Preparative isolation, fractionation and chemical characterization of dissolved organics from natural and industrially derived bitumen-influenced groundwaters from the Athabasca River watershed

Recent analytical advances have provided evidence that groundwater affected by oil sands process-affected water (OSPW) is reaching the Athabasca River at one location. To understand and discriminate the toxicological risks posed by OSPW-influenced groundwater relative to groundwaters associated with natural oil sands deposits, these highly complex mixtures of soluble organics were subjected to toxicological characterization through effects directed analysis. A recently-developed preparative fractionation methodology was applied to bitumen-influenced groundwaters and successfully isolated dissolved organics from both industrial and natural sources into three chemically distinct fractions (F1, F2, F3), enabling multiple toxicological assessments. Analytical techniques included electrospray ionization high resolution mass spectrometry (ESI-HRMS), liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF/MS), gas chromatography mass spectrometry (GC–MS), and synchronous fluorescence spectroscopy (SFS) methods, which did not reveal obvious differences between sources. Comparisons between fractions within each source consistently demonstrated that F3 contained compounds with greater polarity than F2, which in turn was more polar than F1. The abundance of O2 species was confined to F1, including naphthenic acids often cited for being the primary toxicants within bitumen-influenced waters. This result is consistent with earlier work on aged OSPW, as well as with other extraction methods, suggesting that additional factors other than molecular weight and the presence of acid functionalities play a prominent role in defining compound polarities and toxicities within complex bitumen-derived organic mixtures. The similarities in organic abundances, chemical speciation, aromaticity, and double bond equivalents, concomitant with inorganic mixture similarities, demonstrate the resemblances of bitumen-influenced groundwaters regardless of the source, and reinforce the need for more advanced targeted analyses for source differentiation.This work was funded under the Oil Sands Monitoring Program, and is a contribution to the Program, but does not necessarily reflect the position of the Program. Internal resources from Environment and Climate Change Canada were also used to fund this research

Comparison of eye tracking, electrooculography and an auditory brain-computer interface for binary communication: a case study with a participant in the locked-in state

Background In this study, we evaluated electrooculography (EOG), an eye tracker and an auditory brain-computer interface (BCI) as access methods to augmentative and alternative communication (AAC). The participant of the study has been in the locked-in state (LIS) for 6 years due to amyotrophic lateral sclerosis. He was able to communicate with slow residual eye movements, but had no means of partner independent communication. We discuss the usability of all tested access methods and the prospects of using BCIs as an assistive technology. Methods Within four days, we tested whether EOG, eye tracking and a BCI would allow the participant in LIS to make simple selections. We optimized the parameters in an iterative procedure for all systems. Results The participant was able to gain control over all three systems. Nonetheless, due to the level of proficiency previously achieved with his low-tech AAC method, he did not consider using any of the tested systems as an additional communication channel. However, he would consider using the BCI once control over his eye muscles would no longer be possible. He rated the ease of use of the BCI as the highest among the tested systems, because no precise eye movements were required; but also as the most tiring, due to the high level of attention needed to operate the BCI. Conclusions In this case study, the partner based communication was possible due to the good care provided and the proficiency achieved by the interlocutors. To ease the transition from a low-tech AAC method to a BCI once control over all muscles is lost, it must be simple to operate. For persons, who rely on AAC and are affected by a progressive neuromuscular disease, we argue that a complementary approach, combining BCIs and standard assistive technology, can prove valuable to achieve partner independent communication and ease the transition to a purely BCI based approach. Finally, we provide further evidence for the importance of a user-centered approach in the design of new assistive devices

A B2 Repeat Insertion Generates Alternate Structures of the Mouse Muscle [gamma]-Phosphorylase Kinase Gene

A variety of cDNA and genomic clones for the [gamma]-subunit of mouse muscle phosphorylase kinase (Phk-[gamma]M) have been isolated and characterized. The murine gene for Phk-[gamma]M (Phkg) exhibits multiple transcription start sites that are identical in skeletal muscle, cardiac muscle, and brain. The gene is composed of 10 exons and includes a 4.9-kb intron located in the 5' untranslated region. Two mRNA species of 1.75 and 2.55 kb are produced from Phkg in ICR and C57BL/10 mice; these transcripts are colinear throughout the coding region and differ only in the length of the 3' untranslated region. We have mapped the polyadenylation site of the 1.75-kb mRNA to the middle of exon 10; the 2.55-kb mRNA terminates further 3' at the end of a mouse B2 repeat. In Balb/C mice an additional B2 insertion and related genomic rearrangements alter the sequence of Phkg exon 10 and are accompanied by an increase in the quantity of the 1.75-kb transcript and a decrease in the abundance and size of the longer transcript, from 2.55 to 2.35 kb. A PCR assay for sequences contained in exon 10 reveals that the Balb/C 3' gene structure is shared by Mus musculus castaneus and Mus musculus molossinus; the C57BL/10 gene structure is shared by Mus spretus, Mus domesticus, and several strains of laboratory mice. These results suggest that Phkg in Balb/C mice was derived from M. m. molossinus and that Phkg of the other examined laboratory strains was derived from M. domesticus.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30858/1/0000521.pd

Use of pre-industrial floodplain lake sediments to establish baseline river metal concentrations downstream of Alberta oil sands: a new approach for detecting pollution of rivers

In the Alberta oil sands region, insufficient knowledge of pre-disturbance reference conditions has undermined the ability of the Regional Aquatics Monitoring Program (RAMP) to detect pollution of the Athabasca River, because sampling began three decades after the industry started and the river naturally erodes oil-bearing strata. Here, we apply a novel approach to characterize pre-industrial reference metal concentrations in river sediment downstream of Alberta oil sands development by analyzing metal concentrations in sediments deposited in floodplain lakes of the Athabasca Delta during 1700–1916, when they were strongly influenced by Athabasca River floodwaters. We compared results to metal concentrations in surficial bottom sediments sampled by RAMP (2010–2013) at downstream sites of the Athabasca River and distributaries. When normalized to lithium content, concentrations of vanadium (a metal of concern in the oil sands region) and other priority pollutants (Be, Cd, Cr, Cu, Pb, Ni, Zn) in nearly all of the RAMP river sediment samples lie below the upper 95% prediction interval linearly extrapolated from the river-derived lake sediments. Assuming the RAMP protocols obtained recently deposited sediment, this indicates that the metal concentrations in downstream Athabasca River sediment have not increased above pre-disturbance levels. Reference conditions derived from the lake sediment data were used to develop profiles of metal residual concentrations versus time for the RAMP river sediment data, which provides an excellent tool for decision-makers to identify and quantify levels of metal pollution for any given sample, and to monitor for future trends. We recommend that the approach be applied to resurrect the utility of RAMP data at other river sampling locations closer to the development, and for ongoing risk assessment. The approach is also readily transferable to other rivers where insufficient pre-disturbance reference data impairs an ability to determine if industrial activities are polluting downstream ecosystems

Simultaneous Detection of Single Nucleotide Variants and Expression of RNA and Protein in Multiple Myeloma Bone Marrow Aspirates

Introduction: Multiple myeloma (MM) is generally an incurable plasma cell neoplasm that evolves from a premalignant state known as monoclonal gammopathy of undetermined significance (MGUS). Primary genomic events leading to the development of MGUS include hyperdiploidy, translocations involving the immunoglobulin heavy chain genes, and copy number variations. Single-nucleotide variants (SNVs) as well as insertions and deletions are secondary events that trigger progression to active MM. Identifying nucleotide variants that lead to changes in RNA and protein expression is critically important to understanding the biology of the cancer and ultimately identifying therapeutic targets. Analysis of DNA, RNA, and protein has traditionally involved integration of three separate assays and is frequently limited by the availability of sufficient material from MM patient specimens. We used a more efficient approach that simultaneously detects DNA variants, RNA and protein expression in a single sample from as little as 5 ng DNA, 25 ng RNA, and 250 ng protein. We evaluated the NanoString nCounter® Vantage 3D™ DNA:RNA:Protein Heme Assay performed on 1 x 106cells from bone marrow biopsies obtained from patients with MM. Methods: Bone marrow aspirates from 15 patients diagnosed with MM were obtained through an Institutional Review Board approved protocol. Seven patients had newly diagnosed MM and 8 had relapsed disease. DNA, RNA, and protein were extracted from unsorted, cryopreserved, ficoll-hypaque separated bone marrow mononuclear cells and hybridized with optical barcodes designed to detect 124 DNA somatic variants common to hematologic malignancies as well as 180 mRNA transcripts and 38 total and phospho-proteins. We also used the nCounter PanCancer Pathways Panel Assay to measure gene expression of 770 additional genes from 13 cancer-associated canonical pathways. The hybridized probes in each sample were counted using the nCounter Digital Analyzer and statistical analysis was performed using nSolver™ v4.0 alpha software. Results: The percentage of CD138+ bone marrow plasma cells measured by immunohistochemistry at the time of biopsy varied from 44 to 100% in each sample. One or more DNA variants were detected in 3 pre-treatment and 4 relapse samples. Mutations in KRAS, NRAS, and BRAF were most common and 2 patients were found to have variants in both KRAS and NRAS or KRAS and BRAF . Additionally, variants in DNMT3A and IDH2 were detected in 1 patient each. Since KRAS, NRAS, and BRAF are all members of the mitogen-activated protein kinase (MAPK) signaling pathway, a differential gene expression analysis of both RNA and protein was performed comparing samples with and without mutations in these genes. Findings confirmed that a higher level of expression was detectable in MAPK pathway genes, although this result did not reach statistical significance following correction for replicate testing, potentially the consequence of a small sample size. Conclusions: The Vantage 3D DNA:RNA:Protein Heme Assay is a rapid, sensitive and resource sparing platform for the simultaneous detection of DNA variants, RNA transcripts, and protein expression. We show that this method can feasibly be performed on as few as 1 x 106 cryopreserved bone marrow cells in patients with MM and our findings confirm detection of 3 of the most common MM variants. This technology should have broad application in other hematological malignancies and further evaluation of blood and lymph node biopsies from fresh, frozen and formalin-fixed paraffin-embedded (FFPE) samples is warranted. Demirkan:NanoString Technologies: Employment. Meredith:NanoString Technologies: Employment. Meredith:NanoString Technologies: Employment

Maps of study area.

<p>Panel a): map showing locations of near-surface Athabasca oil sands exposures of the McMurray Formation (light grey), the 2009 mining footprint (dark grey) and the downstream Peace-Athabasca Delta (top center box) in northern Alberta, Canada. Top-center box in <b>a)</b> outlines area shown in Panel <b>b)</b>: Map identifying locations of the study lakes (solid circles) PAD 18 (N 58° 53.7′, W 111° 21.7′), PAD 23 (N 58° 23.5′, W 111° 26.6′) and PAD 31 (N 58° 29.6′, W 111° 31.0′) within the Peace-Athabasca Delta. Also shown are locations of the Athabasca River Cutoff (ARC) and the Embarras Breakthrough (EB). The ARC, an engineered channel excavation in 1972, straightened and deepened the Athabasca River at the location of a large meander bend where ice-jam floods occurred, and reduced flood frequency at PAD 23. The EB, a natural avulsion that occurred in 1982, has increased flood frequency at PAD 31 because it directs substantial and increasing Athabasca River flow towards PAD 31 via Mamawi Creek. Further details on these geomorphic changes are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046089#pone.0046089-Wolfe6" target="_blank">[27]</a>.</p

Composition of polycyclic aromatic compounds in river flood sediment and lake sediment cores.

<p>Bar graphs showing average composition of polycyclic aromatic compounds (PACs), expressed as relative concentration (proportion; error bars ±1 SEM) in <b>a)</b> the 2007 Athabasca Delta flood deposit and three intervals of differing flood regime at PAD 31, <b>b)</b> the 2007 Athabasca Delta flood deposit and three intervals of differing flood regime at PAD 23, and <b>c)</b> the 2007 Athabasca Delta flood deposit and two intervals that distinguish pre- and post-1967 onset of major commercial oil sands development at not flood-prone PAD 18 (note different scale of vertical axis). Names of the PAC compounds and the corresponding codes are presented along the lower expanded horizontal axis. Blue vertical bars are PACs identified by SIMPER analysis as river-transported bitumen-associated indicator compounds common in sediments deposited during flood-prone intervals (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046089#pone-0046089-t001" target="_blank">Table 1</a>). Red vertical bars are PACs identified as indicator compounds in sediments deposited during not flood-prone periods.</p

Alignment of duplicate cores.

<p>Graphs showing stratigraphic profiles of organic matter content in duplicate cores taken from each of the three study lakes in the Peace-Athabasca Delta, northern Alberta. One of the cores from each lake was analyzed for ²¹⁰Pb dating and the other provided material for analysis of PACs. Upper panel <b>a)</b> shows the raw data, whereas the lower panel <b>b)</b> shows the data after minor vertical adjustment of the organic matter content profile for the core that was not dated. ²¹⁰Pb-derived dates from the dated core were transferred to the corresponding undated cores used for PAC analyses. No depth adjustments were required for cores from PAD 18.</p