Characterization of the Entner-Doudoroff pathway in Pseudomonas aeruginosa catheter-associated urinary tract infections.

Pseudomonas aeruginosa is an opportunistic nosocomial pathogen responsible for a subset of catheter-associated urinary tract infections (CAUTI). In a murine model of P. aeruginosa CAUTI, we previously demonstrated that urea within urine suppresses quorum sensing and induces the Entner-Doudoroff (E-D) pathway. The E-D pathway consists of the genes zwf, pgl, edd, and eda. Zwf and Pgl convert glucose-6-phosphate into 6-phosphogluconate. Edd hydrolyzes 6-phosphogluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG). Finally, Eda cleaves KDPG to glyceraldehyde-3-phosphate and pyruvate, which enters the citric acid cycle. Here, we generated in-frame E-D mutants in the strain PA14 and assessed their growth phenotypes on chemically defined and complex media. These E-D mutants have a growth defect when grown on glucose or gluconate as the sole carbon source, which is similar to results previously reported for PAO1 mutants lacking E-D genes. RNA-sequencing following short exposure to urine revealed minimal gene regulation differences compared to the wild type. In a murine CAUTI model, virulence testing of E-D mutants revealed that two mutants lacking zwf and pgl showed minor fitness defects. Infection with the ∆pgl strain exhibited a 20% increase in host survival, and the ∆zwf strain displayed decreased colonization of the catheter and kidneys. Consequently, our findings suggest that the E-D pathway in P. aeruginosa is dispensable in this model of CAUTI. IMPORTANCE Prior studies have shown that the Entner-Doudoroff pathway is up-regulated when Pseudomonas aeruginosa is grown in urine. Pseudomonads use the Entner-Doudoroff (E-D) pathway to metabolize glucose instead of glycolysis, which led us to ask whether this pathway is required for urinary tract infection. Here, single-deletion mutants of each gene in the pathway were tested for growth on chemically defined media with single-carbon sources as well as complex media. The effect of each mutant on global gene expression in laboratory media and urine was characterized. The virulence of these mutants in a murine model of catheter-associated urinary tract infection revealed that these mutants had similar levels of colonization indicating that glucose is not the primary carbon source utilized in the urinary tract.

Characterization of the Entner-Douderoff Pathway in Pseudomonas aeruginosa Catheter-associated Urinary Tract Infections.

Pseudomonas aeruginosa is an opportunistic nosocomial pathogen responsible for catheter-associated urinary tract infections (CAUTI). In a murine model of P. aeruginosa CAUTI, we previously demonstrated that urea within urine suppresses quorum sensing and induces the Entner-Douderoff (E-D) pathway. The E-D pathway consists of the genes zwf, pgl, edd, and eda. Zwf and Pgl convert glucose-6-phosphate into 6-phosphogluconate. Edd hydrolyzes 6-phosphogluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG). Finally, Eda cleaves KDPG to glyceraldehyde-3-phosphate and pyruvate, which enters the citric acid cycle. Here, we generated in-frame E-D mutants in strain PA14 and assessed their growth phenotypes on chemically defined media. These E-D mutants have a growth defect when grown on glucose or gluconate as sole carbon source which are similar to results previously reported for PAO1 mutants lacking E-D genes. RNA-sequencing following short exposure to urine revealed minimal gene regulation differences compared to the wild type. In a murine CAUTI model, virulence testing of E-D mutants revealed that two mutants lacking zwf and pgl showed minor fitness defects. Infection with the ∆pgl strain exhibited a 20% increase in host survival, and the ∆zwf strain displayed decreased colonization of the catheter and kidneys. Consequently, our findings suggest that the E-D pathway in P. aeruginosa is dispensable in this model of CAUTI.

Comparative evaluation of filtration and imaging properties of analytical filters for microplastic capture and analysis.

Pollution by microplastics (MPs) is a growing problem that is now well-recognized, as concerning levels of MPs have been found in drinking water, food, and even human tissues. Given the evolving understanding of their toxicological effects on human health, MPs are an area of concern requiring further study. Consequently, there is a need for greater understanding of the performance characteristics of common MP analytical methods and where possible, for standardizing methods and reporting practices. Here, we report our work comparing filtration and imaging properties of five analytical filters suitable for MP capture and analysis. We compared track-etched polycarbonate with (PCTEG) and without gold coating (PCTE), polytetrafluoroethylene (PTFE), porous silicon (PSi), and gold-coated microslit silicon nitride membranes (MSSN-Au). Four of the filter types had a nominal 1.0 µm cut-off, except for PCTEG which had a 0.8 nominal cut-off. We examined the ultrastructure of each membrane type by electron microscopy to understand how their physical properties influence filtration and imaging performance. We compared clean water filtration rates and timed volume passage for each filter in comparison to its porosity and working surface area. We further compared optical microscopy imaging properties for each filter with model MP samples in both bright-field and fluorescent modes with accompanying Nile Red staining. In terms of absolute and surface area-normalized flow rates, our measurements ranked the filters in order of MSSN-Au > PTFE > PCTE > PCTEG > PSi. Similarly, we found MSSN-Au filters compared favorably in terms of optical microscopy performance. Collectively, these data will aid practitioners when choosing analytical filters for MP surveillance and testing.

Continuous dynamics in behavior reveal interactions between perceptual warping in categorization and speech-in-noise perception.

Introduction: Spoken language comprehension requires listeners map continuous features of the speech signal to discrete category labels. Categories are however malleable to surrounding context and stimulus precedence; listeners' percept can dynamically shift depending on the sequencing of adjacent stimuli resulting in a warping of the heard phonetic category. Here, we investigated whether such perceptual warping-which amplify categorical hearing-might alter speech processing in noise-degraded listening scenarios. Methods: We measured continuous dynamics in perception and category judgments of an acoustic-phonetic vowel gradient via mouse tracking. Tokens were presented in serial vs. random orders to induce more/less perceptual warping while listeners categorized continua in clean and noise conditions. Results: Listeners' responses were faster and their mouse trajectories closer to the ultimate behavioral selection (marked visually on the screen) in serial vs. random order, suggesting increased perceptual attraction to category exemplars. Interestingly, order effects emerged earlier and persisted later in the trial time course when categorizing speech in noise. Discussion: These data describe interactions between perceptual warping in categorization and speech-in-noise perception: warping strengthens the behavioral attraction to relevant speech categories, making listeners more decisive (though not necessarily more accurate) in their decisions of both clean and noise-degraded speech.

Perceptual warping exposes categorical representations for speech in human brainstem responses.

The brain transforms continuous acoustic events into discrete category representations to downsample the speech signal for our perceptual-cognitive systems. Such phonetic categories are highly malleable, and their percepts can change depending on surrounding stimulus context. Previous work suggests these acoustic-phonetic mapping and perceptual warping of speech emerge in the brain no earlier than auditory cortex. Here, we examined whether these auditory-category phenomena inherent to speech perception occur even earlier in the human brain, at the level of auditory brainstem. We recorded speech-evoked frequency following responses (FFRs) during a task designed to induce more/less warping of listeners' perceptual categories depending on stimulus presentation order of a speech continuum (random, forward, backward directions). We used a novel clustered stimulus paradigm to rapidly record the high trial counts needed for FFRs concurrent with active behavioral tasks. We found serial stimulus order caused perceptual shifts (hysteresis) near listeners' category boundary confirming identical speech tokens are perceived differentially depending on stimulus context. Critically, we further show neural FFRs during active (but not passive) listening are enhanced for prototypical vs. category-ambiguous tokens and are biased in the direction of listeners' phonetic label even for acoustically-identical speech stimuli. These findings were not observed in the stimulus acoustics nor model FFR responses generated via a computational model of cochlear and auditory nerve transduction, confirming a central origin to the effects. Our data reveal FFRs carry category-level information and suggest top-down processing actively shapes the neural encoding and categorization of speech at subcortical levels. These findings suggest the acoustic-phonetic mapping and perceptual warping in speech perception occur surprisingly early along the auditory neuroaxis, which might aid understanding by reducing ambiguity inherent to the speech signal.

Catheter-associated urinary tract infection by Pseudomonas aeruginosa progresses through acute and chronic phases of infection.

Healthcare-associated infections are major causes of complications that lead to extended hospital stays and significant medical costs. The use of medical devices, including catheters, increases the risk of bacterial colonization and infection through the presence of a foreign surface. Two outcomes are observed for catheterized patients: catheter-associated asymptomatic bacteriuria and catheter-associated urinary tract infection (CAUTI). However, the relationship between these two events remains unclear. To understand this relationship, we studied a murine model of Pseudomonas aeruginosa CAUTI. In this model, we also observe two outcomes in infected animals: acute symptoms that is associated with CAUTI and chronic colonization that is associated with asymptomatic bacteriuria. The timing of the acute outcome takes place in the first week of infection, whereas chronic colonization occurs in the second week of infection. We further showed that mutants lacking genes encoding type III secretion system (T3SS), T3SS effector proteins, T3SS injection pore, or T3SS transcriptional activation all fail to cause acute symptoms of CAUTI. Nonetheless, all mutants defective for T3SS colonized the catheter and bladders at levels similar to the parental strain. In contrast, through induction of the T3SS master regulator ExsA, all infected animals showed acute phenotypes with bacteremia. Our results demonstrated that the acute symptoms, which are analogous to CAUTI, and chronic colonization, which is analogous to asymptomatic bacteriuria, are independent events that require distinct bacterial virulence factors. Experimental delineation of asymptomatic bacteriuria and CAUTI informs different strategies for the treatment and intervention of device-associated infections.

Nonlinear dynamics in auditory cortical activity reveal the neural basis of perceptual warping in speech categorization.

Surrounding context influences speech listening, resulting in dynamic shifts to category percepts. To examine its neural basis, event-related potentials (ERPs) were recorded during vowel identification with continua presented in random, forward, and backward orders to induce perceptual warping. Behaviorally, sequential order shifted individual listeners' categorical boundary, versus random delivery, revealing perceptual warping (biasing) of the heard phonetic category dependent on recent stimulus history. ERPs revealed later (∼300 ms) activity localized to superior temporal and middle/inferior frontal gyri that predicted listeners' hysteresis/enhanced contrast magnitudes. Findings demonstrate that interactions between frontotemporal brain regions govern top-down, stimulus history effects on speech categorization.

Auditory cortex is susceptible to lexical influence as revealed by informational vs. energetic masking of speech categorization.

Speech perception requires the grouping of acoustic information into meaningful phonetic units via the process of categorical perception (CP). Environmental masking influences speech perception and CP. However, it remains unclear at which stage of processing (encoding, decision, or both) masking affects listeners' categorization of speech signals. The purpose of this study was to determine whether linguistic interference influences the early acoustic-phonetic conversion process inherent to CP. To this end, we measured source level, event related brain potentials (ERPs) from auditory cortex (AC) and inferior frontal gyrus (IFG) as listeners rapidly categorized speech sounds along a /da/ to /ga/ continuum presented in three listening conditions: quiet, and in the presence of forward (informational masker) and time-reversed (energetic masker) 2-talker babble noise. Maskers were matched in overall SNR and spectral content and thus varied only in their degree of linguistic interference (i.e., informational masking). We hypothesized a differential effect of informational versus energetic masking on behavioral and neural categorization responses, where we predicted increased activation of frontal regions when disambiguating speech from noise, especially during lexical-informational maskers. We found (1) informational masking weakens behavioral speech phoneme identification above and beyond energetic masking; (2) low-level AC activity not only codes speech categories but is susceptible to higher-order lexical interference; (3) identifying speech amidst noise recruits a cross hemispheric circuit (ACleft â†’ IFGright) whose engagement varies according to task difficulty. These findings provide corroborating evidence for top-down influences on the early acoustic-phonetic analysis of speech through a coordinated interplay between frontotemporal brain areas.

Free Standing, Large-Area Silicon Nitride Membranes for High Toxin Clearance in Blood Surrogate for Small-Format Hemodialysis.

Developing highly-efficient membranes for toxin clearance in small-format hemodialysis presents a fabrication challenge. The miniaturization of fluidics and controls has been the focus of current work on hemodialysis (HD) devices. This approach has not addressed the membrane efficiency needed for toxin clearance in small-format hemodialysis devices. Dr. Willem Kolff built the first dialyzer in 1943 and many changes have been made to HD technology since then. However, conventional HD still uses large instruments with bulky dialysis cartridges made of ~2 m2 of 10 micron thick, tortuous-path membrane material. Portable, wearable, and implantable HD systems may improve clinical outcomes for patients with end-stage renal disease by increasing the frequency of dialysis. The ability of ultrathin silicon-based sheet membranes to clear toxins is tested along with an analytical model predicting long-term multi-pass experiments from single-pass clearance experiments. Advanced fabrication methods are introduced that produce a new type of nanoporous silicon nitride sheet membrane that features the pore sizes needed for middle-weight toxin removal. Benchtop clearance results with sheet membranes (~3 cm2) match a theoretical model and indicate that sheet membranes can reduce (by orders of magnitude) the amount of membrane material required for hemodialysis. This provides the performance needed for small-format hemodialysis.

Development of isoporous microslit silicon nitride membranes for sterile filtration applications.

The widely used 0.2/0.22 µm polymer sterile filters were developed for small molecule and protein sterile filtration but are not well-suited for the production of large nonprotein biological therapeutics, resulting in significant yield loss and production cost increases. Here, we report on the development of membranes with isoporous sub-0.2 µm rectangular prism pores using silicon micromachining to produce microslit silicon nitride (MSN) membranes. The very high porosity (~33%) and ultrathin (200 nm) nature of the 0.2 µm MSN membranes results in a dramatically different structure than the traditional 0.2/0.22 µm polymer sterile filter, which yielded comparable performance properties (including gas and hydraulic permeance, maximum differential pressure tolerance, nanoparticle sieving/fouling behavior). The results from bacteria retention tests, conducted according to the guidance of regulatory agencies, demonstrated that the 0.2 µm MSN membranes can be effectively used as sterile filters. It is anticipated that the results and technologies presented in this study will find future utility in the production of non-protein biological therapeutics and in other biological and biomedical applications.

One-step genome editing of elite crop germplasm during haploid induction.

Genome editing using CRISPR-Cas9 works efficiently in plant cells1, but delivery of genome-editing machinery into the vast majority of crop varieties is not possible using established methods2. We co-opted the aberrant reproductive process of haploid induction (HI)3-6 to induce edits in nascent seeds of diverse monocot and dicot species. Our method, named HI-Edit, enables direct genomic modification of commercial crop varieties. HI-Edit was tested in field and sweet corn using a native haploid-inducer line4 and extended to dicots using an engineered CENH3 HI system7. We also recovered edited wheat embryos using Cas9 delivered by maize pollen. Our data indicate that a transient hybrid state precedes uniparental chromosome elimination in maize HI. Edited haploid plants lack both the haploid-inducer parental DNA and the editing machinery. Therefore, edited plants could be used in trait testing and directly integrated into commercial variety development.

Label-free microarray-based detection of autoantibodies in human serum.

Multiplex assays for autoantibodies have shown utility both in research towards understanding the basic biology of autoimmune disease, and as tools for clinical diagnosis. New label-free multiplex analysis methods have the potential to streamline both the process of assay development and assay workflow. We report fabrication and testing of a 5-plex autoantigen microarray using the Arrayed Imaging Reflectometry (AIR) platform. This label-free technology provides rapid, sensitive, and quantitative detection of an arbitrary number of analytes in a standard multiwell format. In this work, we demonstrate that AIR is able to detect antibodies to Ro60, La/SSB, Scl-70, BicD2, and Ro52 in single-donor human serum samples with multiplex results comparable to singleplex ELISA or Luminex assays.

A label-free, multiplex competitive assay for small molecule pollutants.

Understanding the amount of exposure individuals have had to common chemical pollutants critically requires the ability to detect those compounds in a simple, sensitive, and specific manner. Doing so using label-free biosensor technology has proven challenging, however, given the small molecular weight of many pollutants of interest. To address this issue, we report the development of a pollutant microarray based on the label-free arrayed imaging reflectometry (AIR) detection platform. The sensor is able to detect three common environmental contaminants (benzo[a]pyrene, bisphenol A, and acrolein) in human serum via a competitive binding scheme.

Functionalized Polymer Microgel Particles Enable Customizable Production of Label-Free Sensor Arrays.

Probe molecule immobilization onto surfaces is a critical step in the production of many analytical devices, including labeled and label-free microarrays. New methods to increase the density and uniformity of probe deposition have the potential to significantly enhance the ultimate limits of detection and reproducibility. Hydrogel-based materials have been employed in the past to provide a 3D protein-friendly surface for deposition of antibodies and nucleic acids. However, these methods are susceptible to variation during polymerization of the hydrogel scaffold and provide limited opportunities for tuning deposition parameters on an antibody-by-antibody basis. In this work, a versatile hydrogel nanoparticle deposition method was developed for the production of label-free microarrays and tested in the context of antibody-antigen binding. Poly(N-isopropylacrylamide) nanoparticles (PNIPAM) were conjugated to antibodies using an avidin/biotin system and deposited onto surfaces using a noncontact printing system. After drying, these gel spots formed uniform and thin layers <10 nm in height. The conjugates were characterized with dynamic light scattering, scanning electron microscopy, and atomic force microscopy. We tested this format in the context of tumor necrosis factor-alpha (TNF-α) detection via arrayed imaging reflectometry (AIR), a label-free protein microarray method. This method of probe molecule deposition should be generally useful in the production of microarrays for label-free detection.

Transposon based activation tagging in diploid strawberry and monoploid derivatives of potato.

KEY MESSAGE: Diploid strawberry and potato transformed with a transposon tagging construct exhibited either global (strawberry) or local transposition (potato). An activation tagged, compact-sized strawberry mutant overexpressed the gene adjacent to Ds. As major fruit and vegetable crops, respectively, strawberry and potato are among the first horticultural crops with draft genome sequences. To study gene function, we examined transposon-tagged mutant strategies in model populations for both species, Fragaria vesca and Solanum tuberosum Group Phureja, using the same Activation/Dissociation (Ac/Ds) construct. Early somatic transposition during tissue culture occurred at a frequency of 18.5% in strawberry but not in potato transformants. Green fluorescent protein under a monocot promoter was a more reliable selectable marker in strawberry compared to potato. BASTA (gluphosinate herbicide) resistance served as an effective selectable marker for both species (80 and 85% reliable in strawberry and potato, respectively), although the effective concentration differed (0.5% for strawberry and 0.03% for potato). Transposons preferentially reinserted within genes (exons and introns) in both species. Real-time quantitative PCR revealed enhanced gene expression (670 and 298-fold expression compared to wild type in petiole and leaf tissue, respectively) for an activation tagged strawberry mutant with Ds inserted about 0.6 kb upstream from a gene coding for an epidermis-specific secreted glycoprotein EP1. Our data also suggested that endopolyploid (diploid) cells occurring in leaf explants of monoploid potato were the favored targets of T-DNA integration during transformation. Mutants obtained in these studies provide a useful resource for future genetic studies.

Comparative study of solution-phase and vapor-phase deposition of aminosilanes on silicon dioxide surfaces.

The uniformity of aminosilane layers typically used for the modification of hydroxyl bearing surfaces such as silicon dioxide is critical for a wide variety of applications, including biosensors. However, in spite of many studies that have been undertaken on surface silanization, there remains a paucity of easy-to-implement deposition methods reproducibly yielding smooth aminosilane monolayers. In this study, solution- and vapor-phase deposition methods for three aminoalkoxysilanes differing in the number of reactive groups (3-aminopropyl triethoxysilane (APTES), 3-aminopropyl methyl diethoxysilane (APMDES) and 3-aminopropyl dimethyl ethoxysilane (APDMES)) were assessed with the aim of identifying methods that yield highly uniform and reproducible silane layers that are resistant to minor procedural variations. Silane film quality was characterized based on measured thickness, hydrophilicity and surface roughness. Additionally, hydrolytic stability of the films was assessed via these thickness and contact angle values following desorption in water. We found that two simple solution-phase methods, an aqueous deposition of APTES and a toluene based deposition of APDMES, yielded high quality silane layers that exhibit comparable characteristics to those deposited via vapor-phase methods.

An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation.

Tomato (Solanum lycopersicum) is a model organism for Solanaceae in both molecular and agronomic research. This project utilized Agrobacterium tumefaciens transformation and the transposon-tagging construct Activator (Ac)/Dissociator (Ds)-ATag-Bar_gosGFP to produce activation-tagged and knockout mutants in the processing tomato cultivar M82. The construct carried hygromycin resistance (hyg), green fluorescent protein (GFP), and the transposase (TPase) of maize (Zea mays) Activator major transcript X054214.1 on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds-ATag element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 11,000 selfed and cv M82 backcrossed progeny was produced from the functional T0 line. This population was screened using glufosinate herbicide, hygromycin leaf painting, and multiplex polymerase chain reaction (PCR). Insertion sites of transposed Ds-ATag elements were identified through thermal asymmetric interlaced PCR, and resulting product sequences were aligned to the recently published tomato genome. A population of 509 independent, Ds-only transposant lines spanning all 12 tomato chromosomes has been developed. Insertion site analysis demonstrated that more than 80% of these lines harbored Ds insertions conducive to activation tagging. The capacity of the Ds-ATag element to alter transcription was verified by quantitative real-time reverse transcription-PCR in two mutant lines. The transposon-tagged lines have been immortalized in seed stocks and can be accessed through an online database, providing a unique resource for tomato breeding and analysis of gene function in the background of a commercial tomato cultivar.

Development of a rat model of bisphosphonate-related osteonecrosis of the jaw (BRONJ).

The purpose of this study was to develop a rat model predictive of bisphosphonate-related osteonecrosis of the jaw (BRONJ) after exodontias. Thirty female rats were randomized into 2 groups, control and experimental. The experimental group received 2 intravenous injections of zoledronate (20 µg/kg). The mesial root of the right mandibular first molar was extracted. Rats were euthanized at 0, 4, and 8 weeks. Bone mineral density (BMD), collagen breakdown (pyridinium [PYD]), vascular regeneration (VEGF), and histology were examined. A trend toward higher PYD values was suggested in control vs experimental groups after wounding. Serum VEGF increased significantly after wounding for both control and experimental groups. After 8 weeks, VEGF continued to rise for the experimental group only. In the extraction socket area, BMD was significantly lower after wounding in control vs. zoledronate-treated rats. Histology sections from experimental groups showed bacteria and bone necrosis. Consistent findings of BRONJ features similar to those in humans were observed after zoledronate treatment.

Analysis of inflammatory biomarkers by Arrayed Imaging Reflectometry.

Levels of serum cytokines are important markers for a broad range of human health conditions, ranging from infectious disease and cancer, to pollutant exposure and stress. In the interest of developing new rapid label-free methods for profiling serum cytokines, we have examined the utility of Arrayed Imaging Reflectometry (AIR) microarrays for this application. We find that AIR is readily able to profile 14 cytokines and other inflammatory biomarker proteins in a background of buffered bovine serum albumin or 1% bovine serum with performance metrics comparable to singleplex ELISA, but in a multiplex, chip-based, reagentless format. Further experiments with interferon-gamma (IFN-γ) demonstrated that the concentration of bovine serum could be increased to at least 20% without changing the overall analytical profile or limit of detection (<10 pg/mL).