Publications by authors named "Susan Long"

46 Publications

Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs.

medRxiv 2021 Feb 3. Epub 2021 Feb 3.

Background: Wastewater surveillance for SARS-CoV-2 is an emerging approach to help identify the risk of a COVID-19 outbreak. This tool can contribute to public health surveillance at both community (wastewater treatment system) and institutional (e.g., colleges, prisons, nursing homes) scales.

Objectives: This research aims to understand the successes, challenges, and lessons learned from initial wastewater surveillance efforts at colleges and university systems to inform future research, development and implementation.

Methods: This paper presents the experiences of 25 college and university systems in the United States that monitored campus wastewater for SARS-CoV-2 during the fall 2020 academic period. We describe the broad range of approaches, findings, resource needs, and lessons learned from these initial efforts. These institutions range in size, social and political geographies, and include both public and private institutions.

Discussion: Our analysis suggests that wastewater monitoring at colleges requires consideration of information needs, local sewage infrastructure, resources for sampling and analysis, college and community dynamics, approaches to interpretation and communication of results, and follow-up actions. Most colleges reported that a learning process of experimentation, evaluation, and adaptation was key to progress. This process requires ongoing collaboration among diverse stakeholders including decision-makers, researchers, faculty, facilities staff, students, and community members.
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http://dx.doi.org/10.1101/2021.02.01.21250952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872386PMC
February 2021

Inoculum microbiome composition impacts fatty acid product profile from cellulosic feedstock.

Bioresour Technol 2021 Mar 13;323:124532. Epub 2020 Dec 13.

Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA. Electronic address:

Conversion of organic wastes to fatty acids rather than methane through anaerobic digestion-based technologies has considerable promise. However, the relationships between microbiome structure and fatty acids produced from cellulosic feedstocks are not well understood. This study investigated the nature of those relationships for anaerobic digester sludge, bison rumen, and cattle rumen inocula grown on cellulose. Acetic acid production was highest in anaerobic sludge reactors, while propionic acid production was highest in cattle rumen reactors. Butyric and pentanoic acid were produced at the highest rates in bison rumen before Day 5. Reactor microbiomes remained distinct, despite identical operating conditions. Novel associations linked Alistipes with butyric acid production and Eubacterium nodatum and Clostridiales bacterium with pentanoic acid production. This study provides new insights into the ability of microbiomes to convert cellulose to different fatty acid mixtures and adds impetus for the rewiring of anaerobic digestion to generate high-value products.
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http://dx.doi.org/10.1016/j.biortech.2020.124532DOI Listing
March 2021

Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium.

Appl Microbiol Biotechnol 2019 May 9;103(10):4177-4192. Epub 2019 Apr 9.

Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.

Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.
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http://dx.doi.org/10.1007/s00253-019-09762-7DOI Listing
May 2019

Impact of primary carbon sources on microbiome shaping and biotransformation of pharmaceuticals and personal care products.

Biodegradation 2019 06 28;30(2-3):127-145. Epub 2019 Feb 28.

Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO, 80523, USA.

Knowledge of the conditions that promote the growth and activity of pharmaceutical and personal care product (PPCP)-degrading microorganisms within mixed microbial systems are needed to shape microbiomes in biotreatment reactors and manage process performance. Available carbon sources influence microbial community structure, and specific carbon sources could potentially be added to end-of-treatment train biotreatment systems (e.g., soil aquifer treatment [SAT]) to select for the growth and activity of a range of microbial phylotypes that collectively degrade target PPCPs. Herein, the impacts of primary carbon sources on PPCP biodegradation and microbial community structure were explored to identify promising carbon sources for PPCP biotreatment application. Six types of primary carbon sources were investigated: casamino acids, two humic acid and peptone mixtures (high and low amounts of humic acid), molasses, an organic acids mixture, and phenol. Biodegradation was tracked for five PPCPs (diclofenac, 5-fluorouracil, gemfibrozil, ibuprofen, and triclosan). Primary carbon sources were found to differentially impact microbial community structures and rates and efficiencies of PPCP biotransformation. Of the primary carbon sources tested, casamino acids, organic acids, and phenol showed the fastest biotransformation; however, on a biomass-normalized basis, both humic acid-peptone mixtures showed comparable or superior biotransformation. By comparing microbial communities for the different primary carbon sources, abundances of unclassified Beijerinckiaceae, Beijerinckia, Sphingomonas, unclassified Sphingomonadaceae, Flavobacterium, unclassified Rhizobiales, and Nevskia were statistically linked with biotransformation of specific PPCPs.
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http://dx.doi.org/10.1007/s10532-019-09871-0DOI Listing
June 2019

Child's play: Harnessing play and curiosity motives to improve child handwashing in a humanitarian setting.

Int J Hyg Environ Health 2019 03 13;222(2):177-182. Epub 2018 Sep 13.

Department for Disease Control, London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London, WC1E 7HT, UK.

In humanitarian emergency settings there is need for low cost and rapidly deployable interventions to protect vulnerable children, in- and out-of-school, from diarrhoeal diseases. Handwashing with soap can greatly reduce diarrhoea but interventions specifically targeting children's handwashing behaviour in humanitarian settings have not been tested. Traditional children's handwashing promotion interventions have been school-focused, resource-intensive and reliant on health-based messaging. However, recent research from non-humanitarian settings and targeting adults suggests that theory-based behaviour change interventions targeting specific motives may be more effective than traditional handwashing interventions. In this proof-of-concept study we test, for the first time, the distribution of a modified soap bar, designed to appeal to the motives of play and curiosity, in a household-level, rapidly deployable, handwashing promotion intervention for older children in a humanitarian setting - an internally displaced persons camp in Iraqi Kurdistan. Out of five total blocks within the camp, one was assigned to intervention and one to control. 40 households from each assigned block were then randomly chosen for inclusion in the study and the practice of handwashing with soap at key times was measured at baseline and four weeks after intervention delivery. Children in intervention households received transparent soaps with embedded toys, delivered within a short, fun, and interactive household session with minimal, non-health-based, messaging. The control group received plain soap delivered in a short standard, health-based, hygiene promotion session. At the 4-week follow-up, children in the intervention group were 4 times more likely to wash their hands with soap after key handwashing occasions than expected in the counterfactual (if there had been no intervention) based on the comparison to children in the control group (adjusted RR = 3.94, 95% CI 1.59-9.79). We show that distributing soaps with toys embedded inside, in a rapidly deployable intervention, can improve child handwashing behaviour in a humanitarian emergency context. Further studies are needed to determine the longer-term behavioural and health impact of such an intervention when delivered at a greater scale in a humanitarian context.
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http://dx.doi.org/10.1016/j.ijheh.2018.09.002DOI Listing
March 2019

Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles.

ACS Sustain Chem Eng 2018 Sep;6(9):11642-11652

Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095.

Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7751626PMC
September 2018

Ambient-temperature co-digestion of low-solids municipal and industrial waste mixtures: Insights from molecular analyses.

J Air Waste Manag Assoc 2018 11 12;68(11):1148-1158. Epub 2018 Sep 12.

h Department of Civil and Environmental Engineering , Colorado State University , Fort Collins , CO.

The performance of ambient temperature anaerobic co-digestion was investigated for mixtures of six substrates: canned tomato and salsa waste, portable toilet waste, septic tank waste, winery waste, beer and cider waste, and fats, oils, and grease (FOG). Laboratory semi-continuous reactor studies and molecular biological analyses revealed that beer/winery, and tomato/FOG/winery/beer mixtures resulted in the best performance in terms of biogas production (515 and 371 mL CH4/g VS, respectively) and methanogenic populations. A portable toilet/septage mixture resulted in the overall poorest performance and inhibition of microbial activity was evident. Average methane content was ~70% for all mixtures tested. The findings of this study reveal that healthy methanogen populations were present, further supporting the feasibility of biogas production via the novel feedstock mixtures in ambient temperature lagoons. Implications: Disposal of septic tank waste and other high chemical oxygen demand (COD) 10 industrial food processing waste at a small wastewater treatment plant is uncommon, because it can upset the treatment process and requires additional power for treatment. Ambient-temperature covered lagoon digesters can be an alternative low-cost technology for co-digestion of these recalcitrant waste streams while generating bioenergy. The results of this study demonstrated that there is potential for implementation of unheated covered lagoon digester systems 15 for conversion of liquid wastes for production of renewable biomethane while eliminating the need to treat these wastes at a wastewater treatment plant.
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http://dx.doi.org/10.1080/10962247.2018.1479667DOI Listing
November 2018

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells.

Biotechnol Biofuels 2018 23;11:121. Epub 2018 Apr 23.

1Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, USA.

Background: Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole.

Results: To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic (90.9 ± 3.3%) during initial biofilm formation to dominance by , particularly (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition.

Conclusions: The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.
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http://dx.doi.org/10.1186/s13068-018-1111-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5913794PMC
April 2018

Rural surgery: High pressure but rewarding.

Authors:
Susan Long

Bull Am Coll Surg 2017 01;102(1):55-7

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January 2017

Impact of inoculum sources on biotransformation of pharmaceuticals and personal care products.

Water Res 2017 11 21;125:227-236. Epub 2017 Aug 21.

Colorado State University, Department of Civil and Environmental Engineering, USA. Electronic address:

Limited knowledge of optimal microbial community composition for PPCP biotreatment, and of the microbial phylotypes that drive biotransformation within mixed microbial communities, has hindered the rational design and operation of effective and reliable biological PPCP treatment technologies. Herein, bacterial community composition was investigated as an isolated variable within batch biofilm reactors via comparison of PPCP removals for three distinct inocula. Inocula pre-acclimated to model PPCPs were derived from activated sludge (AS), ditch sediment historically-impacted by wastewater treatment plant effluent (Sd), and material from laboratory-scale soil aquifer treatment (SAT) columns. PPCP removals were found to be substantially higher for AS- and Sd-derived inocula compared to the SAT-derived inocula despite comparable biomass. Removal patterns differed among the 6 model compounds examined (diclofenac, 5-fluorouracil, gabapentin, gemfibrozil, ibuprofen, and triclosan) indicating differences in biotransformation mechanisms. Sphingomonas, Beijerinckia, Methylophilus, and unknown Cytophagaceae were linked with successful PPCP biodegradation via next-generation sequencing of 16S rRNA genes over time. Results indicate the criticality of applying engineering approaches to control bacterial community compositions in biotreatment systems.
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http://dx.doi.org/10.1016/j.watres.2017.08.041DOI Listing
November 2017

Enhanced anaerobic digestion performance via combined solids- and leachate-based hydrolysis reactor inoculation.

Bioresour Technol 2016 Nov 10;220:94-103. Epub 2016 Aug 10.

Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA. Electronic address:

Suboptimal conditions in anaerobic digesters (e.g., presence of common inhibitors ammonia and salinity) limit waste hydrolysis and lead to unstable performance and process failures. Application of inhibitor-tolerant inocula improves hydrolysis, but approaches are needed to establish and maintain these desired waste-hydrolyzing bacteria in high-solids reactors. Herein, performance was compared for leach bed reactors (LBRs) seeded with unacclimated or acclimated inoculum (0-60% by mass) at start-up and over long-term operation. High quantities of inoculum (∼60%) increase waste hydrolysis and are beneficial at start-up or when inhibitors are increasing. After start-up (∼112days) with high inoculum quantities, leachate recirculation leads to accumulation of inhibitor-tolerant hydrolyzing bacteria in leachate. During long-term operation, low inoculum quantities (∼10%) effectively increase waste hydrolysis relative to without solids-derived inoculum. Molecular analyses indicated that combining digested solids with leachate-based inoculum doubles quantities of Bacteria contacting waste over a batch and supplies additional desirable phylotypes Bacteriodes and Clostridia.
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http://dx.doi.org/10.1016/j.biortech.2016.08.024DOI Listing
November 2016

Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body.

Appl Microbiol Biotechnol 2016 Apr 22;100(7):3347-60. Epub 2015 Dec 22.

Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO, 80523, USA.

Advances in our understanding of the microbial ecology at sites impacted by light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies, support longevity models, and develop culture-independent molecular tools. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct zones were identified based on microbial community structure and geochemical data: (i) an aerobic, low-contaminant mass zone at the top of the vadose zone; (ii) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone; (iii) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone; and (iv) an anaerobic, low-contaminant mass zone below the LNAPL body. Evidence suggested that hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zone III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, in the LNAPL body below the water table. Observed phylotypes were linked with in situ anaerobic hydrocarbon degradation in LNAPL-impacted soils.
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http://dx.doi.org/10.1007/s00253-015-7106-zDOI Listing
April 2016

Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.

Proc Natl Acad Sci U S A 2015 Apr 18;112(14):4322-7. Epub 2015 Mar 18.

Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210; College of Pharmacy, The Ohio State University, Columbus, OH 43210

Immunoglobulins (Ig) are produced by B lymphocytes as secreted antibodies or as part of the B-cell receptor. There is tremendous diversity of potential Ig transcripts (>1 × 10(12)) as a result of hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments into a complete transcript, and the process of somatic hypermutation at individual nucleotides. This recombination and mutation process takes place in the maturing B cell and is responsible for the diversity of potential epitope recognition. Cancers arising from mature B cells are characterized by clonal production of Ig heavy (IGH@) and light chain transcripts, although whether the sequence has undergone somatic hypermutation is dependent on the maturation stage at which the neoplastic clone arose. Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults and arises from a mature B cell with either mutated or unmutated IGH@ transcripts, the latter having worse prognosis and the assessment of which is routinely performed in the clinic. Currently, IGHV mutation status is assessed by Sanger sequencing and comparing the transcript to known germ-line genes. In this paper, we demonstrate that complete IGH@ V-D-J sequences can be computed from unselected RNA-seq reads with results equal or superior to the clinical procedure: in the only discordant case, the clinical transcript was out-of-frame. Therefore, a single RNA-seq assay can simultaneously yield gene expression profile, SNP and mutation information, as well as IGHV mutation status, and may one day be performed as a general test to capture multidimensional clinically relevant data in CLL.
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http://dx.doi.org/10.1073/pnas.1503587112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394264PMC
April 2015

Priorities, strategies, and accountability measures in interprofessional education.

J Allied Health 2014 Aug;43(3):e37-44

University of Arkansas for Medical Sciences, College of Health Professions, 4301 W. Markham Street, #619, Little Rock, AR 72205, USA. Tel 501-686-6854, fax 501-686-6855.

Purpose: The purpose of this pilot study was to identify the priorities, strategies, and accountability measures for interprofessional education (IPE) being used by health professions programs, allied health colleges, and/or universities.

Method: An electronic survey was sent to 114 deans, associate deans, and directors (program, clinical education, graduate studies) at six institutions with allied health programs, including three academic medical centers and three comprehensive public institutions. The survey consisted of basic demographic questions and questions assessing knowledge of the Interprofessional Education Collaborative (IPEC) concepts of IPE, program-specific accreditation requirements for IPE, and institutional priorities, strategies, and accountability measures for IPE activities.

Results: An overall response rate of 50% (57/114) was achieved with representation from a total of 34 different allied health programs. Chi-squared statistics showed statistically significant differences (p<0.05) between the frequencies of survey responses and institutional types in the inclusion of IPE in the college/school's vision, the physical space available to accommodate IPE needs, and the commitment to set aside time for IPE.

Conclusion: This study found that there is not a clear mandate or direction from most allied health disciplinary accrediting bodies for IPE. While there appears to be distinct movement by institutions to hold programs accountable for IPE and to integrate IPE into the curricula, barriers remain that have slowed the desired degree of implementation of an interprofessional curricula. While institutions, college, and/or programs may be slow to formally include IPE in its vision, this study found that, in general, support is being provided for IPE activities.
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August 2014

Dental hygiene students' perceptions of distance learning: do they change over time?

J Dent Hyg 2014 Feb;88(1):30-5

Purpose: The University of Arkansas for Medical Sciences dental hygiene program established a distant site where the didactic curriculum was broadcast via interactive video from the main campus to the distant site, supplemented with on-line learning via Blackboard. This study compared the perceptions of students towards distance learning as they progressed through the 21 month curriculum. Specifically, the study sought to answer the following questions: Is there a difference in the initial perceptions of students on the main campus and at the distant site toward distance learning? Do students' perceptions change over time with exposure to synchronous distance learning over the course of the curriculum?

Methods: All 39 subjects were women between the ages of 20 and 35 years. Of the 39 subjects, 37 were Caucasian and 2 were African-American. A 15-question Likert scale survey was administered at 4 different periods during the 21 month program to compare changes in perceptions toward distance learning as students progressed through the program. An independent sample t-test and ANOVA were utilized for statistical analysis.

Results: At the beginning of the program, independent samples t-test revealed that students at the main campus (n=34) perceived statistically significantly higher effectiveness of distance learning than students at the distant site (n=5). Repeated measures of ANOVA revealed that perceptions of students at the main campus on effectiveness and advantages of distance learning statistically significantly decreased whereas perceptions of students at distant site statistically significantly increased over time. Distance learning in the dental hygiene program was discussed, and replication of the study with larger samples of students was recommended.
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February 2014

Temperature impacts on anaerobic biotransformation of LNAPL and concurrent shifts in microbial community structure.

Biodegradation 2014 Jul 29;25(4):569-85. Epub 2014 Jan 29.

Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO, 80523, USA.

Thermally-enhanced bioremediation is a promising treatment approach for petroleum contamination; however, studies examining temperature effects on anaerobic biodegradation in zones containing light non-aqueous phase liquids (LNAPLs) are lacking. Herein, laboratory microcosm studies were conducted for a former refinery to evaluate LNAPL transformation, sulfate reduction, and methane generation over a one-year period for temperatures ranging from 4 to 40 °C, and microbial community shifts were characterized. Temperatures of 22 and 30 °C significantly increased total biogas generation compared to lower (4 and 9 °C) and higher temperatures (35 and 40 °C; p < 0.1). Additionally, at 22 and 30 °C methane generation commenced ~6 months earlier than for 35 and 40 °C. Statistically significant biodegradation of benzene, toluene and xylenes was observed at elevated temperatures but not at lower temperatures (p < 0.1). Additionally, a novel differential chromatogram approach was developed to overcome challenges associated with resolving losses in complex mixtures of hydrocarbons, and application of this method revealed greater losses of hydrocarbons at 22 and 30 °C as compared to lower and higher temperatures. Finally, molecular biology assays revealed that the composition and activity of microbial communities shifted in a temperature-dependent manner. Collectively, results demonstrated that anaerobic biodegradation processes can be enhanced by increasing the temperature of LNAPL-containing soils, but biodegradation does not simply increase as temperature increases likely due to a lack of microorganisms that thrive at temperatures well above the historical high temperatures for a site. Rather, optimal degradation is achieved by holding soils at the high end of, or slightly higher than, their natural range.
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http://dx.doi.org/10.1007/s10532-014-9682-5DOI Listing
July 2014

Imidazopyridazine hepatitis C virus polymerase inhibitors. Structure-activity relationship studies and the discovery of a novel, traceless prodrug mechanism.

J Med Chem 2014 Mar 23;57(5):1964-75. Epub 2013 Nov 23.

GlaxoSmithKline Research & Development , 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States.

By reducing the basicity of the core heterocycle in a series of HCV NS5B inhibitors, the hERG liability was reduced. The SAR was then systematically explored in order to increase solubility and enable dose escalation while retaining potency. During this exploration, a facile decarboxylation was noted and was exploited as a novel prodrug mechanism. The synthesis and characterization of these prodrugs and their utilization in chronic toxicity studies are presented.
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http://dx.doi.org/10.1021/jm401337xDOI Listing
March 2014

Microbial community acclimation enhances waste hydrolysis rates under elevated ammonia and salinity conditions.

Bioresour Technol 2013 Oct 15;146:15-22. Epub 2013 Jul 15.

Department of Civil and Environmental Engineering, Colorado State University, 1372 Campus Delivery, Fort Collins, CO 80523, USA. Electronic address:

Hydrolysis rates under potentially inhibitory concentrations of ammonia and salinity were investigated for two model feedstocks (manure and food waste). Rates were determined under a range of ammonia and salinity concentrations (1.0-10.0 g TAN [total ammonia nitrogen] L(-1) and 3.9-20.0 g sodium L(-1)) with unacclimated and acclimated microbial inocula. Microbial community changes as a function of acclimation and feedstock were also investigated. Using unacclimated inocula, hydrolysis was found to be severely inhibited for elevated ammonia and salinity (~4 to 10-fold, respectively) or hydrolysis was not detected. However, for inocula acclimated over 2-4 months, statistically significant inhibition generally was not detectable. Molecular analyses demonstrated that microbial community composition changed during acclimation, and bacterial communities under elevated ammonia were distinct from communities under elevated salinity. Feedstock source also had a major influence on bacterial community structure.
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http://dx.doi.org/10.1016/j.biortech.2013.06.081DOI Listing
October 2013

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress.

Water Res 2013 Sep 18;47(14):5316-25. Epub 2013 Jun 18.

Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, USA.

Sulfate-reducing permeable reactive zones (SR-PRZs) are microbially-driven anaerobic systems designed for the removal of heavy metals and sulfate in mine drainage. Environmental perturbations, such as oxygen exposure, may adversely affect system stability and long-term performance. The objective of this study was to examine the effect of two successive aerobic stress events on the performance and microbial community composition of duplicate laboratory-scale lignocellulosic SR-PRZs operated using the following microbial community management strategies: biostimulation with ethanol or carboxymethylcellulose; bioaugmentation with sulfate-reducing or cellulose-degrading enrichments; inoculation with dairy manure only; and no inoculation. A functional gene-based approach employing terminal restriction fragment length polymorphism and quantitative polymerase chain reaction targeting genes of sulfate-reducing (dsrA), cellulose-degrading (cel5, cel48), fermentative (hydA), and methanogenic (mcrA) microbes was applied. In terms of performance (i.e., sulfate removal), biostimulation with ethanol was the only strategy that clearly had an effect (positive) following exposure to oxygen. In terms of microbial community composition, significant shifts were observed over the course of the experiment. Results suggest that exposure to oxygen more strongly influenced microbial community shifts than the different microbial community management strategies. Sensitivity to oxygen exposure varied among different populations and was particularly pronounced for fermentative bacteria. Although the community structure remained altered after exposure, system performance recovered, indicating that SR-PRZ microbial communities were functionally redundant. Results suggest that pre-exposure to oxygen might be a more effective strategy to improve the resilience of SR-PRZ microbial communities relative to bioaugmentation or biostimulation.
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http://dx.doi.org/10.1016/j.watres.2013.06.014DOI Listing
September 2013

The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants.

J Microbiol Methods 2013 Sep 25;94(3):224-31. Epub 2013 Jun 25.

Department of Civil and Environmental Engineering, Colorado State University, 1372 Campus Delivery, Fort Collins, CO 80523, USA.

Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences.
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http://dx.doi.org/10.1016/j.mimet.2013.06.013DOI Listing
September 2013

Stability enhancement of drug layered pellets in a fixed dose combination tablet.

AAPS PharmSciTech 2013 Mar 15;14(1):312-20. Epub 2013 Jan 15.

GlaxoSmithKline R&D, New Frontiers Science Park, Third Avenue, Harlow, Essex, UK, CM19 5AW.

The purpose of this research was to develop a stable fixed dose combination tablet for a model DPP-IV inhibitor and metformin hydrochloride. The dipeptidyl peptidase IV (DPP-IV) inhibitor was particularly challenging to formulate due to its significant chemical instability and moisture sensitivity. Various formulation strategies were investigated and placed on accelerated stability to determine the lead approach and critical quality attributes. The lead formulation investigated was a drug layered pellet containing the DPP-IV inhibitor, which was further coated with various seal coats and moisture barriers, then compressed into a tablet with compression aids and granulated metformin hydrochloride. The investigations revealed that the drug layered pellets compressed into a fixed dose combination tablet yielded a unique stability enhancement. The stability was highly dependent on the final tablet water content and could be further improved by the addition of moisture barrier coatings. A fundamental understanding of the key critical quality attributes for the fixed dose combination product containing a DPP-IV inhibitor and metformin hydrochloride as an oral solid dosage form were established. This research identified a formulation approach to enable a successful commercial product to be developed.
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http://dx.doi.org/10.1208/s12249-012-9911-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581657PMC
March 2013

Bodies, technologies, and aging in Japan: thinking about old people and their silver products.

Authors:
Susan O Long

J Cross Cult Gerontol 2012 Jun;27(2):119-37

Department of Sociology, John Carroll University, University Heights, OH 44118, USA.

Contemporary Japan is known both for its high tech culture and its rapidly aging population, with 22 % of people currently 65 years and older. Yet there has been little attention to the material culture of the elderly. This paper explores the way aging bodies, official ideology, and consumption of what are called "assistive devices" and "life technologies" come together in the experience of frail old people who depend not only on human caregivers but on "things" such as walkers, kidney dialysis machines, and electric massage chairs. It begins to consider the questions: What technology to aid failing bodies is available, and to whom? How does the advocacy of independence create new forms of consumption? How do "things" mediate ideological change regarding elder care and help to create new understandings of self and one's relation to others? Data come from interviews conducted in 2003-2007 as part of a study of elder care in Japan under the public long term care insurance system that began in 2000. These interviews point both to acceptance of the technology as a way to avoid over-dependence on caregivers, and to resistance to the limitations of aging and to its 21st century definition by the state.
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http://dx.doi.org/10.1007/s10823-012-9164-3DOI Listing
June 2012

Autohydrogenotrophic perchlorate reduction kinetics of a microbial consortium in the presence and absence of nitrate.

Water Res 2011 Dec 19;45(19):6593-601. Epub 2011 Oct 19.

Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, 1 University Station C1786, Austin, TX 78712-0273, USA.

This is the first study to model the effects of nitrate on autohydrogenotrophic perchlorate biokinetics. Batch experiments demonstrated that the presence of nitrate significantly inhibited perchlorate degradation by a hydrogen-oxidizing, perchlorate-reducing microbial consortium. However, the consortium was capable of significant perchlorate reduction while the bulk of the nitrate was still present. Results showed that a modified competitive inhibition model successfully predicted autohydrogenotrophic perchlorate degradation in the presence of nitrate (initial concentrations of ∼230 μg ClO(4)(-)/L and 2.2-4.6 mg NO(3)(-)-N/L). The model describes perchlorate degradation as a function of the biomass, perchlorate, hydrogen, and nitrate concentrations, as well as the single-component perchlorate (28 μg/L), hydrogen (2.3 × 10(-6) M (aq)), and nitrate (0.15 mg/L as N) half-saturation coefficients (K(s)) and perchlorate maximum substrate utilization rate (k) (1.8 μg ClO(4)(-)/mg TSS-hr). Single-component parameters were obtained through a series of batch experiments performed under perchlorate-, nitrate-, and hydrogen-limiting conditions with initial concentrations of 80-340 μg ClO(4)(-)/L, 2.7-3.6 mg NO(3)(-)-N/L, and 1%-3% H(2) (g) by volume.
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http://dx.doi.org/10.1016/j.watres.2011.10.007DOI Listing
December 2011

Quantitative measurement of direct nitrous oxide emissions from microalgae cultivation.

Environ Sci Technol 2011 Nov 6;45(21):9449-56. Epub 2011 Oct 6.

Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado, 80523-1374 United States.

Although numerous lifecycle assessments (LCA) of microalgae-based biofuels have suggested net reductions of greenhouse gas emissions, limited experimental data exist on direct emissions from microalgae cultivation systems. For example, nitrous oxide (N(2)O) is a potent greenhouse gas that has been detected from microalgae cultivation. However, little quantitative experimental data exist on direct N(2)O emissions from microalgae cultivation, which has inhibited LCA performed to date. In this study, microalgae species Nannochloropsis salina was cultivated with diurnal light-dark cycling using a nitrate nitrogen source. Gaseous N(2)O emissions were quantitatively measured using Fourier transform infrared spectrometry. Under a nitrogen headspace (photobioreactor simulation), the reactors exhibited elevated N(2)O emissions during dark periods, and reduced N(2)O emissions during light periods. Under air headspace conditions (open pond simulation), N(2)O emissions were negligible during both light and dark periods. Results show that N(2)O production was induced by anoxic conditions when nitrate was present, suggesting that N(2)O was produced by denitrifying bacteria within the culture. The presence of denitrifying bacteria was verified through PCR-based detection of norB genes and antibiotic treatments, the latter of which substantially reduced N(2)O emissions. Application of these results to LCA and strategies for growth management to reduce N(2)O emissions are discussed.
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http://dx.doi.org/10.1021/es202573fDOI Listing
November 2011

qPCR assays to quantify genes and gene expression associated with microbial perchlorate reduction.

J Microbiol Methods 2010 Nov 16;83(2):270-4. Epub 2010 Sep 16.

The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 1 University Station C1786, Austin, TX 78712, United States.

Quantitative PCR (qPCR) assays targeting cld (developed in this work) and pcrA (previously described) were used to quantify these perchlorate-related genes in a perchlorate-reducing enrichment culture. Transcript copies were quantified in perchlorate-reducing Rhodocyclaceae strain JDS4. Oxygen and nitrate inhibited expression of cld and pcrA.
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http://dx.doi.org/10.1016/j.mimet.2010.09.002DOI Listing
November 2010

Podcasting: making waves in millennial education.

J Nurses Staff Dev 2010 May-Jun;26(3):96-101; quiz 102-3

James Sprunt Community College, Kenansville, North Carolina, USA.

Podcasting is a useful addition to the repertoire of distance learning technologies that provides a fresh and mobile learning option particularly for millennial learners. Nurse educators should capitalize on this new educational approach, which has much to offer in the line of audio recordings.
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http://dx.doi.org/10.1097/NND.0b013e3181993a6fDOI Listing
January 2011

Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung.

J Bacteriol 2009 Jun 27;191(11):3492-503. Epub 2009 Mar 27.

Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA.

Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats, ranging from soil to immunocompromised people. The formation of surface-associated communities called biofilms is one factor thought to enhance colonization and persistence in these diverse environments. Another factor is the ability of P. aeruginosa to diversify genetically, generating phenotypically distinct subpopulations. One manifestation of diversification is the appearance of colony morphology variants on solid medium. Both laboratory biofilm growth and chronic cystic fibrosis (CF) airway infections produce rugose small-colony variants (RSCVs) characterized by wrinkled, small colonies and an elevated capacity to form biofilms. Previous reports vary on the characteristics attributable to RSCVs. Here we report a detailed comparison of clonally related wild-type and RSCV strains isolated from both CF sputum and laboratory biofilm cultures. The clinical RSCV had many characteristics in common with biofilm RSCVs. Transcriptional profiling and Biolog phenotypic analysis revealed that RSCVs display increased expression of the pel and psl polysaccharide gene clusters, decreased expression of motility functions, and a defect in growth on some amino acid and tricarboxylic acid cycle intermediates as sole carbon sources. RSCVs also elicited a reduced chemokine response from polarized airway epithelium cells compared to wild-type strains. A common feature of all RSCVs analyzed in this study is increased levels of the intracellular signaling molecule cyclic di-GMP (c-di-GMP). To assess the global transcriptional effects of elevated c-di-GMP levels, we engineered an RSCV strain that had elevated c-di-GMP levels but did not autoaggregate. Our results showed that about 50 genes are differentially expressed in response to elevated intracellular c-di-GMP levels. Among these genes are the pel and psl genes, which are upregulated, and flagellum and pilus genes, which are downregulated. RSCV traits such as increased exopolysaccharide production leading to antibiotic tolerance, altered metabolism, and reduced immunogenicity may contribute to increased persistence in biofilms and in the airways of CF lungs.
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http://dx.doi.org/10.1128/JB.00119-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681918PMC
June 2009

Factor structure of PTSD in a community sample of sexual assault survivors.

J Trauma Dissociation 2008 ;9(4):507-24

Department of Criminology, Law, Justice, University of Illinois at Chicago, IL 60607, USA.

Recent factor analytic research on posttraumatic stress disorder (PTSD) has questioned the 3-factor structure of the diagnosis as codified in the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV), proposing that a 4-factor model may more accurately reflect the phenomenology of the disorder. Confirmatory factor analyses of the Posttraumatic Stress Diagnostic Scale (E. B. Foa, 1995) were used to conduct model tests of the structure of PTSD in a large sample (N = 967) of adult female sexual assault survivors. A model specifying 4 correlated factors of reexperiencing, effortful avoidance, dysphoria, and hyperarousal provided the best fit to the data, although no model fits were excellent (including that of the traditional DSM-IV 3-factor model). Tests of measurement invariance across race and education suggest that differences may exist in the underlying factor structure of PTSD.
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http://dx.doi.org/10.1080/15299730802223370DOI Listing
May 2009

Exploring the relationships of women's sexual assault disclosure, social reactions, and problem drinking.

J Interpers Violence 2008 Sep 28;23(9):1235-57. Epub 2008 Feb 28.

University of Illinois at Chicago.

The goal of this exploratory study was to examine correlates of sexual assault disclosure and social reactions in female victims with and without drinking problems. An ethnically diverse sample of sexual assault survivors was recruited from college, community, and mental health agencies. Ethnic minority women were less likely to disclose assault, and women with a greater number of traumatic life events disclosed assault more often. Although there were no differences in disclosure likelihood by drinking status; of those disclosing, problem drinkers told more support sources and received more negative and positive social reactions than nonproblem drinkers. Correlates of receiving negative social reactions were similar for normal and problem drinkers; however, negative social reactions to assault disclosure were related to more problem drinking for women with less frequent social interaction. Implications for future research and possible support interventions with problem-drinking victims are provided.
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http://dx.doi.org/10.1177/0886260508314298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863580PMC
September 2008

Women's experiences of male-perpetrated sexual assault by sexual orientation.

Violence Vict 2007 ;22(6):684-701

Department of Psychology, University of Illinois at Chicago 60607, USA.

This study examined differences in male-perpetrated adult sexual assault experiences among women of various sexual orientations using a large urban convenience sample (N = 1,022). Results showed many similarities in disclosure to others, perceived helpfulness, and attributions of blame, but there were also differences by sexual orientation. Heterosexual women were more likely to experience completed sexual assault than lesbian or bisexual women. Lesbians were more likely to be assaulted by relatives than bisexual or heterosexual women. Finally, bisexual women disclosed the assault to the greatest number of formal support sources, were most likely to tell a romantic partner about the assault, received the fewest positive social reactions overall, and had higher posttraumatic stress disorder (PTSD) symptomatology.
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http://dx.doi.org/10.1891/088667007782793138DOI Listing
March 2008