Publications by authors named "Daniel E Williams"

19 Publications

  • Page 1 of 1

Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.

Environ Sci Technol 2021 09 2;55(18):12683-12693. Epub 2021 Sep 2.

Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States.

Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.
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http://dx.doi.org/10.1021/acs.est.1c00802DOI Listing
September 2021

High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus.

Mol Microbiol 2021 08 3;116(2):397-415. Epub 2021 Apr 3.

Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia.

Endolysin enzymes from bacteriophage cause bacterial lysis by degrading the peptidoglycan cell wall. The streptococcal C1 phage endolysin PlyC, is the most potent endolysin described to date and can rapidly lyse group A, C, and E streptococci. PlyC is known to bind the Group A streptococcal cell wall, but the specific molecular target or the binding site within PlyC remain uncharacterized. Here we report for the first time, that the polyrhamnose backbone of the Group A streptococcal cell wall is the binding target of PlyC. We have also characterized the putative rhamnose binding groove of PlyC and found four key residues that were critical to either the folding or the cell wall binding action of PlyC. Based on our results, we suggest that the interaction between PlyC and the cell wall may not be a high-affinity interaction as previously proposed, but rather a high avidity one, allowing for PlyC's remarkable lytic activity. Resistance to our current antibiotics is reaching crisis levels and there is an urgent need to develop the antibacterial agents with new modes of action. A detailed understanding of this potent endolysin may facilitate future developments of PlyC as a tool against the rise of antibiotic resistance.
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http://dx.doi.org/10.1111/mmi.14719DOI Listing
August 2021

Insights into community of photosynthetic microorganisms from permafrost.

FEMS Microbiol Ecol 2020 11;96(12)

Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia.

This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01-0.45% and Chlorophyta (green algae) 0.01-0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.
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http://dx.doi.org/10.1093/femsec/fiaa229DOI Listing
November 2020

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer.

Chemosphere 2020 Sep 10;255:126951. Epub 2020 May 10.

University of Washington, Department of Civil and Environmental Engineering, Seattle, WA, USA.

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.
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http://dx.doi.org/10.1016/j.chemosphere.2020.126951DOI Listing
September 2020

Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach.

Front Plant Sci 2020 28;11:180. Epub 2020 Feb 28.

Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.

Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot () genotypes with contrasting bloom dates and peach () genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box () genes , , and ). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.
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http://dx.doi.org/10.3389/fpls.2020.00180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059448PMC
February 2020

Structural Studies of Thyroid Peroxidase Show the Monomer Interacting With Autoantibodies in Thyroid Autoimmune Disease.

Endocrinology 2020 02;161(2)

Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Thyroid peroxidase (TPO) is a critical membrane-bound enzyme involved in the biosynthesis of multiple thyroid hormones, and is a major autoantigen in autoimmune thyroid diseases such as destructive (Hashimoto) thyroiditis. Here we report the biophysical and structural characterization of a novel TPO construct containing only the ectodomain of TPO and lacking the propeptide. The construct was enzymatically active and able to bind the patient-derived TR1.9 autoantibody. Analytical ultracentrifugation data suggest that TPO can exist as both a monomer and a dimer. Combined with negative stain electron microscopy and molecular dynamics simulations, these data show that the TR1.9 autoantibody preferentially binds the TPO monomer, revealing conformational changes that bring together previously disparate residues into a continuous epitope. In addition to providing plausible structural models of a TPO-autoantibody complex, this study provides validated TPO constructs that will facilitate further characterization, and advances our understanding of the structural, functional, and antigenic characteristics of TPO, an autoantigen implicated in some of the most common autoimmune diseases.
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http://dx.doi.org/10.1210/endocr/bqaa016DOI Listing
February 2020

Thyroid Peroxidase as an Autoantigen in Hashimoto's Disease: Structure, Function, and Antigenicity.

Horm Metab Res 2018 Dec 25;50(12):908-921. Epub 2018 Oct 25.

Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Human thyroid peroxidase (TPO), is an important enzyme responsible for the biosynthesis of thyroid hormones and is a major autoantigen in autoimmune thyroid diseases (AITDs) such as the destructive Hashimoto's thyroiditis. Although the structure of TPO has yet to be determined, its extracellular domain consists of three regions that exhibit a high degree of sequence similarity to domains of known three-dimensional structure: the myeloperoxidase (MPO)-like domain, complement control protein (CCP)-like domain, and epidermal growth factor (EGF)-like domain. Homology models of TPO can therefore be constructed, providing some structural context to its known function, as well as facilitating the mapping of regions that are responsible for its autoantigenicity. In this review, we highlight recent progress in this area, in particular how a molecular modelling approach has advanced the visualisation and interpretation of epitope mapping studies for TPO, facilitating the dissection of the interplay between TPO protein structure, function, and autoantigenticity.
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http://dx.doi.org/10.1055/a-0717-5514DOI Listing
December 2018

Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval.

J Forensic Sci 2015 Jul 24;60(4):844-50. Epub 2015 Mar 24.

Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996.

Bacteria are taphonomic agents of human decomposition, potentially useful for estimating postmortem interval (PMI) in late-stage decomposition. Bone samples from 12 individuals and three soil samples were analyzed to assess the effects of decomposition and advancing time on bacterial communities. Results indicated that partially skeletonized remains maintained a presence of bacteria associated with the human gut, whereas bacterial composition of dry skeletal remains maintained a community profile similar to soil communities. Variation in the UniFrac distances was significantly greater between groups than within groups (p < 0.001) for the unweighted metric and not the weighted metric. The members of the bacterial communities were more similar within than between decomposition stages. The oligotrophic environment of bone relative to soft tissue and the physical protection of organic substrates may preclude bacterial blooms during the first years of skeletonization. Therefore, community membership (unweighted) may be better for estimating PMI from skeletonized remains than community structure (weighted).
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http://dx.doi.org/10.1111/1556-4029.12744DOI Listing
July 2015

Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from bangladesh.

Genome Announc 2014 Nov 20;2(6). Epub 2014 Nov 20.

The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport.
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http://dx.doi.org/10.1128/genomeA.01170-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239352PMC
November 2014

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples.

FEMS Microbiol Ecol 2014 Jan 17;87(1):217-30. Epub 2013 Oct 17.

University of Tennessee, Knoxville, TN, USA.

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.
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http://dx.doi.org/10.1111/1574-6941.12219DOI Listing
January 2014

Unsealed tubewells lead to increased fecal contamination of drinking water.

J Water Health 2012 Dec;10(4):565-78

Department of Earth & Planetary Sciences, University of Tennessee, Knoxville, TN 37996-1410, USA.

Bangladesh is underlain by shallow aquifers in which millions of drinking water wells are emplaced without annular seals. Fecal contamination has been widely detected in private tubewells. To evaluate the impact of well construction on microbial water quality 35 private tubewells (11 with intact cement platforms, 19 without) and 17 monitoring wells (11 with the annulus sealed with cement, six unsealed) were monitored for culturable Escherichia coli over 18 months. Additionally, two 'snapshot' sampling events were performed on a subset of wells during late-dry and early-wet seasons, wherein the fecal indicator bacteria (FIB) E. coli, Bacteroidales and the pathogenicity genes eltA (enterotoxigenic E. coli; ETEC), ipaH (Shigella) and 40/41 hexon (adenovirus) were detected using quantitative polymerase chain reaction (qPCR). No difference in E. coli detection frequency was found between tubewells with and without platforms. Unsealed private wells, however, contained culturable E. coli more frequently and higher concentrations of FIB than sealed monitoring wells (p < 0.05), suggestive of rapid downward flow along unsealed annuli. As a group the pathogens ETEC, Shigella and adenovirus were detected more frequently (10/22) during the wet season than the dry season (2/20). This suggests proper sealing of private tubewell annuli may lead to substantial improvements in microbial drinking water quality.
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http://dx.doi.org/10.2166/wh.2012.102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612880PMC
December 2012

Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater.

Sci Total Environ 2012 Aug 14;431:314-22. Epub 2012 Jun 14.

Department of Civil Engineering and Engineering Mechanics, Columbia University, NY, USA.

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.
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http://dx.doi.org/10.1016/j.scitotenv.2012.05.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587152PMC
August 2012

Implications of fecal bacteria input from latrine-polluted ponds for wells in sandy aquifers.

Environ Sci Technol 2012 Feb 11;46(3):1361-70. Epub 2012 Jan 11.

Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Tennessee 37996-1410, United States.

Ponds receiving latrine effluents may serve as sources of fecal contamination to shallow aquifers tapped by millions of tube-wells in Bangladesh. To test this hypothesis, transects of monitoring wells radiating away from four ponds were installed in a shallow sandy aquifer underlying a densely populated village and monitored for 14 months. Two of the ponds extended to medium sand. Another pond was sited within silty sand and the last in silt. The fecal indicator bacterium E. coli was rarely detected along the transects during the dry season and was only detected near the ponds extending to medium sand up to 7 m away during the monsoon. A log-linear decline in E. coli and Bacteroidales concentrations with distance along the transects in the early monsoon indicates that ponds excavated in medium sand were the likely source of contamination. Spatial removal rates ranged from 0.5 to 1.3 log(10)/m. After the ponds were artificially filled with groundwater to simulate the impact of a rain storm, E. coli levels increased near a pond recently excavated in medium sand, but no others. These observations show that adjacent sediment grain-size and how recently a pond was excavated influence the how much fecal contamination ponds receiving latrine effluents contribute to neighboring groundwater.
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http://dx.doi.org/10.1021/es202773wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602418PMC
February 2012

Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44.

J Bacteriol 2011 Sep 8;193(18):5009-10. Epub 2011 Jul 8.

Center for Environmental Biotechnology, 676 Dabney Hall, University of Tennessee, Knoxville, TN 37996, USA.

Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ∼6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.
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http://dx.doi.org/10.1128/JB.05530-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165646PMC
September 2011

Impact of population and latrines on fecal contamination of ponds in rural Bangladesh.

Sci Total Environ 2011 Aug 31;409(17):3174-82. Epub 2011 May 31.

Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, TN 37996-1410, USA.

A majority of households in Bangladesh rely on pond water for hygiene. Exposure to pond water fecal contamination could therefore still contribute to diarrheal disease despite the installation of numerous tubewells for drinking. The objectives of this study are to determine the predominant sources (human or livestock) of fecal pollution in ponds and examine the association between local population, latrine density, latrine quality and concentrations of fecal bacteria and pathogens in pond water. Forty-three ponds were analyzed for E. coli using culture-based methods and E. coli, Bacteroidales and adenovirus using quantitative PCR. Population and sanitation spatial data were collected and measured against pond fecal contamination. Humans were the dominant source of fecal contamination in 79% of the ponds according to Bacteroidales measurements. Ponds directly receiving latrine effluent had the highest concentrations of fecal indicator bacteria (up to 10⁶ Most Probable Number (MPN) of culturable E. coli per 100 mL). Concentrations of fecal indicator bacteria correlated with population surveyed within a distance of 30-70 m (p<0.05) and total latrines surveyed within 50-70 m (p<0.05). Unsanitary latrines (visible effluent or open pits) within the pond drainage basin were also significantly correlated to fecal indicator concentrations (p<0.05). Water in the vast majority of the surveyed ponds contained unsafe levels of fecal contamination attributable primarily to unsanitary latrines, and to lesser extent, to sanitary latrines and cattle. Since the majority of fecal pollution is derived from human waste, continued use of pond water could help explain the persistence of diarrheal disease in rural South Asia.
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http://dx.doi.org/10.1016/j.scitotenv.2011.04.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150537PMC
August 2011

Viruses and bacteria in karst and fractured rock aquifers in East Tennessee, USA.

Ground Water 2011 Jan-Feb;49(1):98-110

Clancy Environmental Consultants, Inc., Saint Albans, VT 05478, USA.

A survey of enteric viruses and indicator bacteria was carried out in eight community water supply sources (four wells and four springs) in East Tennessee. Seven sites derived their water from carbonate aquifers and one from fractured sandstone. Four of the sites were deemed "low-risk" based on prior monitoring of fecal indicators and factors such as presence of thick layers of overlying sediments. The remaining sites were deemed "high-risk." Enteric viruses (enterovirus and reovirus) were detected by cell culture at least once in seven of the eight wells or springs including all but one of the four low-risk sites. Viral RNA, however, was not detected in any of the samples by reverse transcription-polymerase chain reaction. Conventional indicators of microbial contamination (Escherichia coli and total coliform bacteria) were detected together with culturable viruses in seven of nine virus positive samples. Bacteroides, an alternative fecal indicator which has not previously been used in groundwater investigations, was also detected in all but one of the samples containing E. coli or total coliform bacteria, as well as in one sample where viruses were present in the absence of other bacterial indicators. The study highlights some of the challenges involved in surveys of virus occurrence and indicates that culturable enteric viruses in East Tennessee karst aquifers may be more widespread than previously observed in studies of karst aquifers in Pennsylvania (8%), the Ozark region of Missouri (< 1%), or several other states covered in a national microbial water quality survey conducted by the U.S. Environmental Protection Agency (43%).
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http://dx.doi.org/10.1111/j.1745-6584.2010.00698.xDOI Listing
April 2011

PM(2.5) Characterization for Time Series Studies: Organic Molecular Marker Speciation Methods and Observations from Daily Measurements in Denver.

Atmos Environ (1994) 2009 Apr;43(12):2018-2030

Department of Civil, Environmental and Architectural Engineering, College of Engineering and Applied Science, University of Colorado, Boulder, CO 80309, USA.

Particulate matter less than 2.5 microns in diameter (PM(2.5)) has been shown to have a wide range of adverse health effects and consequently is regulated in accordance with the US-EPA's National Ambient Air Quality Standards. PM(2.5) originates from multiple primary sources and is also formed through secondary processes in the atmosphere. It is plausible that some sources form PM(2.5) that is more toxic than PM(2.5) from other sources. Identifying the responsible sources could provide insight into the biological mechanisms causing the observed health effects and provide a more efficient approach to regulation. This is the goal of the Denver Aerosol Sources and Health (DASH) study, a multi-year PM(2.5) source apportionment and health study.The first step in apportioning the PM(2.5) to different sources is to determine the chemical make-up of the PM(2.5). This paper presents the methodology used during the DASH study for organic speciation of PM(2.5). Specifically, methods are covered for solvent extraction of non-polar and semi-polar organic molecular markers using gas chromatography-mass spectrometry (GC-MS). Vast reductions in detection limits were obtained through the use of a programmable temperature vaporization (PTV) inlet along with other method improvements. Results are presented for the first 1.5 years of the DASH study revealing seasonal and source-related patterns in the molecular markers and their long-term correlation structure. Preliminary analysis suggests that point sources are not a significant contributor to the organic molecular markers measured at our receptor site. Several motor vehicle emission markers help identify a gasoline/diesel split in the ambient data. Findings show both similarities and differences when compared with other cities where similar measurements and assessments have been made.
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http://dx.doi.org/10.1016/j.atmosenv.2009.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678721PMC
April 2009

Selection of cell lines with enhanced invasive phenotype from xenografts of the human prostate cancer cell line WPE1-NB26.

J Exp Ther Oncol 2005 ;5(2):111-23

Department of Zoology, Michigan State University, East Lansing, Ml 48824, USA.

Prostate cancer is a leading cause of death from cancer in American men and metastasis the main cause of death. To better understand the disease and accelerate development of new therapies, in vivo models that reflect different disease stages are needed. A family of cell lines that mimics multiple steps in cancer development and tumor progression has been developed in our laboratory from the parent, non-tumorigenic, RWPE-1 cell line by transformation with N-methyl-N-nitrosourea (MNU). The MNU cell lines mimic multiple steps in tumor progression where WPE1-NB26 is the most malignant cell line. WPE1-NB26 cells form metastases in the lungs of athymic, male, nude mice after intravenous injection. Two new cell lines, WPE1-NB26-64 and WPE1-NB26-65, showing more malignant characteristics than the parent WPE1-NB26 cell line, were derived from tumors after subcutaneous injection of WPE1-NB26 cells into nude mice. The WPE1-NB26-64 and WPE1-NB26-65 cell lines show an increase in anchorage-dependent growth and invasive ability as compared to the parent WPE1-NB26 cells. While the parent WPE1-NB26 cells express barely detectable levels, the new cell lines produce high levels of matrix metalloproteinase MMP-2 and detectable levels of MMP-9. By immunostaining, all three cell lines were positive for cytokeratins CK18 and CK5/14. These cell lines, having the same lineage, represent additional steps in the multi-step process of tumor progression and provide novel and useful cell models for studies on tumor progression and for drug development for the treatment of prostate cancer.
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March 2006

17alpha-ethynylestradiol-induced vitellogenin gene transcription quantified in livers of adult males, larvae, and gills of fathead minnows (Pimephales promelas).

Environ Toxicol Chem 2002 Nov;21(11):2385-93

National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency, Cincinnati, Ohio 45268 , USA.

We have applied a method for quantifying relative levels of messenger RNA (mRNA) transcription to assess chemically induced gene expression in fathead minnows (Pimephales promelas). Synthetic oligonucleotides designed for the fathead minnow vitellogenin gene transcription product were used in a reverse transcription polymerase chain reaction (RT-PCR) protocol. This sensitive and rapid strategy detected vitellogenin gene transcription in livers of male fathead minnows exposed to concentrations as low as 2 ng/L of the endocrine-disrupting compound 17alpha-ethynylestradiol for 24 h. Surprisingly, vitellogenin transcription products also were detected in gill tissue and in 48-h-old posthatch fathead minnow larvae. Relative levels of vitellogenin gene induction among individuals were quantified in a single-step reaction (PCR multiplex) with 18S rRNA universal primers and Competimers concurrently with fathead minnow vitellogenin oligonucleotides. This quantitative approach will markedly enhance detection of the first cellular event of estrogenic exposure to aquatic ecosystems in both field and laboratory systems. Use of the model provides sensitivity of detection at a concentration below those that cause mortality or visible signs of stress in fish or other aquatic organisms. The model may also provide an in vivo screening method for estrogenlike endocrine-disrupting compounds.
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November 2002
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