Characterization of a Stenotrophomonas maltophilia Bacteriophage

Stenotrophomonas maltophilia is a ubiquitous Gram-negative, multidrug resistant, opportunistic bacterial pathogen that causes various infections in humans. Recently, the use of bacteriophages as therapeutic agents, has gained interest as an alternative to traditional antibiotics. This thesis describes the isolation, purification, and characterization of S. maltophilia bacteriophage Bfi2 and discusses its activity against related, and often co-isolated, bacterial pathogens. Amplification of the phage resulted in clear, well-defined plaques and a titer of 1.73 ± 0.38 x 1011 PFU/ml. Bfi2 demonstrated the ability to lyse 55% of the S. maltophilia strains tested, suggesting that it has a moderate host range. However, the phage did not show cross taxonomic order infectivity, as the other bacterial species tested were not susceptible to infection. Efficiency of plating (EOP) assays shown Bfi2 to be nearly half as effective against another susceptible strain of S. maltophilia, F7221, compared to the host strain. Digestion of Bfi2 nucleic acid by type II restriction endonucleases, and visualization of products by agarose gel electrophoresis, indicated that the phage contained a dsDNA genome with an estimated size of 66.5 kb. Electron microscopy determined that Bfi2 has an icosahedral capsid 75.3 ± 3.3 nm by 69.6 ± 3.9 nm and a flexible, non-contractile tail 154.2 ± 4.6 nm by 9.3 ± 0.5 nm. Together, electron microscopy and genomic analysis suggests that Bfi2 likely belongs to the family Siphoviridae, with a B1 morphotype. Bfi2 was found to be stable at a temperature of 30°C. However, Bfi2 became increasingly unstable at 50°C over time, and quickly lost activity at 60°C. Moreover, Bfi2 was found to be stable at pH 5, 7, and 9. The kinetics of Bfi2 adsorption to host cells were determined. Bfi2 was found to have a relatively high adsorption efficiency, where ~97% of phages were adsorbed to host cells after 15 minutes of incubation. The adsorption rate constant (k) of Bfi2 was calculated to be ~2.15 ± 0.06 x 10-9 ml min-1 at a multiplicity of infection (MOI) of 0.05. Bfi2 may be suitable for future therapeutic applications based on its lytic activity and moderate host range

Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations.

The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments. Genes associated with cofactor biosynthesis and one-carbon metabolism showed habitat specificity, and protein-coding genes of unknown function and membrane transport proteins were under positive selection across each habitat. Characterized by different median ratios of nonsynonymous to synonymous evolutionary changes (dN/dS ratios) and a limited but statistically significant negative correlation between the dN/dS ratio and codon usage bias between habitats, the free-living and core genotypes were observed to be evolving under strong purifying selection pressure. Highlighting the potential role of genetic adaptation to the local environment, the two-component system protein-coding genes were highly stable (dN/dS ratio, < 0.03). These results suggest that despite the impact of the habitat on genetic diversity, and hence niche partition, strong environmental selection pressure maintains a conserved core genome for Polynucleobacter populations. IMPORTANCE Understanding the biological factors influencing habitat-wide genetic endemism is important for explaining observed biogeographic patterns. Polynucleobacter is a genus of bacteria that seems to have found a way to colonize myriad freshwater ecosystems and by doing so has become one of the most abundant bacteria in these environments. We sequenced metagenomes from locations across the Chicago River system and assembled Polynucleobacter genomes from different sites and compared how the nucleotide composition, gene codon usage, and the ratio of synonymous (codes for the same amino acid) to nonsynonymous (codes for a different amino acid) mutations varied across these population genomes at each site. The environmental pressures at each site drove purifying selection for functional traits that maintained a streamlined core genome across the Chicago River Polynucleobacter population while allowing for site-specific genomic adaptation. These adaptations enable Polynucleobacter to become dominant across different riverine environmental gradients

Recovery Act - Demonstration of Sodium Ion Battery for Grid Level Applications

Aquion Energy received a $5.179 million cooperative research agreement under the Department of Energyâs Smart Grid Demonstration Program â Demonstration of Promising Energy Storage Technologies (Program Area 2.5) of FOA DE-FOE-0000036. The main objective of this project was to demonstrate Aquionâs low cost, grid-scale, ambient temperature sodium ion energy storage device. The centerpiece of the technology is a novel hybrid energy storage chemistry that has been proven in a laboratory environment. The objective was to translate these groundbreaking results from the small-batch, small-cell test environment to the pilot scale to enable significant numbers of multiple ampere-hour cells to be manufactured and assembled into test batteries. Aquion developed a proof of concept demonstration unit that showed similar performance and major cost improvement over existing technologies. Beyond minimizing cell and system cost, Aquion built a technology that is safe, environmentally benign and durable over many thousands of cycles as used in a variety of grid support roles. As outlined in the Program documents, the original goals of the project were to demonstrate a unit that: 1. Has a projected capital cost of less than$250/kWh at the pack level 2. A deep discharge cycle life of > 10,000 cycles 3. A volumetric energy density of >20 kWh/m3 4. Projected calendar life of over 10 years 5. A device that contains no hazardous materials and retains best in class safety characteristics. Through the course of this project Aquion developed its aqueous electrolyte electrochemical energy storage device to the point where large demonstration units (> 10 kWh) were able to function in grid-supporting functions detailed by their collaborators. Aquionâs final deliverable was an ~15 kWh system that has the ability to perform medium to long duration (> 2 hours) charge and discharge functions approaching 95% DC-DC efficiency. The system has functioned, and continues to function as predicted with no indication that it will not tolerate well beyond 10 calendar years and 10,000 cycles. It has been in continuous operation for more than 1 year with 1,000 cycles (of varying depth of discharge, including 100% depth of discharge) and no identifiable degradation to the system. The final thick electrode cell structure has shown an energy density of 25 kWh/m3 at a five hour (or greater) discharge time. The primary chemistry has remained non-toxic, containing no acids or other corrosive chemicals, and the battery units have passed numerous safety tests, including flame resistance testing. These tests have verified the claim that the device is safe to use and contains no hazardous materials. Current projections show costs at the pack level to offer best in class value and are competitive with lead-acid batteries, factoring in LCOE

Athletic equipment microbiota are shaped by interactions with human skin

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412

Left atrial reservoir strain by speckle tracking echocardiography : association with exercise capacity in chronic kidney disease

BACKGROUND: Left atrial (LA) function plays a pivotal role in modulating left ventricular performance. The aim of our study was to evaluate the relationship between resting LA function by strain analysis and exercise capacity in patients with chronic kidney disease (CKD) and evaluate its utility compared with exercise E/e’. METHODS AND RESULTS: Consecutive patients with stage 3 and 4 CKD without prior cardiac history were prospectively recruited from outpatient nephrology clinics and underwent clinical evaluation and resting and exercise stress echocardiography. Resting echocardiographic parameters including E/e’ and phasic LA strain (LA reservoir [LASr], conduit, and contractile strain) were measured and compared with exercise E/e’. A total of 218 (63.9±11.7 years, 64% men) patients with CKD were recruited. Independent clinical parameters associated with exercise capacity were age, estimated glomerular filtration rate, body mass index, and sex (P<0.01 for all), while independent resting echocardiographic parameters included E/e’, LASr, and LA contractile strain (P<0.01 for all). Among resting echocardiographic parameters, LASr demonstrated the strongest positive correlation to metabolic equivalents achieved (r=0.70; P<0.01). Receiver operating characteristic curves demonstrated that LASr (area under the curve, 0.83) had similar diagnostic performance as exercise E/e’ (area under the curve, 0.79; P=0.20 on DeLong test). A model combining LASr and clinical metrics showed robust association with metabolic equivalents achieved in patients with CKD. CONCLUSIONS: LASr, a marker of decreased LA compliance is an independent correlate of exercise capacity in patients with stage 3 and 4 CKD, with similar diagnostic value to exercise E/e’. Thus, LASr may serve as a resting biomarker of functional capacity in this population

Direct Molecular Detection and Genotyping of Borrelia burgdorferi from Whole Blood of Patients with Early Lyme Disease

Direct molecular tests in blood for early Lyme disease can be insensitive due to low amount of circulating Borrelia burgdorferi DNA. To address this challenge, we have developed a sensitive strategy to both detect and genotype B. burgdorferi directly from whole blood collected during the initial patient visit. This strategy improved sensitivity by employing 1.25 mL of whole blood, a novel pre-enrichment of the entire specimen extract for Borrelia DNA prior to a multi-locus PCR and electrospray ionization mass spectrometry detection assay. We evaluated the assay on blood collected at the initial presentation from 21 endemic area patients who had both physician-diagnosed erythema migrans (EM) and positive two-tiered serology either at the initial visit or at a follow-up visit after three weeks of antibiotic therapy. Results of this DNA analysis showed detection of B. burgdorferi in 13 of 21 patients (62%). In most cases the new assay also provided the B. burgdorferi genotype. The combined results of our direct detection assay with initial physician visit serology resulted in the detection of early Lyme disease in 19 of 21 (90%) of patients at the initial visit. In 5 of 21 cases we demonstrate the ability to detect B. burgdorferi in early Lyme disease directly from whole blood specimens prior to seroconversion