Daniel J Hassett

Cincinnati Eye Hospital, Cincinnati, Ohio, United States

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Publications (128)492.01 Total impact

  • Gihoon Choi · Daniel J. Hassett · Seokheun Choi
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    ABSTRACT: There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in the MFC performance can be achieved with the development of a new technique in synthetic biology that regulates microbial metabolic pathways or controls their gene expression. For this new direction, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for high-throughput and rapid characterization of microbial electricity-producing capability. Spatially distinct 48 wells of the sensor array were prepared by patterning 48 hydrophilic reservoirs in paper with hydrophobic wax boundaries. The paper-based platform exploited the ability of paper to quickly wick fluid and promote bacterial attachment to the anode pads, resulting in an instant current generation upon loading of a bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impact the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants in P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identify which of the genes in P. aeruginosa trigger higher power density.
    The Analyst 04/2015; 140(12). DOI:10.1039/C5AN00492F · 4.11 Impact Factor
  • G. Choi · A. Fraiwan · D.J. Hassett · S. Choi
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    ABSTRACT: We demonstrate the use of a paper-based sensing platform for rapid and high-throughput characterization of microbial electricity-generating capabilities. For the first time, a 48-well microbial fuel cell (MFC) array was fabricated on paper substrates, providing 48 high-throughput measurements and highly comparable performance characteristics in a reliable manner. Spatially distinct 48 wells of the sensor array were prepared by patterning 48 hydrophilic reservoirs in paper with hydrophobic wax boundaries. The paper-based platform exploited the ability of paper to quickly wick fluid and promote bacterial attachment to the gold anode pads, resulting in an instant current generation upon loading of bacterial inoculum and catholyte. This paper-based 48-well MFC array does not require external pumps/tubings and represents the most rapid and the highest throughput test platform for electrogenic bacterial screening.
    Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS) 02/2015; 2015:577-580. DOI:10.1109/MEMSYS.2015.7051021
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    ABSTRACT: The majority of antibiotic-induced diarrhea is caused by Clostridium difficile (C. difficile). Hospitalizations for Clostridium difficile infection (CDI) have tripled in the last decade, emphasizing the need to better understand how the organism colonizes the intestine and maintain infection. The mucus provides an interface for bacterial-host interactions and changes in intestinal mucus have been linked host health. To assess mucus production and composition in healthy and CDI patients, the main mucins MUC1 and MUC2 and mucus oligosaccharides were examined. In comparison to healthy patients, CDI patients demonstrated decreased MUC2 with no changes in surface MUC1. Although MUC1 did not change at the level of the epithelia, MUC1 was the primary constituent of secreted mucus in CDI patients. CDI mucus also exhibited decreased N-Acetylgalactosamine (GalNAc), increased N-Acetylglucosamine(GlcNAc) and increased terminal galactose residues. Increased galactose in CDI biopsies are of particular interest since terminal galactose sugars are known as C. difficile toxin A receptor in animals. In vitro, C. difficile is capable of metabolizing fucose, mannose, galactose, GlcNAc, and GalNAc for growth under healthy stool conditions (low [Na(+)], pH 6.0). Injection of C. difficile into human intestinal organoids (HIOs) demonstrated that C. difficile alone is sufficient to reduce MUC2 production, but is not capable of altering host mucus oligosaccharide composition. We also demonstrate that C. difficile binds preferentially to mucus extracted from CDI patients compared with healthy patients. Our results provide insight into a mechanism of C. difficile colonization and may provide novel target(s) for the development of alternative therapeutic agents. Copyright © 2014, American Journal of Physiology- Gastrointestinal and Liver Physiology.
    AJP Gastrointestinal and Liver Physiology 12/2014; 308(6):ajpgi.00091.2014. DOI:10.1152/ajpgi.00091.2014 · 3.80 Impact Factor
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    ABSTRACT: Clostridium difficile infection (CDI) is principally responsible for hospital acquired, antibiotic-induced diarrhea and colitis and represents a significant financial burden on our healthcare system. Little is known about C. difficile proliferation requirements and a better understanding of these parameters are critical for development of new therapeutic targets. In cell lines, C. difficile toxin B has been shown to inhibit Na(+)/H(+) Exchanger 3 (NHE3) and loss of NHE3 in mice results in an altered intestinal environment coupled with a transformed gut microbiota composition. However, this has yet to be established in vivo in humans. We hypothesize that C. difficile toxin inhibits NHE3, resulting in alteration of the intestinal environment and gut microbiota. Our results demonstrate that CDI patient biopsies have decreased NHE3 expression and CDI stool has elevated Na(+) and are more alkaline compared to stool from healthy individuals. CDI stool microbiota have increased Bacteroidetes and Proteobacteria and decreased Firmicutes phyla compared with healthy patients. In vitro, C. difficile grows optimally in the presence of elevated Na(+) and alkaline pH, conditions which correlate to changes observed in CDI patients. To confirm that inhibition of NHE3 was specific to C. difficile, human intestinal organoids (HIOs) were injected with C. difficile or healthy and CDI stool supernatant. Injection of C. difficile and CDI stool decreased NHE3 mRNA and protein expression compared with healthy stool and control HIOs. Together these data demonstrate that C. difficile inhibits NHE3 in vivo which creates an altered environment favored by C. difficile. Copyright © 2014, American Journal of Physiology- Gastrointestinal and Liver Physiology.
    AJP Gastrointestinal and Liver Physiology 12/2014; 308(6):ajpgi.00090.2014. DOI:10.1152/ajpgi.00090.2014 · 3.80 Impact Factor
  • Arwa Fraiwan · Daniel J. Hassett · Seokheun Choi
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    ABSTRACT: Due to an increased concern about the global energy crisis and environmental pollution, microbial fuel cells (MFCs) have been a major focus for renewable energy production. To date, however, a surprisingly small number of bacterial strains and their optimal growth conditions have been investigated for use in MFCs, revealing a crucial lack of fundamental knowledge as to which bacteria species or consortia may be best suited for generating power in MFCs. This lack of knowledge is due to the fact that current screening methods are depending on larger scale two-bottle MFCs that require long start-up times, as well as the inability of conventional MFC arrays to generate electricity in a reliable, robust, and reproducible manner. In particular, the influence of light on the bacterial growth conditions and their power generation has not been fully reported because conventional MFC's opaque device/anode configuration leads to inefficient light penetration. This paper presents a miniaturized high-throughput parallel analyses platform not only for the screening/characterization of the electrochemical activities of electrogenic bacteria but also for investigation of the effect of light on bioelectricity generated from eight different microbial consortia in anode or cathode compartment; wild-type Shewanella oneidensis MR-1, Synechocystis sp. PCC 6803, wild-type Pseudomonas aeruginosa PAO1, and isogenic nirS, lasl, bdlA, and rpoS mutants, respectively. The array consists of nine MFC units with (i) transparent thin gold anode on PMMA layers for efficient light penetration and (ii) independent microfluidic accesses allowing for long term analysis ability without contamination from chamber to chamber during operation. Each MFC unit contains vertically stacked 57 μl anode/cathode chambers separated by a proton exchange membrane. S. oneidensis displayed the highest current generation among all the consortia, 4-fold higher than that of wild-type P. aeruginosa PAO1. However, all the other mutants produced significantly low current outputs. Current production by Synechocystis sp. PCC 6803 demonstrated a positive response upon illumination and a subsequent decrease of output in the dark while other MFC units showed negligible light responses.
    Journal of Renewable and Sustainable Energy 11/2014; 6(6):063110. DOI:10.1063/1.4902094 · 0.90 Impact Factor
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    ABSTRACT: Here, we constructed stable, chromosomal, constitutively expressed, green and red fluorescent protein (GFP and RFP) as reporters in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei. Using bioinformatic approaches and other experimental analyses, we identified P0253 and P1 as potent promoters that drive the optimal expression of fluorescent reporters in single copy in B. anthracis and Burkholderia spp. as well as their surrogate strains, respectively. In comparison, Y. pestis and its surrogate strain need two chromosomal copies of cysZK promoter (P2cysZK) for optimal fluorescence. The P0253-, P2cysZK-, and P1-driven GFP and RFP fusions were first cloned into the vectors pRP1028, pUC18R6KT-mini-Tn7T-Km, pmini-Tn7-gat, or their derivatives. The resultant constructs were delivered into the respective surrogates and subsequently into the select agent strains. The chromosomal GFP- and RFP-tagged strains exhibited bright fluorescence at an exposure time of less than 200 msec and displayed the same virulence traits as their wild-type parental strains. The utility of the tagged strains was proven by the macrophage infection assays and lactate dehydrogenase release analysis. Such strains will be extremely useful in high-throughput screens for novel compounds that could either kill these organisms, or interfere with critical virulence processes in these important bioweapon agents and during infection of alveolar macrophages.
    MicrobiologyOpen 10/2014; 3(5). DOI:10.1002/mbo3.192 · 2.21 Impact Factor
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    ABSTRACT: The human pathogen Pseudomonas aeruginosa is capable of causing both acute and chronic infections. Differences in virulence are attributable to the mode of growth: bacteria growing planktonically cause acute infections, while bacteria growing in matrix-enclosed aggregates known as biofilms are associated with chronic, persistent infections. While the contribution of the planktonic and biofilm modes of growth to virulence is now widely accepted, little is known about the role of dispersion in virulence, the active process by which biofilm bacteria switch back to the planktonic mode of growth. Here, we demonstrate that P. aeruginosa dispersed cells display a virulence phenotype distinct from those of planktonic and biofilm cells. While the highest activity of cytotoxic and degradative enzymes capable of breaking down polymeric matrix components was detected in supernatants of planktonic cells, the enzymatic activity of dispersed cell supernatants was similar to that of biofilm supernatants. Supernatants of non-dispersing ΔbdlA biofilms were characterized by a lack of many of the degradative activities. Expression of genes contributing to the virulence of P. aeruginosa was nearly 30-fold reduced in biofilm cells relative to planktonic cells. Gene expression analysis indicated dispersed cells, while dispersing from a biofilm and returning to the single cell lifestyle, to be distinct from both biofilm and planktonic cells, with virulence transcript levels being reduced up to 150-fold compared to planktonic cells. In contrast, virulence gene transcript levels were significantly increased in non-dispersing ΔbdlA and ΔdipA biofilms compared to wild-type planktonic cells. Despite this, bdlA and dipA inactivation, resulting in an inability to disperse in vitro, correlated with reduced pathogenicity and competitiveness in cross-phylum acute virulence models. In contrast, bdlA inactivation rendered P. aeruginosa more persistent upon chronic colonization of the murine lung, overall indicating that dispersion may contribute to both acute and chronic infections.
    PLoS Pathogens 06/2014; 10(6):e1004168. DOI:10.1371/journal.ppat.1004168 · 7.56 Impact Factor
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    ABSTRACT: Pseudomonas aeruginosa (PA) is a common bacterial pathogen, responsible for a high incidence of nosocomial and respiratory infections. KatA is the major catalase of PA that detoxifies hydrogen peroxide (H2O2), a reactive oxygen intermediate generated during aerobic respiration. Paradoxically, PA displays elevated KatA activity under anaerobic growth conditions where the substrate of KatA, H2O2, is not produced. The aim of the present study is to elucidate the mechanism underlying this phenomenon and define the role of KatA in PA during anaerobiosis using genetic, biochemical and biophysical approaches. We demonstrated that anaerobic wild-type PAO1 cells yielded higher levels of katA transcription and expression than aerobic cells, whereas a nitrite reductase mutant ΔnirS produced ∼50% the KatA activity of PAO1, suggesting that a basal NO level was required for the increased KatA activity. We also found that transcription of the katA gene was controlled, in part, by the master anaerobic regulator, ANR. A ΔkatA mutant and a mucoid mucA22 ΔkatA bacteria demonstrated increased sensitivity to acidified nitrite (an NO generator) in anaerobic planktonic and biofilm cultures. EPR spectra of anaerobic bacteria showed that levels of dinitrosyl iron complexes (DNIC), indicators of NO stress, were increased significantly in the ΔkatA mutant, and dramatically in a ΔnorCB mutant compared to basal levels of DNIC in PAO1 and ΔnirS mutant. Expression of KatA dramatically reduced the DNIC levels in ΔnorCB mutant. We further revealed direct NO-KatA interactions in vitro using EPR, optical spectroscopy and X-ray crystallography. KatA has a 5-coordinate high spin ferric heme that binds NO without prior reduction of the heme iron (Kd ∼6 μM). Collectively, we conclude that KatA is expressed to protect PA against NO generated during anaerobic respiration. We proposed that such protective effects of KatA may involve buffering of free NO when potentially toxic concentrations of NO are approached.
    PLoS ONE 03/2014; 9(3):e91813. DOI:10.1371/journal.pone.0091813 · 3.23 Impact Factor
  • Daniel J Hassett · Michael T Borchers · Ralph J Panos
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    ABSTRACT: Chronic obstructive pulmonary disease (COPD), a disease manifested by significantly impaired airflow, afflicts ∼14.2 million cases in the United States alone with an estimated 63 million people world-wide. Although there are a number of causes, the predominant cause is excessive tobacco smoke. In fact, in China, there have been estimates of 315,000,000 people that smoke. Other less frequent causes are associated with indirect cigarette smoke, air pollutants, biomass fuels, and genetic mutations. COPD is often associated with heart disease, lung cancer, osteoporosis and conditions can worsen in patients with sudden falls. COPD also affects both innate and adaptive immune processes. Cigarette smoke increases the expression of matrix metalloproteases and proinflammatory chemokines and increases lung titers of natural killer cells and neutrophils. Yet, neutrophil reactive oxygen species (ROS) mediated by the phagocytic respiratory burst and phagocytosis is impaired by nicotine. In contrast to innate immunity in COPD, dendritic cells represent leukocytes recruited to the lung that link the innate immune responses to adaptive immune responses by activating naïve T cells through antigen presentation. The autoimmune process that is also a significant part of inflammation associated with COPD. Moreover, coupled with restricted FEV1 values, are the prevalence of patients with single or multiple infections by bacteria, viruses and fungi. Finally, we focus on one of the more problematic infectious agents, the Gram-negative opportunistic pathogenic bacterium, Pseudomonas aeruginosa. Specifically, we delve into the development of highly problematic biofilm infections that are highly refractory to conventional antibiotic therapies in COPD. We offer a non-conventional, biocidal treatment that may be effective for COPD airway infections as well as with combinations of current antibiotic regimens for more effective treatment outcomes and relief for patients with COPD.
    The Journal of Microbiology 03/2014; 52(3):211-26. DOI:10.1007/s12275-014-4068-2 · 1.44 Impact Factor
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    ABSTRACT: Bioenergy Research: Advances and Applications, (2014) 513pp. 978-0-444-59561-4
    01/2014: pages 1-513; Elsevier B.V..
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    ABSTRACT: We have developed an array of six MEMS (micro-electro-mechanical systems) microbial fuel cells (MFCs), a compact and reliable platform for rapid screening of electrochemically active bacteria. The MFC array contains vertically stacked 1.5 μL anode/cathode chambers separated by a proton exchange membrane (PEM), and represents the smallest MEMS MFC array currently available. Each layer, except for the PEM, was micro-patterned by using laser micromachining and was precisely aligned. Within just 5 h, we successfully determined the electricity generation capacity of two known bacterial electrogens (wild-type S. oneidensis and P. aeruginosa) and another metabolically more voracious organism with 4 isogenic mutants constructed with the hypothesis that such mutations could alter their electrogenic properties. Genetically engineered genes in P. aeruginosa including nirS (nitrite reductase), lasl (N-(3-oxododecanoyl)-l-homoserine lactone synthase), bdlA (biofiilm dispersion locus) and pilT (controls the number of Type IV pili on the poles of the bacteria) sensitively showed different efficiencies of extracellular electron transfer to the anode in the significantly reduced micro-chambers. In addition, the percent deviation of all six MFC units was less than 1.4% from their open circuit voltages recorded, which is far less than that of mL-sized MFC arrays (25%) and even MEMS MFC arrays (>8%). This analytical platform would provide the practical tools for fundamental study and characterization of the behavior and physiology of microorganisms and their interaction with MFCs with a greater level of insight and productivity.
    Sensors and Actuators A Physical 10/2013; 201:532-537. DOI:10.1016/j.sna.2012.10.025 · 1.90 Impact Factor
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    ABSTRACT: Changes in the intestinal microbiota have been linked to diabetes, obesity, IBD, and Clostridium difficile-associated disease. Despite this, it remains unclear how the intestinal environment, set by ion transport, affects luminal and mucosa-associated bacterial composition. Na(+)/H(+)-Exchanger isoform 3 (NHE3), a target of C. difficile toxin B, plays an integral role in intestinal Na(+) absorption. Thus, the NHE3-deficient mouse model was chosen to examine the effect of pH and ion composition on bacterial growth. We hypothesized that ion transport-induced change in the intestinal environment would lead to alteration of the microbiota. Region-specific changes in ion composition and pH correlated with region-specific alteration of luminal and mucosal-associated bacteria with general decreases in Firmicutes and increases in Bacteroidetes members. Bacteroides thetaiotaomicron increased in NHE3(-/-) terminal ileum and was examined in vitro to determine if altered Na(+) was sufficient to affect growth. Increased in vitro growth of B. thetaiotaomicron occurred in 43 mM Na(+) correlating with the NHE3(-/-) mouse terminal ileum [Na(+)]. NHE3(-/-) terminal ileum displayed increased fut2 mRNA and fucosylation correlating with B. thetaiotaomicron growth. Inoculation of B. thetaiotaomicron in WT and NHE3-/- terminal ileum organoids displayed increased fut2 and fucosylation, indicating that B. thetaiotaomicron alone is sufficient for the increased fucosylation seen in vivo. These data demonstrate that loss of NHE3 alters the intestinal environment leading to region-specific changes in bacteria and shed light on the growth requirements of some gut microbiota members, which is vital for creating better treatments of complex diseases with an altered gut microbiota.
    AJP Gastrointestinal and Liver Physiology 09/2013; 305(10). DOI:10.1152/ajpgi.00184.2013 · 3.80 Impact Factor
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    ABSTRACT: Here, we constructed stable, constitutively expressed, chromosomal green (GFP) and red fluorescent (RFP) reporters in the genome of the surrogate strain, Francisella tularensis spp. holarctica LVS (herein LVS), and the select agent, F. tularensis Schu S4. A bioinformatic approach was used to identify constitutively expressed genes. Two promoter regions upstream of the FTT1794 and rpsF(FTT1062) genes were selected and fused with GFP and RFP reporter genes in pMP815, respectively. While the LVS strains with chromosomally integrated reporter fusions exhibited fluorescence, we were unable to deliver the same fusions into Schu S4. Neither a temperature-sensitive Francisella replicon nor a pBBR replicon in the modified pMP815 derivatives facilitated integration. However, a mini-Tn7 integration system was successful at integrating the reporter fusions into the Schu S4 genome. Finally, fluorescent F. tularensis LVS and a mutant lacking MglA were assessed for growth in monocyte-derived macrophages (MDMs). As expected, when compared to wild-type bacteria, replication of an mglA mutant was significantly diminished, and the overall level of fluorescence dramatically decreased with infection time. The utility of the fluorescent Schu S4 strain was also examined within infected MDMs treated with clarithromycin and enrofloxacin. Taken together, this study describes the development of an important reagent for F. tularensis research, especially since the likelihood of engineered antibiotic resistant strains will emerge with time. Such strains will be extremely useful in high-throughput screens for novel compounds that could interfere with critical virulence processes in this important bioweapons agent and during infection of alveolar macrophages.
    Applied Microbiology and Biotechnology 07/2013; 97(20). DOI:10.1007/s00253-013-5081-9 · 3.34 Impact Factor
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    ABSTRACT: The opportunistic pathogen Pseudomomas aeruginosa produces multiple pigments during in vitro culture and in vivo during colonization of burn wounds and in the airways of cystic fibrosis (CF) patients. One pigment is a deep "merlot" colored compound known as aeruginosin A (AA). However, the red pigment(s) of P. aeruginosa are often collectively called pyorubrin, of which there is no known chemical composition. Here, we purified and confirmed by mass spectrometry and assessed the physicochemical properties of AA (2-amino-6-carboxy-10-methylphenazinium betaine) by first focusing on its ability to redox-cycle using cyclic voltammetry and its spectroscopic (as well as fluorescent) properties, experiments that were conducted at physiological pH. AA exhibited reversible electrochemistry at a glassy carbon electrode within a potential range of -500 mV to -200 mV. Electrochemical anodic and cathodic peak currents were observed at -327 mV and -360 mV, respectively, with a low formal reduction potential of -343.5 mV vs. Ag/AgCl. AA absorbed at 516 nm and fluoresced at 606 nm. Results from the spectro-electrochemistry of PR revealed that its strongest fluorescence was in its parent or oxidized form. Production of AA by P. aeruginosa was found to be controlled by the rhl component of the inter-cellular signaling system known as quorum sensing and was produced maximally during the stationary growth phase. However, unlike its downstream blue redox-active toxin, pyocyanin (PYO), AA had no adverse effects on methicillin-resistant Staphylococcus aureus USA300, Escherichia coli DH5-α or human keratinocytes. We close with some thoughts on the potential commercial use(s) of AA.
    Microbiology 06/2013; 159(Pt_8). DOI:10.1099/mic.0.065235-0 · 2.56 Impact Factor
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    A. Fraiwan · S. Sundermier · D. Han · A. J. Steckl · D. J. Hassett · S. Choi
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    ABSTRACT: In this work, a microfabricated anode based on gold coated poly(ϵ-caprolactone) fiber was developed that outperformed gold microelectrode by a factor of 2.65-fold and even carbon paper by 1.39-fold. This is a result of its ability to three-dimensionally interface with bacterial biofilm, the metabolic “engines” of the microbial fuel cell (MFC). We also examined unavoidable issues as the MFC is significantly reduced in size (e.g. to the microscale); (1) bubble production or movement into the microchamber and (2) high sensitivity to flow rate variations. In fact, intentionally induced bubble generation in the anodic chamber reduced the MFC current density by 33% and the MFC required 4 days to recover its initial performance. Under different flow rates in the anode chamber, the current densities were almost constant, however, the current increased up to 38% with increasing flow rate in the cathode.
    Fuel Cells 06/2013; 13(3). DOI:10.1002/fuce.201200225 · 2.08 Impact Factor
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    Minghua Zhou · Hongyu Wang · Daniel J. Hassett · Tingyue Gu
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    ABSTRACT: Bioenergy is a renewable energy that plays an indispensable role in meeting today's ever increasing energy needs. Unlike biofuels, microbial fuel cells (MFCs) convert energy harvested from redox reactions directly into bioelectricity. MFCs can utilize low-grade organic carbons (fuels) in waste streams. The oxidation of the fuel molecules requires biofilm catalysis. In recent years, MFCs have also been used in the electrolysis mode to produce bioproducts in laboratory tests. MFCs research has intensified in the past decade and the maximum MFCs power density output has been increased greatly and many types of waste streams have been tested. However, new breakthroughs are needed for MFCs to be practical in wastewater treatment and power generation beyond powering small sensor devices. To reduce capital and operational costs, simple and robust membrane-less MFCs reactors are desired, but these reactors require highly efficient biofilms. Newly discovered conductive cell aggregates, improved electron transport through hyperpilation via mutation or genetic recombination and other advances in biofilm engineering present opportunities. This review is an update on the recent advances on MFCs designs and operations. © 2012 Society of Chemical Industry
    Journal of Chemical Technology & Biotechnology 04/2013; 88(4). DOI:10.1002/jctb.4004 · 2.35 Impact Factor
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    ABSTRACT: High-throughput screening (HTS) of 42 865 compounds was performed to identify compounds that inhibit formation of or kill Staphylococcus epidermidis RP62a biofilms. Three biological processes were assayed, including (1) growth of planktonic/biofilm bacteria, (2) assessment of metabolically active biofilm bacteria using a resazurin assay, and (3) assessment of biofilm biomass by crystal violet staining. After completing the three tiers (primary screening, hit confirmation, and dose-response curves), 352 compounds (representing ~0.8%) were selected as confirmed hit compounds from the HTS assay. The compounds were divided into groups based on their effectiveness on S. epidermidis biofilm properties. The majority of these affected both inhibition and killing of bacterial biofilm cultures. Only 16 of the confirmed hit compounds that have either an AC50 lower than 10 µM and/or Sconst ≥70 from those processed were selected for further study by confocal laser scanning microscopy (CLSM). The CLSM was used to evaluate the confirmed hit compounds on (1) inhibition of biofilm formation and (2) killing of preexisting S. epidermidis biofilms. Taken together, with further testing (e.g., disease-related conditions), such compounds may have applications as broad antimicrobial/antibiofilm use for prophylactic or therapeutic intervention to combat infections in surgical and intensive care clinics and battlefield settings.
    Journal of Biomolecular Screening 03/2013; 18(7). DOI:10.1177/1087057113481499 · 2.42 Impact Factor
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    Jingyuan Deng · Shengchang Su · Xiaodong Lin · Daniel J Hassett · Long Jason Lu
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    ABSTRACT: Large-scale systematic analysis of gene essentiality is an important step closer toward unraveling the complex relationship between genotypes and phenotypes. Such analysis cannot be accomplished without unbiased and accurate annotations of essential genes. In current genomic databases, most of the essential gene annotations are derived from whole-genome transposon mutagenesis (TM), the most frequently used experimental approach for determining essential genes in microorganisms under defined conditions. However, there are substantial systematic biases associated with TM experiments. In this study, we developed a novel Poisson model-based statistical framework to simulate the TM insertion process and subsequently correct the experimental biases. We first quantitatively assessed the effects of major factors that potentially influence the accuracy of TM and subsequently incorporated relevant factors into the framework. Through iteratively optimizing parameters, we inferred the actual insertion events occurred and described each gene's essentiality on probability measure. Evaluated by the definite mapping of essential gene profile in Escherichia coli, our model significantly improved the accuracy of original TM datasets, resulting in more accurate annotations of essential genes. Our method also showed encouraging results in improving subsaturation level TM datasets. To test our model's broad applicability to other bacteria, we applied it to Pseudomonas aeruginosa PAO1 and Francisella tularensis novicida TM datasets. We validated our predictions by literature as well as allelic exchange experiments in PAO1. Our model was correct on six of the seven tested genes. Remarkably, among all three cases that our predictions contradicted the TM assignments, experimental validations supported our predictions. In summary, our method will be a promising tool in improving genomic annotations of essential genes and enabling large-scale explorations of gene essentiality. Our contribution is timely considering the rapidly increasing essential gene sets. A Webserver has been set up to provide convenient access to this tool. All results and source codes are available for download upon publication at http://research.cchmc.org/essentialgene/.
    PLoS ONE 03/2013; 8(3):e58178. DOI:10.1371/journal.pone.0058178 · 3.23 Impact Factor
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    A Fraiwan · S Sundermier · D Han · A Steckl · D J Hassett · S Choi
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    ABSTRACT: Driven by increasing concerns over the energy-climate crisis and environment pollution, microbial fuel cells (MFCs) have been a major focus for renewable energy production. With the successful validation of conceptual macro-sized MFCs as a low-cost renewable energy technology, recent research has focused on miniaturizing MFCs for powering small portable electronics. However, existing micro-sized MEMS MFCs are generally limited by their relatively low power density due to the lack of fundamental knowledge and information on MEMS MFCs. In this paper, we identified the main limiting factors in developing and operating MEMS MFCs and provided suggestions to more effectively improve their performance.
    Proceedings of PowerMEMS; 12/2012
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    Minlu Zhang · Shengchang Su · Raj K Bhatnagar · Daniel J Hassett · Long J Lu
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    ABSTRACT: Pseudomonas aeruginosa (PA) is a ubiquitous opportunistic pathogen that is capable of causing highly problematic, chronic infections in cystic fibrosis and chronic obstructive pulmonary disease patients. With the increased prevalence of multi-drug resistant PA, the conventional "one gene, one drug, one disease" paradigm is losing effectiveness. Network pharmacology, on the other hand, may hold the promise of discovering new drug targets to treat a variety of PA infections. However, given the urgent need for novel drug target discovery, a PA protein-protein interaction (PPI) network of high accuracy and coverage, has not yet been constructed. In this study, we predicted a genome-scale PPI network of PA by integrating various genomic features of PA proteins/genes by a machine learning-based approach. A total of 54,107 interactions covering 4,181 proteins in PA were predicted. A high-confidence network combining predicted high-confidence interactions, a reference set and verified interactions that consist of 3,343 proteins and 19,416 potential interactions was further assembled and analyzed. The predicted interactome network from this study is the first large-scale PPI network in PA with significant coverage and high accuracy. Subsequent analysis, including validations based on existing small-scale PPI data and the network structure comparison with other model organisms, shows the validity of the predicted PPI network. Potential drug targets were identified and prioritized based on their essentiality and topological importance in the high-confidence network. Host-pathogen protein interactions between human and PA were further extracted and analyzed. In addition, case studies were performed on protein interactions regarding anti-sigma factor MucA, negative periplasmic alginate regulator MucB, and the transcriptional regulator RhlR. A web server to access the predicted PPI dataset is available at http://research.cchmc.org/PPIdatabase/.
    PLoS ONE 07/2012; 7(7):e41202. DOI:10.1371/journal.pone.0041202 · 3.23 Impact Factor

Publication Stats

6k Citations
492.01 Total Impact Points


  • 2014
    • Cincinnati Eye Hospital
      Cincinnati, Ohio, United States
  • 1994–2014
    • University of Cincinnati
      • Department of Molecular Genetics, Biochemistry, and Microbiology
      Cincinnati, Ohio, United States
  • 2009
    • The Ohio State University
      Columbus, Ohio, United States
  • 2006
    • University of Southampton
      • Centre for Biological Sciences
      Southampton, England, United Kingdom
  • 2001–2006
    • Montana State University
      • Department of Land Resources and Environmental Sciences
      Bozeman, MT, United States
  • 2002
    • Winthrop University Hospital
      مينيولا, New York, United States
  • 1999
    • Howard Hughes Medical Institute
      Ashburn, Virginia, United States
    • Colorado State University
      Fort Collins, Colorado, United States
  • 1996–1997
    • The University of Calgary
      • Department of Microbiology, Immunology and Infectious Diseases
      Calgary, Alberta, Canada
  • 1995
    • Cincinnati Children's Hospital Medical Center
      • Department of Pediatrics
      Cincinnati, OH, United States
    • University of Tennessee
      • Department of Microbiology
      Knoxville, Tennessee, United States
  • 1987–1994
    • University of North Carolina at Chapel Hill
      • • Department of Medicine
      • • Department of Microbiology and Immunology
      Chapel Hill, NC, United States
    • Duke University Medical Center
      Durham, North Carolina, United States