the processed data, and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .dat, .R, .ref, or .xml