Cassette bacteria detection system. [for monitoring the sterility of regenerated water in spacecraft

NASA Technical Reports Server (NTRS)

1974-01-01

The design, fabrication, and testing of an automatic bacteria detection system, with a zero-g capability, based on the filter-capable approach, and intended for monitoring the sterility of regenerated water in spacecraft is discussed. The principle of detection is based on measuring the increase in chemiluminescence produced by the action of bacterial porphyrins on a luminol-hydrogen peroxide mixture. Viable organisms are detected by comparing the signal of an incubated water sample with an unincubated control. High signals for the incubated water sample indicate the presence of viable organisms.

Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria

PubMed Central

Kim, Jinjoo; Kim, Hansol; Park, Ji Ho; Jon, Sangyong

2017-01-01

The polymerase chain reaction (PCR) has been an essential tool for diagnosis of infectious diseases, but conventional PCR still has some limitations with respect to applications to point-of-care (POC) diagnostic systems that require rapid detection and miniaturization. Here we report a light-based PCR method, termed as photo-PCR, which enables rapid detection of bacteria in a single step. In the photo-PCR system, poly(enthylene glycol)-modified gold nanorods (PEG-GNRs), used as a heat generator, are added into the PCR mixture, which is subsequently periodically irradiated with a 808-nm laser to create thermal cycling. Photo-PCR was able to significantly reduce overall thermal cycling time by integrating bacterial cell lysis and DNA amplification into a single step. Furthermore, when combined with KAPA2G fast polymerase and cooling system, the entire process of bacterial genomic DNA extraction and amplification was further shortened, highlighting the potential of photo-PCR for use in a portable, POC diagnostic system. PMID:29071186

Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria.

PubMed

Blaustein, Ryan A; Shelton, Daniel R; Van Kessel, Jo Ann S; Karns, Jeffrey S; Stocker, Matthew D; Pachepsky, Yakov A

2016-01-01

The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hot spot for proliferation and gene exchange. Pipe-based irrigation systems that utilize surface waters may contribute to the dissemination of antibiotic-resistant bacteria in a similar manner. We conducted irrigation events at a perennial stream on a weekly basis for 1 month, and the concentrations of total heterotrophic bacteria, total coliforms, and fecal coliforms, as well as the concentrations of these bacterial groups that were resistant to ampicillin and tetracycline, were monitored at the intake water. Prior to each of the latter three events, residual pipe water was sampled and 6-in. sections of pipeline (coupons) were detached from the system, and biofilm from the inner-wall was removed and analyzed for total protein content and the above bacteria. Isolates of biofilm-associated bacteria were screened for resistance to a panel of seven antibiotics, representing five antibiotic classes. All of the monitored bacteria grew substantially in the residual water between irrigation events, and the biomass of the biofilm steadily increased from week to week. The percentages of biofilm-associated isolates that were resistant to antibiotics on the panel sometimes increased between events. Multiple-drug resistance was observed for all bacterial groups, most often for fecal coliforms, and the distributions of the numbers of antibiotics that the total coliforms and fecal coliforms were resistant to were subject to change from week to week. Results from this study highlight irrigation waters as a potential source for antibiotic-resistant bacteria, which can subsequently become incorporated into and proliferate within irrigation pipe-based biofilms.

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria.

PubMed

Strauss, Christian; Endimiani, Andrea; Perreten, Vincent

2015-01-01

A rapid and simple DNA labeling system has been developed for disposable microarrays and has been validated for the detection of 117 antibiotic resistance genes abundant in Gram-positive bacteria. The DNA was fragmented and amplified using phi-29 polymerase and random primers with linkers. Labeling and further amplification were then performed by classic PCR amplification using biotinylated primers specific for the linkers. The microarray developed by Perreten et al. (Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., Frey, J., 2005. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J.Clin.Microbiol. 43, 2291-2302.) was improved by additional oligonucleotides. A total of 244 oligonucleotides (26 to 37 nucleotide length and with similar melting temperatures) were spotted on the microarray, including genes conferring resistance to clinically important antibiotic classes like β-lactams, macrolides, aminoglycosides, glycopeptides and tetracyclines. Each antibiotic resistance gene is represented by at least 2 oligonucleotides designed from consensus sequences of gene families. The specificity of the oligonucleotides and the quality of the amplification and labeling were verified by analysis of a collection of 65 strains belonging to 24 species. Association between genotype and phenotype was verified for 6 antibiotics using 77 Staphylococcus strains belonging to different species and revealed 95% test specificity and a 93% predictive value of a positive test. The DNA labeling and amplification is independent of the species and of the target genes and could be used for different types of microarrays. This system has also the advantage to detect several genes within one bacterium at once, like in Staphylococcus aureus strain BM3318, in which up to 15 genes were detected. This new microarray-based detection system offers a large potential for applications in clinical diagnostic, basic research, food safety and

Quaternized magnetic nanoparticles-fluorescent polymer system for detection and identification of bacteria.

PubMed

Wan, Yi; Sun, Yan; Qi, Peng; Wang, Peng; Zhang, Dun

2014-05-15

Nanomaterial-based 'chemical nose' sensor with sufficient sensing specificity is a useful analytical tool for the detection of toxicologically important substances in complicated biological systems. A sensor array containing three quaternized magnetic nanoparticles (q-MNPs)-fluorescent polymer systems has been designed to identify and quantify bacteria. The bacterial cell membranes disrupt the q-MNP-fluorescent polymer, generating unique fluorescence response array. The response intensity of the array is dependent on the level of displacement determined by the relative q-MNP-fluorescent polymer binding strength and bacteria cells-MNP interaction. These characteristic responses show a highly repeatable bacteria cells and can be differentiated by linear discriminant analysis (LDA). Based on the array response matrix from LDA, our approach has been used to measure bacteria with an accuracy of 87.5% for 10(7) cfu mL(-1) within 20 min. Combined with UV-vis measurement, the method can be successfully performed to identify and detect eight different pathogen samples with an accuracy of 96.8%. The measurement system has a potential for further applications and provides a facile and simple method for the rapid analysis of protein, DNA, and pathogens. Copyright © 2013 Elsevier B.V. All rights reserved.

Design of a Microcomputer-Based Adaptive Testing System.

ERIC Educational Resources Information Center

Vale, C. David

This paper explores the feasibility of developing a single-user microcomputer-based testing system. Testing literature was surveyed to discover types of test items that might be used in the system and to compile a list of strategies that such a system might use. Potential users were surveyed. Several were interviewed, and a questionnaire was…

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system.

PubMed

Zarkasi, K Z; Abell, G C J; Taylor, R S; Neuman, C; Hatje, E; Tamplin, M L; Katouli, M; Bowman, J P

2014-07-01

The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated. Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. Faecal bacterial communities were highly dynamic but largely similar between randomly selected fish. In postsmolt, the faecal bacteria population was dominated by Gram-positive fermentative bacteria; however, by midsummer, members of the family Vibrionaceae predominated. As fish progressed towards harvest, a range of different bacterial genera became more prominent corresponding to a decline in Vibrionaceae. The sampled fish were fed two different commercial diet series with slightly different protein, lipid and digestible energy level; however, the effect of these differences was minimal. The overall data demonstrated dynamic hind gut communities in salmon that were related to season and fish growth phases but were less influenced by differences in commercial diets used routinely within the farm system studied. This study provides understanding of farmed salmon GI bacterial communities and describes the relative impact of diet, environmental and farm factors. © 2014 The Society for Applied Microbiology.

Development of an in vitro Assay, Based on the BioFilm Ring Test®, for Rapid Profiling of Biofilm-Growing Bacteria

PubMed Central

Di Domenico, Enea G.; Toma, Luigi; Provot, Christian; Ascenzioni, Fiorentina; Sperduti, Isabella; Prignano, Grazia; Gallo, Maria T.; Pimpinelli, Fulvia; Bordignon, Valentina; Bernardi, Thierry; Ensoli, Fabrizio

2016-01-01

Microbial biofilm represents a major virulence factor associated with chronic and recurrent infections. Pathogenic bacteria embedded in biofilms are highly resistant to environmental and chemical agents, including antibiotics and therefore difficult to eradicate. Thus, reliable tests to assess biofilm formation by bacterial strains as well as the impact of chemicals or antibiotics on biofilm formation represent desirable tools for a most effective therapeutic management and microbiological risk control. Current methods to evaluate biofilm formation are usually time-consuming, costly, and hardly applicable in the clinical setting. The aim of the present study was to develop and assess a simple and reliable in vitro procedure for the characterization of biofilm-producing bacterial strains for future clinical applications based on the BioFilm Ring Test® (BRT) technology. The procedure developed for clinical testing (cBRT) can provide an accurate and timely (5 h) measurement of biofilm formation for the most common pathogenic bacteria seen in clinical practice. The results gathered by the cBRT assay were in agreement with the traditional crystal violet (CV) staining test, according to the κ coefficient test (κ = 0.623). However, the cBRT assay showed higher levels of specificity (92.2%) and accuracy (88.1%) as compared to CV. The results indicate that this procedure offers an easy, rapid and robust assay to test microbial biofilm and a promising tool for clinical microbiology. PMID:27708625

A WWW-based information system on resistance of bacteria to antibiotics.

PubMed

Schindler, J; Schindler, Z; Schindler, J

1998-01-01

The information system on resistance of bacteria to antibiotics (WARN--World Antibiotic Resistance Network) is implemented as a WWW server at Charles University in Prague (http:/(/)www.warn.cas.cz). Its main goal is to give information about problems of antibiotic resistance of bacteria and to process data on isolated strains. The WARN web-site contains six main topics. Four of them form the core of the system: Topics of Interest bring information on selected timely topics in antibiotic resistance--pneumococci, staphylococci, beta-lactamases, glycopeptide--and aminoglycoside resistance. Global Monitor brings references and reports on resistance in the world as well as recommended method of surveillance. The topic Data contains raw data on strains in particular countries and hospitals. Data can be viewed in their original form as a list of records (strains) or processed to provide statistics about the resistance rates in the selected country or hospital respectively. The topic Search allows one to search for one or several terms in the whole document. Counts of accessed pages show, that there is a standing demand for information about the serious problems of antibiotic therapy of infectious diseases.

Autotransporter-based cell surface display in Gram-negative bacteria.

PubMed

Nicolay, Toon; Vanderleyden, Jos; Spaepen, Stijn

2015-02-01

Cell surface display of proteins can be used for several biotechnological applications such as the screening of protein libraries, whole cell biocatalysis and live vaccine development. Amongst all secretion systems and surface appendages of Gram-negative bacteria, the autotransporter secretion pathway holds great potential for surface display because of its modular structure and apparent simplicity. Autotransporters are polypeptides made up of an N-terminal signal peptide, a secreted or surface-displayed passenger domain and a membrane-anchored C-terminal translocation unit. Genetic replacement of the passenger domain allows for the surface display of heterologous passengers. An autotransporter-based surface expression module essentially consists of an application-dependent promoter system, a signal peptide, a passenger domain of interest and the autotransporter translocation unit. The passenger domain needs to be compatible with surface translocation although till now no general rules have been determined to test this compatibility. The autotransporter technology for surface display of heterologous passenger domains is critically discussed for various applications.

Rapid Methods for Biochemical Testing of Anaerobic Bacteria

PubMed Central

Schreckenberger, Paul C.; Blazevic, Donna J.

1974-01-01

Rapid biochemical tests for nitrate, indole, gelatin, starch, esculin, and o-nitrophenyl-β-D-galactopyranoside were performed on 112 strains of anaerobic bacteria. All tests were incubated under aerobic conditions, and results were recorded within 4 h. The tests for nitrate, indole, and starch showed a 95% or greater correlation when compared to the standard biochemical tests. Tests for esculin and gelatin showed an agreement of 86 and 77%, respectively. PathoTec test strips for nitrate, indole, esculin, o-nitrophenyl-β-D-galactopyranoside, Voges-Proskauer, and urease were also tested and showed encouraging results. PMID:4613268

Quantifying the extruded bacteria following use of two rotary instrumentation systems.

PubMed

Mohammadi, Zahed; Khademi, Abbasali

2007-01-01

All instrumentation techniques have been reported to be associated with extrusion of infected debris. The aim of this study was to evaluate the number of bacteria extruded apically from extracted teeth ex vivo after canal instrumentation using the two engine-driven techniques utilizing nickel-titanium instruments (Flex Master and Mtwo). Seventy extracted maxillary central incisor teeth were used. Access cavities were prepared and root canals were then contaminated with a suspension of Enterococcus faecalis and dried. The contaminated roots were divided into two experimental groups of 30 teeth each and one control group of 10 teeth. Group 1, Flex Master; Group2, Mtwo; Group 3, control group: no instrumentation was attempted. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples from the vials were incubated in culture media for 24 h. Colonies of bacteria were counted and the results were given as number of colony-forming units. The obtained data were analyzed using the Kruskal-Wallis one-way analysis of variance and Mann-Whitney U-tests, with α = 0.05 as the level for statistical significance. Findings showed that there was no significant difference as to the number of extruded bacteria between two engine-driven systems (P>0.05). Both engine-driven Nickel-Titanium systems extruded bacteria through the apical foramen.

Micro-motors: A motile bacteria based system for liposome cargo transport.

PubMed

Dogra, Navneet; Izadi, Hadi; Vanderlick, T Kyle

2016-07-05

Biological micro-motors (microorganisms) have potential applications in energy utilization and nanotechnology. However, harnessing the power generated by such motors to execute desired work is extremely difficult. Here, we employ the power of motile bacteria to transport small, large, and giant unilamellar vesicles (SUVs, LUVs, and GUVs). Furthermore, we demonstrate bacteria-bilayer interactions by probing glycolipids inside the model membrane scaffold. Fluorescence Resonance Energy Transfer (FRET) spectroscopic and microscopic methods were utilized for understanding these interactions. We found that motile bacteria could successfully propel SUVs and LUVs with a velocity of 28 μm s(-1) and 13 μm s(-1), respectively. GUVs, however, displayed Brownian motion and could not be propelled by attached bacteria. Bacterial velocity decreased with the larger loaded cargo, which agrees with our calculations of loaded bacteria swimming at low Reynolds number.

Apical extrusion of bacteria when using reciprocating single-file and rotary multifile instrumentation systems.

PubMed

Tinoco, J M; De-Deus, G; Tinoco, E M B; Saavedra, F; Fidel, R A S; Sassone, L M

2014-06-01

To evaluate ex vivo, apical bacterial extrusion associated with two reciprocating single-file systems (WaveOne and Reciproc) compared with a conventional multifile rotary system (BioRace). Forty-five human single-rooted mandibular incisors were used. Endodontic access cavities were prepared, and root canals were contaminated with an Enterococcus faecalis suspension. Following incubation at 37 °C for thirty days, the contaminated teeth were divided into three groups of 15 specimens each (G1 - Reciproc, G2 - WaveOne and G3 - BioRace). Positive and negative controls consisted of 5 infected teeth and 3 uninfected incisors that were instrumented with one of the tested NiTi systems, respectively. Bacteria extruded from the apical foramen during instrumentation were collected into vials containing 0.9% NaCl. The microbiological samples were taken from the vials and incubated in brain heart agar medium for 24 h. The resulting bacterial titre, in colony-forming units (CFU) per mL, was determined, and these data were analysed by Wilcoxon matched-pairs signed rank test and Kruskal-Wallis H-test. The level of significance was set at α = 0.05. No significant difference was found in the number of CFU between the two reciprocating systems (P = 0.41). The conventional multifile rotary system group was associated with significantly higher CFU than both of the two reciprocating groups (P = 0.01). All instrumentation systems extruded bacteria beyond the foramen. However, both reciprocating single-file systems extruded fewer bacteria apically than the conventional multifile rotary system. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

On-chip concentration of bacteria using a 3D dielectrophoretic chip and subsequent laser-based DNA extraction in the same chip

NASA Astrophysics Data System (ADS)

Cho, Yoon-Kyoung; Kim, Tae-hyeong; Lee, Jeong-Gun

2010-06-01

We report the on-chip concentration of bacteria using a dielectrophoretic (DEP) chip with 3D electrodes and subsequent laser-based DNA extraction in the same chip. The DEP chip has a set of interdigitated Au post electrodes with 50 µm height to generate a network of non-uniform electric fields for the efficient trapping by DEP. The metal post array was fabricated by photolithography and subsequent Ni and Au electroplating. Three model bacteria samples (Escherichia coli, Staphylococcus epidermidis, Streptococcus mutans) were tested and over 80-fold concentrations were achieved within 2 min. Subsequently, on-chip DNA extraction from the concentrated bacteria in the 3D DEP chip was performed by laser irradiation using the laser-irradiated magnetic bead system (LIMBS) in the same chip. The extracted DNA was analyzed with silicon chip-based real-time polymerase chain reaction (PCR). The total process of on-chip bacteria concentration and the subsequent DNA extraction can be completed within 10 min including the manual operation time.

Heterotrophic bacteria in an air-handling system.

PubMed Central

Hugenholtz, P; Fuerst, J A

1992-01-01

Heterotrophic bacteria from structural surfaces, drain pan water, and the airstream of a well-maintained air-handling system with no reported building-related illness were enumerated. Visually the system appeared clean, but large populations of bacteria were found on the fin surface of the supply-side cooling coils (10(5) to 10(6) CFU cm-2), in drain pan water (10(5) to 10(7) CFU ml-1), and in the sump water of the evaporative condenser (10(5) CFU ml-1). Representative bacterial colony types recovered from heterotrophic plate count cultures on R2A medium were identified to the genus level. Budding bacteria belonging to the genus Blastobacter dominated the supply surface of the coil fins, the drain pan water, and the postcoil air. These data and independent scanning electron microscopy indicated that a resident population of predominantly Blastobacter bacteria was present as a biofilm on the supply-side cooling coil fins. Images PMID:1476435

Heterotrophic bacteria in an air-handling system.

PubMed

Hugenholtz, P; Fuerst, J A

1992-12-01

Heterotrophic bacteria from structural surfaces, drain pan water, and the airstream of a well-maintained air-handling system with no reported building-related illness were enumerated. Visually the system appeared clean, but large populations of bacteria were found on the fin surface of the supply-side cooling coils (10(5) to 10(6) CFU cm-2), in drain pan water (10(5) to 10(7) CFU ml-1), and in the sump water of the evaporative condenser (10(5) CFU ml-1). Representative bacterial colony types recovered from heterotrophic plate count cultures on R2A medium were identified to the genus level. Budding bacteria belonging to the genus Blastobacter dominated the supply surface of the coil fins, the drain pan water, and the postcoil air. These data and independent scanning electron microscopy indicated that a resident population of predominantly Blastobacter bacteria was present as a biofilm on the supply-side cooling coil fins.

Comparison of apical extrusion of intracanal bacteria by various glide-path establishing systems: an in vitro study.

PubMed

Dagna, Alberto; El Abed, Rashid; Hussain, Sameeha; Abu-Tahun, Ibrahim H; Visai, Livia; Bertoglio, Federico; Bosco, Floriana; Beltrami, Riccardo; Poggio, Claudio; Kim, Hyeon-Cheol

2017-11-01

This study compared the amount of apically extruded bacteria during the glide-path preparation by using multi-file and single-file glide-path establishing nickel-titanium (NiTi) rotary systems. Sixty mandibular first molar teeth were used to prepare the test apparatus. They were decoronated, blocked into glass vials, sterilized in ethylene oxide gas, infected with a pure culture of Enterococcus faecalis, randomly assigned to 5 experimental groups, and then prepared using manual stainless-steel files (group KF) and glide-path establishing NiTi rotary files (group PF with PathFiles, group GF with G-Files, group PG with ProGlider, and group OG with One G). At the end of canal preparation, 0.01 mL NaCl solution was taken from the experimental vials. The suspension was plated on brain heart infusion agar and colonies of bacteria were counted, and the results were given as number of colony-forming units (CFU). The manual instrumentation technique tested in group KF extruded the highest number of bacteria compared to the other 4 groups ( p < 0.05). The 4 groups using rotary glide-path establishing instruments extruded similar amounts of bacteria. All glide-path establishment instrument systems tested caused a measurable apical extrusion of bacteria. The manual glide-path preparation showed the highest number of bacteria extruded compared to the other NiTi glide-path establishing instruments.

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik's Cube of Clinical Microbiology?

PubMed

Gajdács, Márió; Spengler, Gabriella; Urbán, Edit

2017-11-07

Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.

A microcomputer-based testing station for dynamic and static testing of protective relay systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, W.J.; Li, R.J.; Gu, J.C.

1995-12-31

Dynamic and static relay performance testing before installation in the field is a subject of great interest to utility relay engineers. The common practice in utility testing of new relays is to put the new unit to be tested in parallel with an existing functioning relay in the system, wait until an actual transient occurs and then observe and analyze the performance of new relay. It is impossible to have a thorough test of the protective relay system through this procedure. An equipment, Microcomputer-Based Testing Station (or PC-Based Testing Station), that can perform both static and dynamic testing of themore » relay is described in this paper. The Power System Simulation Laboratory at the University of Texas at Arlington is a scaled-down, three-phase, physical power system which correlates well with the important components for a real power system and is an ideal facility for the dynamic and static testing of protective relay systems. A brief introduction to the configuration of this laboratory is presented. Test results of several protective functions by using this laboratory illustrate the usefulness of this test set-up.« less

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach

PubMed Central

2012-01-01

Background Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data. PMID:22759462

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach.

PubMed

Ratkovic, Zorana; Golik, Wiktoria; Warnier, Pierre

2012-06-26

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

Versatile plasmid-based expression systems for Gram-negative bacteria--General essentials exemplified with the bacterium Ralstonia eutropha H16.

PubMed

Gruber, Steffen; Schwab, Helmut; Koefinger, Petra

2015-12-25

The Gram-negative bacterium Escherichia coli is currently the most efficient and widely used prokaryotic host for recombinant protein and metabolite production. However, due to some limitations and to various interesting features of other Gram-negative bacteria efficient vector systems applicable to a broad range are desired. Basic building blocks for plasmid-based vectors include besides the need for a suitable selection marker in the first line a proper replication and maintenance system. In addition to these basic requirements, further elements are needed for Gram-negative bacteria beyond E. coli, such as Pseudomonas pudita, Ralstonia eutropha, Burkholderia glumae or Acinetobacter sp.. Established building blocks have to be adapted and new building blocks providing the desired functions need to be identified and exploited. This minireview addresses so far described and used genetic elements for broad host range replication, efficient plasmid maintenance, and conjugative plasmid transfer as well as expression elements and protein secretion signals. The industrially important bacterium R. eutropha H16 was chosen as a model organism to provide specific data on the effectivity and utility of building blocks based on such genetic elements. Copyright © 2015 Elsevier B.V. All rights reserved.

Capillary-tube-based oxygen/argon micro-plasma system for the inactivation of bacteria suspended in aqueous solution.

PubMed

Weng, Chih-Chiang; Liao, Juinn-Der; Chen, Hsin-Hung; Lin, Tung-Yi; Huang, Chih-Ling

2011-09-01

An aqueous solution containing Escherichia coli can be completely inactivated within a short treatment time using a capillary-tube-based oxygen/argon micro-plasma source. A capillary-tube-based oxygen/argon micro-plasma system with a hollow inner electrode was ignited by a 13.56 MHz radio frequency power supply with a matching network and characterised by optical emission spectroscopy. An aqueous solution containing E. coli was then treated at various the working distances, plasma exposure durations, and oxygen ratios in argon micro-plasma. The treated bacteria were then assessed and qualitatively investigated. The morphologies of treated bacteria were examined using a scanning electron microscope (SEM). In the proposed oxygen/argon micro-plasma system, the intensities of the main emission lines of the excited species, nitric oxide (NO), hydrated oxide (OH), argon (Ar), and atomic oxygen (O), fluctuated with the addition of oxygen to argon micro-plasma. Under a steady state of micro-plasma generation, the complete inactivation of E. coli in aqueous solution was achieved within 90 s of argon micro-plasma exposure time with a working distance of 3 mm. SEM micrographs reveal obvious morphological damage to the treated E. coli. The addition of oxygen to argon micro-plasma increased the variety of O-containing excited species. At a given supply power, the relative intensities of the excited species, NO and OH, correlated with the ultraviolet (UV) intensity, decreased. For the proposed capillary-tube-based micro-plasma system with a hollow inner electrode, the oxygen/argon micro-plasma source is efficient in inactivating E. coli in aqueous solution. The treatment time required for the inactivation process decreases with decreasing working distance or the increasing synthesised effect of reactive species and UV intensity.

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR

PubMed Central

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-01

AIM: To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. METHODS: Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. RESULTS: cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. CONCLUSION: The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well. PMID:22294830

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR.

PubMed

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-21

To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well.

Isolation, amplification and characterization of foodborne pathogen disease bacteria gene for rapid kit test development

NASA Astrophysics Data System (ADS)

Nurjayadi, M.; Santoso, I.; Kartika, I. R.; Kurniadewi, F.; Saamia, V.; Sofihan, W.; Nurkhasanah, D.

2017-07-01

There is a lot of public concern over food safety. Food-safety cases recently, including many food poisoning cases in both the developed and developing countries, considered to be the national security threats which involved police investigation. Quick and accurate detection methods are needed to handle the food poisoning cases with a big number of sufferers at the same time. Therefore, the research is aimed to develop a specific, sensitive, and rapid result molecular detection tool for foodborne pathogen bacteria. We, thus, propose genomic level approach with Polymerase Chain Reaction. The research has successfully produced a specific primer to perform amplification to fim-C S. typhi, E. coli, and pef Salmonella typhimurium genes. The electrophoresis result shows that amplification products are 95 base pairs, 121 base pairs, and 139 base pairs; and all three genes are in accordance with the size of the in silico to third genes bacteria. In conclusion, the research has been successfully designed a specific detection tool to three foodborne pathogen bacteria genes. Further stages test and the uses of Real-time PCR in the detection are still in the trial process for better detection method.

[Clinical application of testing methods on acid-fast bacteria].

PubMed

Ichiyama, Satoshi; Suzuki, Katsuhiro

2005-02-01

Clinical bacteriology pertaining to acid-fast bacteria has made marked advances over the past decade, initiated by the development of a DNA probe kit for identification of acid-fast bacteria. Wide-spread use of nucleic acid amplification for rapid detection of tubercle bacillus contributed more greatly than any other factor to such advances in this field. At present, 90% of all kits used for nucleic acid amplification in the world are consumed in Japan. Unfortunately, not a few clinicians in Japan have a false idea that the smear method and nucleic acid amplification are necessary but culture is not. In any event nucleic acid amplification has exerted significant impacts on the routine works at bacteriology laboratories. Among others, collecting bacteria by pretreatment with NALC-NaOH has simplified the introduction of the collective mode smear method and liquid media. Furthermore, as clinicians have become increasingly more experienced with various methods of molecular biology, it now seems possible to apply these techniques for detection of genes encoding drug resistance and for utilization of molecular epidemiology in routine laboratory works. Meanwhile, attempts to diagnose acid-fast bacteriosis by checking blood for antibody have also been made, primarily in Japan. At present, two kits for detecting antibodies to glycolipids (LAM, TDM, etc.) are covered by national health insurance in Japan. We have an impression that in Japan clinicians do not have adequate knowledge and skill to make full use of these new testing methods clinically. We, as the chairmen of this symposium, hope that this symposium will help clinicians increase their skill related to new testing methods, eventually leading to stimulation of advances in clinical practices related to acid-fast bacteria in Japan. 1. Smear microscopy by concentration method and broth culture system: Kazunari TSUYUGUCHI (Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center) Smear

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology?

PubMed Central

Gajdács, Márió; Spengler, Gabriella; Urbán, Edit

2017-01-01

Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria. PMID:29112122

TEXSYS. [a knowledge based system for the Space Station Freedom thermal control system test-bed

NASA Technical Reports Server (NTRS)

Bull, John

1990-01-01

The Systems Autonomy Demonstration Project has recently completed a major test and evaluation of TEXSYS, a knowledge-based system (KBS) which demonstrates real-time control and FDIR for the Space Station Freedom thermal control system test-bed. TEXSYS is the largest KBS ever developed by NASA and offers a unique opportunity for the study of technical issues associated with the use of advanced KBS concepts including: model-based reasoning and diagnosis, quantitative and qualitative reasoning, integrated use of model-based and rule-based representations, temporal reasoning, and scale-up performance issues. TEXSYS represents a major achievement in advanced automation that has the potential to significantly influence Space Station Freedom's design for the thermal control system. An overview of the Systems Autonomy Demonstration Project, the thermal control system test-bed, the TEXSYS architecture, preliminary test results, and thermal domain expert feedback are presented.

Space Launch System Base Heating Test: Environments and Base Flow Physics

NASA Technical Reports Server (NTRS)

Mehta, Manish; Knox, Kyle; Seaford, Mark; Dufrene, Aaron

2016-01-01

NASA MSFC and CUBRC designed and developed a 2% scale SLS propulsive wind tunnel test program to investigate base flow effects during flight from lift-off to MECO. This type of test program has not been conducted in 40+ years during the NASA Shuttle Program. Dufrene et al paper described the operation, instrumentation type and layout, facility and propulsion performance, test matrix and conditions and some raw results. This paper will focus on the SLS base flow physics and the generation and results of the design environments being used to design the thermal protection system.

Requirements-Based Conformance Testing of ARINC 653 Real-Time Operating Systems

NASA Astrophysics Data System (ADS)

Maksimov, Andrey

2010-08-01

Requirements-based testing is emphasized in avionics certification documents because this strategy has been found to be the most effective at revealing errors. This paper describes the unified requirements-based approach to the creation of conformance test suites for mission-critical systems. The approach uses formal machine-readable specifications of requirements and finite state machine model for test sequences generation on-the-fly. The paper also presents the test system for automated test generation for ARINC 653 services built on this approach. Possible application of the presented approach to various areas of avionics embedded systems testing is discussed.

Evaluation of Verigene Blood Culture Test Systems for Rapid Identification of Positive Blood Cultures.

PubMed

Kim, Jae-Seok; Kang, Go-Eun; Kim, Han-Sung; Kim, Hyun Soo; Song, Wonkeun; Lee, Kyu Man

2016-01-01

The performance of molecular tests using the Verigene Gram-Positive and Gram-Negative Blood Culture nucleic acid tests (BC-GP and BC-GN, resp.; Naosphere, Northbrook, IL, USA) was evaluated for the identification of microorganisms detected from blood cultures. Ninety-nine blood cultures containing Gram-positive bacteria and 150 containing Gram-negative bacteria were analyzed using the BC-GP and BC-GN assays, respectively. Blood cultures were performed using the Bactec blood culture system (BD Diagnostic Systems, Franklin Lakes, NJ, USA) and conventional identification and antibiotic-susceptibility tests were performed using a MicroScan system (Siemens, West Sacramento, CA, USA). When a single strain of bacteria was isolated from the blood culture, Verigene assays correctly identified 97.9% (94/96) of Gram-positive bacteria and 93.8% (137/146) of Gram-negative bacteria. Resistance genes mecA and vanA were correctly detected by the BC-GP assay, while the extended-spectrum β-lactamase CTX-M and the carbapenemase OXA resistance gene were detected from 30 cases cultures by the BC-GN assay. The BC-GP and BC-GN assays showed high agreement with conventional identification and susceptibility tests. These tests are useful for rapid identification of microorganisms and the detection of clinically important resistance genes from positive Bactec blood cultures.

Comparative evaluation of apical extrusion of bacteria using hand and rotary systems : An in vitro study

PubMed Central

Ghivari, Sheetal B; Kubasad, Girish C; Deshpande, Preethi

2012-01-01

Aim: To evaluate the bacteria extruded apically during root canal preparation using two hand and rotary instrumentation techniques. Materials and Methods: Eighty freshly extracted mandibular premolars were mounted in bacteria collection apparatus. Root canals were contaminated with the pure culture of Enterococcus fecalis (ATCC 29212) and dried at 37°C for 24 h. Bacteria extruded were collected, incubated in brain heart infusion agar for 24 h at 36°C and the colony forming units (CFU) were counted. Statistical Analysis: The mean number of colony forming units were calculated by One-way ANOVA and comparison between the groups made by multiple comparison (Dunnet D) test. Results: The step-back technique extruded highest number of bacteria in comparison to other hand and rotary Ni–Ti systems. Conclusion: Under the limitation of this study all hand and rotary instrumentation techniques extruded bacteria. Among all the instrumentation techniques step-back technique extruded more number of bacteria and K-3 system the least. Further in vivo research in this direction could provide more insight into the biologic factors associated and focus on bacterial species that essentially play a major role in post instrumentation flare-ups. PMID:22368332

Gas Chromatographic Presumptive Test for Coliform Bacteria in Water

PubMed Central

Newman, Judith S.; O'Brien, R. T.

1975-01-01

A gas chromatographic procedure which shows promise as a presumptive test for coliform bacteria in water is described. Total coliform bacteria concentrations were determined from the incubation times at 37 C required for ethanol to be produced. Fecal coliform densities were determined in a similar manner at 44.5 C. The culture medium was filter sterilized M-9 salts supplemented with 1% lactose, 0.1% Casamino Acids, and 0.1% yeast extract. Best results were obtained when the initial total coliform concentrations were 5 per ml or higher and when fecal coliform concentrations were 50 per ml or higher. Minimum detection times at these concentrations were 9 and 12 h, respectively. PMID:1103731

In vitro evaluation of apical extrusion of bacteria following use of new rotary instrumentation system.

PubMed

Mohammadi, Zahed

2009-04-01

The aim of this study was to evaluate the number of bacteria extruded apically from extracted teeth ex vivo after canal instrumentation using two engine-driven nickel-titanium instruments (Flex Master and V-Taper). Seventy extracted maxillary central incisor teeth were used. After preparing access cavities, root canals were contaminated with a suspension of Enterococcus faecalis, then dried. The contaminated roots were divided into two experimental groups of 30 teeth each and one control group of 10 teeth. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples from the vials were incubated in culture media for 24 hours. Colonies of bacteria were counted, and the results were given as number of colony-forming units. The data obtained were analyzed using the Kruskal-Wallis one-way analysis of variance and Mann-Whitney U-tests, with alpha = 0.05 as the level for statistical significance. Results showed that there was no significant difference as to the number of extruded bacteria between the two engine-driven systems (P > 0.05). Both engine-driven nickel-titanium systems extruded bacteria through the apical foramen.

Current and future prospects for CRISPR-based tools in bacteria

PubMed Central

Luo, Michelle L.; Leenay, Ryan T.; Beisel, Chase L.

2015-01-01

CRISPR-Cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. This article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. Recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural diversity of CRISPR-Cas systems, and the untapped potential of CRISPR-based DNA acquisition. Overall, these systems have formed the basis of an ever-expanding genetic toolbox and hold tremendous potential for our future understanding and engineering of the bacterial world. PMID:26460902

Current and future prospects for CRISPR-based tools in bacteria.

PubMed

Luo, Michelle L; Leenay, Ryan T; Beisel, Chase L

2016-05-01

CRISPR-Cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. This article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. Recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural diversity of CRISPR-Cas systems, and the untapped potential of CRISPR-based DNA acquisition. Overall, these systems have formed the basis of an ever-expanding genetic toolbox and hold tremendous potential for our future understanding and engineering of the bacterial world. © 2015 Wiley Periodicals, Inc.

Heterotrophic bacteria in drinking water distribution system: a review.

PubMed

Chowdhury, Shakhawat

2012-10-01

The microbiological quality of drinking water in municipal water distribution systems (WDS) depends on several factors. Free residual chlorine and/or chloramines are typically used to minimize bacterial recontamination and/or regrowth in WDS. Despite such preventive measures, regrowth of heterotrophic (HPC) and opportunistic bacteria in bulk water and biofilms has yet to be controlled completely. No approach has shown complete success in eliminating biofilms or HPC bacteria from bulk water and pipe surfaces. Biofilms can provide shelter for pathogenic bacteria and protect these bacteria from disinfectants. Some HPC bacteria may be associated with aesthetic and non-life threatening diseases. Research to date has achieved important success in understanding occurrence and regrowth of bacteria in bulk water and biofilms in WDS. To achieve comprehensive understanding and to provide efficient control against bacteria regrowth, future research on bacteria regrowth dynamics and their implications is warranted. In this study, a review was performed on the literature published in this area. The findings and limitations of these papers are summarized. Occurrences of bacteria in WDS, factors affecting bacteria regrowth in bulk water and biofilms, bacteria control strategies, sources of nutrients, human health risks from bacterial exposure, modelling of bacteria regrowth and methods of bacteria sampling and detection and quantification are investigated. Advances to date are noted, and future research needs are identified. Finally, research directions are proposed to effectively control HPC and opportunistic bacteria in bulk water and biofilms in WDS.

Antimicrobial susceptibility testing of veterinary clinical isolates with the Sceptor System.

PubMed Central

Papp, J R; Muckle, C A

1991-01-01

The Sceptor System (Becton Dickinson) was compared with an agar dilution method for antimicrobial susceptibility testing of veterinary clinical isolates. The results indicate that the Sceptor System may be used to test gram-positive and fastidious gram-negative bacteria. PMID:1864944

Space Launch System Base Heating Test: Environments and Base Flow Physics

NASA Technical Reports Server (NTRS)

Mehta, Manish; Knox, Kyle S.; Seaford, C. Mark; Dufrene, Aaron T.

2016-01-01

The NASA Space Launch System (SLS) vehicle is composed of four RS-25 liquid oxygen- hydrogen rocket engines in the core-stage and two 5-segment solid rocket boosters and as a result six hot supersonic plumes interact within the aft section of the vehicle during ight. Due to the complex nature of rocket plume-induced ows within the launch vehicle base during ascent and a new vehicle con guration, sub-scale wind tunnel testing is required to reduce SLS base convective environment uncertainty and design risk levels. This hot- re test program was conducted at the CUBRC Large Energy National Shock (LENS) II short-duration test facility to simulate ight from altitudes of 50 kft to 210 kft. The test program is a challenging and innovative e ort that has not been attempted in 40+ years for a NASA vehicle. This presentation discusses the various trends of base convective heat ux and pressure as a function of altitude at various locations within the core-stage and booster base regions of the two-percent SLS wind tunnel model. In-depth understanding of the base ow physics is presented using the test data, infrared high-speed imaging and theory. The normalized test design environments are compared to various NASA semi- empirical numerical models to determine exceedance and conservatism of the ight scaled test-derived base design environments. Brief discussion of thermal impact to the launch vehicle base components is also presented.

Space Launch System Base Heating Test: Environments and Base Flow Physics

NASA Technical Reports Server (NTRS)

Mehta, Manish; Knox, Kyle S.; Seaford, C. Mark; Dufrene, Aaron T.

2016-01-01

The NASA Space Launch System (SLS) vehicle is composed of four RS-25 liquid oxygen-hydrogen rocket engines in the core-stage and two 5-segment solid rocket boosters and as a result six hot supersonic plumes interact within the aft section of the vehicle during flight. Due to the complex nature of rocket plume-induced flows within the launch vehicle base during ascent and a new vehicle configuration, sub-scale wind tunnel testing is required to reduce SLS base convective environment uncertainty and design risk levels. This hot-fire test program was conducted at the CUBRC Large Energy National Shock (LENS) II short-duration test facility to simulate flight from altitudes of 50 kft to 210 kft. The test program is a challenging and innovative effort that has not been attempted in 40+ years for a NASA vehicle. This paper discusses the various trends of base convective heat flux and pressure as a function of altitude at various locations within the core-stage and booster base regions of the two-percent SLS wind tunnel model. In-depth understanding of the base flow physics is presented using the test data, infrared high-speed imaging and theory. The normalized test design environments are compared to various NASA semi-empirical numerical models to determine exceedance and conservatism of the flight scaled test-derived base design environments. Brief discussion of thermal impact to the launch vehicle base components is also presented.

Comparison of spot esculin hydrolysis with the PathoTec strip test for rapid differentiation of anaerobic bacteria.

PubMed Central

Qadri, S M; Johnson, S; Smith, J C; Zubairi, S; Gillum, R L

1981-01-01

The ability of several anaerobic bacteria to hydrolyze esculin to esculetin is used by clinical microbiologists and taxonomists in the differentiation and identification of both gram-positive and gram-negative microorganisms. Conventional methods used for determining esculin hydrolysis by anaerobic bacteria require 24 to 48 h for completion. In this paper we evaluate two procedures which yield rapid results. A total of 738 anaerobic bacteria were used in this study. A total of 99% of the esculin-hydrolyzing anaerobic bacteria gave positive results with the spot test in 1 h, whereas the other test method, the PathoTec strip test (General Diagnostics, Morris Plains, N.J.), required 4 h for 96% of the strains tested to yield positive reactions. Both tests showed a 100% specificity when compared with the standard broth test and are easy to perform, accurate, and economical. The spot test is superior to the PathoTec strip test in yielding results more rapidly. PMID:7016896

An Approach to Model Based Testing of Multiagent Systems

PubMed Central

Nadeem, Aamer

2015-01-01

Autonomous agents perform on behalf of the user to achieve defined goals or objectives. They are situated in dynamic environment and are able to operate autonomously to achieve their goals. In a multiagent system, agents cooperate with each other to achieve a common goal. Testing of multiagent systems is a challenging task due to the autonomous and proactive behavior of agents. However, testing is required to build confidence into the working of a multiagent system. Prometheus methodology is a commonly used approach to design multiagents systems. Systematic and thorough testing of each interaction is necessary. This paper proposes a novel approach to testing of multiagent systems based on Prometheus design artifacts. In the proposed approach, different interactions between the agent and actors are considered to test the multiagent system. These interactions include percepts and actions along with messages between the agents which can be modeled in a protocol diagram. The protocol diagram is converted into a protocol graph, on which different coverage criteria are applied to generate test paths that cover interactions between the agents. A prototype tool has been developed to generate test paths from protocol graph according to the specified coverage criterion. PMID:25874263

A novel PMT test system based on waveform sampling

NASA Astrophysics Data System (ADS)

Yin, S.; Ma, L.; Ning, Z.; Qian, S.; Wang, Y.; Jiang, X.; Wang, Z.; Yu, B.; Gao, F.; Zhu, Y.; Wang, Z.

2018-01-01

Comparing with the traditional test system based on a QDC and TDC and scaler, a test system based on waveform sampling is constructed for signal sampling of the 8"R5912 and the 20"R12860 Hamamatsu PMT in different energy states from single to multiple photoelectrons. In order to achieve high throughput and to reduce the dead time in data processing, the data acquisition software based on LabVIEW is developed and runs with a parallel mechanism. The analysis algorithm is realized in LabVIEW and the spectra of charge, amplitude, signal width and rising time are analyzed offline. The results from Charge-to-Digital Converter, Time-to-Digital Converter and waveform sampling are discussed in detailed comparison.

Assessment of pathogenesis of infective endocarditis by plasma IgG antibody titer test against periodontal bacteria.

PubMed

Isoshima, Daichi; Yamashiro, Keisuke; Matsunaga, Kazuyuki; Shinobe, Michitaka; Nakanishi, Nagako; Nakanishi, Izumi; Omori, Kazuhiro; Yamamoto, Tadashi; Takashiba, Shogo

2017-10-01

Oral bacteria cause infective endocarditis (IE), so severe periodontitis is thought to be high risk for IE. We suggest the identification of high-risk patients by an IgG antibody titer test against periodontal bacteria might become common screening test.

Testing expert systems

NASA Technical Reports Server (NTRS)

Chang, C. L.; Stachowitz, R. A.

1988-01-01

Software quality is of primary concern in all large-scale expert system development efforts. Building appropriate validation and test tools for ensuring software reliability of expert systems is therefore required. The Expert Systems Validation Associate (EVA) is a validation system under development at the Lockheed Artificial Intelligence Center. EVA provides a wide range of validation and test tools to check correctness, consistency, and completeness of an expert system. Testing a major function of EVA. It means executing an expert system with test cases with the intent of finding errors. In this paper, we describe many different types of testing such as function-based testing, structure-based testing, and data-based testing. We describe how appropriate test cases may be selected in order to perform good and thorough testing of an expert system.

Effects of symbiotic bacteria on chemical sensitivity of Daphnia magna.

PubMed

Manakul, Patcharaporn; Peerakietkhajorn, Saranya; Matsuura, Tomoaki; Kato, Yasuhiko; Watanabe, Hajime

2017-07-01

The crustacean zooplankton Daphnia magna has been widely used for chemical toxicity tests. Although abiotic factors have been well documented in ecotoxicological test protocols, biotic factors that may affect the sensitivity to chemical compounds remain limited. Recently, we identified symbiotic bacteria that are critical for the growth and reproduction of D. magna. The presence of symbiotic bacteria on Daphnia raised the question as to whether these bacteria have a positive or negative effect on toxicity tests. In order to evaluate the effects of symbiotic bacteria on toxicity tests, bacteria-free Daphnia were prepared, and their chemical sensitivities were compared with that of Daphnia with symbiotic bacteria based on an acute immobilization test. The Daphnia with symbiotic bacteria showed higher chemical resistance to nonylphenol, fenoxycarb, and pentachlorophenol than bacteria-free Daphnia. These results suggested potential roles of symbiotic bacteria in the chemical resistance of its host Daphnia. Copyright © 2017 Elsevier Ltd. All rights reserved.

Space Launch System Base Heating Test: Experimental Operations & Results

NASA Technical Reports Server (NTRS)

Dufrene, Aaron; Mehta, Manish; MacLean, Matthew; Seaford, Mark; Holden, Michael

2016-01-01

NASA's Space Launch System (SLS) uses four clustered liquid rocket engines along with two solid rocket boosters. The interaction between all six rocket exhaust plumes will produce a complex and severe thermal environment in the base of the vehicle. This work focuses on a recent 2% scale, hot-fire SLS base heating test. These base heating tests are short-duration tests executed with chamber pressures near the full-scale values with gaseous hydrogen/oxygen engines and RSRMV analogous solid propellant motors. The LENS II shock tunnel/Ludwieg tube tunnel was used at or near flight duplicated conditions up to Mach 5. Model development was based on the Space Shuttle base heating tests with several improvements including doubling of the maximum chamber pressures and duplication of freestream conditions. Test methodology and conditions are presented, and base heating results from 76 runs are reported in non-dimensional form. Regions of high heating are identified and comparisons of various configuration and conditions are highlighted. Base pressure and radiometer results are also reported.

Coliform Bacteria and Nitrogen Fixation in Pulp and Paper Mill Effluent Treatment Systems

PubMed Central

Gauthier, Francis; Neufeld, Josh D.; Driscoll, Brian T.; Archibald, Frederick S.

2000-01-01

The majority of pulp and paper mills now biotreat their combined effluents using activated sludge. On the assumption that their wood-based effluents have negligible fixed N, and that activated-sludge microorganisms will not fix significant N, these mills routinely spend large amounts adding ammonia or urea to their aeration tanks (bioreactors) to permit normal biomass growth. N2 fixation in seven Eastern Canadian pulp and paper mill effluent treatment systems was analyzed using acetylene reduction assays, quantitative nitrogenase (nifH) gene probing, and bacterial isolations. In situ N2 fixation was undetectable in all seven bioreactors but was present in six associated primary clarifiers. One primary clarifier was studied in greater detail. Approximately 50% of all culturable cells in the clarifier contained nifH, of which >90% were Klebsiella strains. All primary-clarifier coliform bacteria growing on MacConkey agar were identified as klebsiellas, and all those probed contained nifH. In contrast, analysis of 48 random coliform isolates from other mill water system locations showed that only 24 (50%) possessed the nifH gene, and only 13 (27%) showed inducible N2-fixing activity. Thus, all the pulp and paper mill primary clarifiers tested appeared to be sites of active N2 fixation (0.87 to 4.90 mg of N liter−1 day−1) and a microbial community strongly biased toward this activity. This may also explain why coliform bacteria, especially klebsiellas, are indigenous in pulp and paper mill water systems. PMID:11097883

Presence of archaea and selected bacteria in infected root canal systems.

PubMed

Brzezińska-Błaszczyk, Ewa; Pawłowska, Elżbieta; Płoszaj, Tomasz; Witas, Henryk; Godzik, Urszula; Agier, Justyna

2018-05-01

Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson's χ 2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student's t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.

Recombinant Salmonella Bacteria Vectoring HIV/AIDS Vaccines

PubMed Central

Chin’ombe, Nyasha; Ruhanya, Vurayai

2013-01-01

HIV/AIDS is an important public health problem globally. An affordable, easy-to-deliver and protective HIV vaccine is therefore required to curb the pandemic from spreading further. Recombinant Salmonella bacteria can be harnessed to vector HIV antigens or DNA vaccines to the immune system for induction of specific protective immunity. These are capable of activating the innate, humoral and cellular immune responses at both mucosal and systemic compartments. Several studies have already demonstrated the utility of live recombinant Salmonella in delivering expressed foreign antigens as well as DNA vaccines to the host immune system. This review gives an overview of the studies in which recombinant Salmonella bacteria were used to vector HIV/AIDS antigens and DNA vaccines. Most of the recombinant Salmonella-based HIV/AIDS vaccines developed so far have only been tested in animals (mainly mice) and are yet to reach human trials. PMID:24478808

Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection.

PubMed

Zelenin, Sergey; Ramachandraiah, Harisha; Faridi, Asim; Russom, Aman

2017-01-01

Bacterial blood stream infection (BSI) potentially leads to life-threatening clinical conditions and medical emergencies such as severe sepsis, septic shock, and multi organ failure syndrome. Blood culturing is currently the gold standard for the identification of microorganisms and, although it has been automated over the decade, the process still requires 24-72 h to complete. This long turnaround time, especially for the identification of antimicrobial resistance, is driving the development of rapid molecular diagnostic methods. Rapid detection of microbial pathogens in blood related to bloodstream infections will allow the clinician to decide on or adjust the antimicrobial therapy potentially reducing the morbidity, mortality, and economic burden associated with BSI. For molecular-based methods, there is a lot to gain from an improved and straightforward method for isolation of bacteria from whole blood for downstream processing.We describe a microfluidic-based sample-preparation approach that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.

International Space Station Bacteria Filter Element Post-Flight Testing and Service Life Prediction

NASA Technical Reports Server (NTRS)

Perry, J. L.; von Jouanne, R. G.; Turner, E. H.

2003-01-01

The International Space Station uses high efficiency particulate air (HEPA) filters to remove particulate matter from the cabin atmosphere. Known as Bacteria Filter Elements (BFEs), there are 13 elements deployed on board the ISS's U.S. Segment. The pre-flight service life prediction of 1 year for the BFEs is based upon performance engineering analysis of data collected during developmental testing that used a synthetic dust challenge. While this challenge is considered reasonable and conservative from a design perspective, an understanding of the actual filter loading is required to best manage the critical ISS Program resources. Thus testing was conducted on BFEs returned from the ISS to refine the service life prediction. Results from this testing and implications to ISS resource management are discussed. Recommendations for realizing significant savings to the ISS Program are presented.

MICROBIOLOGICAL CHARACTERIZATION OF BACTERIA INHABITING A WATER DISTRIBUTION SYSTEM SIMULATOR

EPA Science Inventory

The impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia oxidizing bacteria (AOB) inhabiting a water distribution system simulator was investigated. Notable changes in bacterial densities were observed during this monitoring study. For e...

Design and evaluation of a wireless sensor network based aircraft strength testing system.

PubMed

Wu, Jian; Yuan, Shenfang; Zhou, Genyuan; Ji, Sai; Wang, Zilong; Wang, Yang

2009-01-01

The verification of aerospace structures, including full-scale fatigue and static test programs, is essential for structure strength design and evaluation. However, the current overall ground strength testing systems employ a large number of wires for communication among sensors and data acquisition facilities. The centralized data processing makes test programs lack efficiency and intelligence. Wireless sensor network (WSN) technology might be expected to address the limitations of cable-based aeronautical ground testing systems. This paper presents a wireless sensor network based aircraft strength testing (AST) system design and its evaluation on a real aircraft specimen. In this paper, a miniature, high-precision, and shock-proof wireless sensor node is designed for multi-channel strain gauge signal conditioning and monitoring. A cluster-star network topology protocol and application layer interface are designed in detail. To verify the functionality of the designed wireless sensor network for strength testing capability, a multi-point WSN based AST system is developed for static testing of a real aircraft undercarriage. Based on the designed wireless sensor nodes, the wireless sensor network is deployed to gather, process, and transmit strain gauge signals and monitor results under different static test loads. This paper shows the efficiency of the wireless sensor network based AST system, compared to a conventional AST system.

Design and Evaluation of a Wireless Sensor Network Based Aircraft Strength Testing System

PubMed Central

Wu, Jian; Yuan, Shenfang; Zhou, Genyuan; Ji, Sai; Wang, Zilong; Wang, Yang

2009-01-01

The verification of aerospace structures, including full-scale fatigue and static test programs, is essential for structure strength design and evaluation. However, the current overall ground strength testing systems employ a large number of wires for communication among sensors and data acquisition facilities. The centralized data processing makes test programs lack efficiency and intelligence. Wireless sensor network (WSN) technology might be expected to address the limitations of cable-based aeronautical ground testing systems. This paper presents a wireless sensor network based aircraft strength testing (AST) system design and its evaluation on a real aircraft specimen. In this paper, a miniature, high-precision, and shock-proof wireless sensor node is designed for multi-channel strain gauge signal conditioning and monitoring. A cluster-star network topology protocol and application layer interface are designed in detail. To verify the functionality of the designed wireless sensor network for strength testing capability, a multi-point WSN based AST system is developed for static testing of a real aircraft undercarriage. Based on the designed wireless sensor nodes, the wireless sensor network is deployed to gather, process, and transmit strain gauge signals and monitor results under different static test loads. This paper shows the efficiency of the wireless sensor network based AST system, compared to a conventional AST system. PMID:22408521

Directed transport of bacteria-based drug delivery vehicles: bacterial chemotaxis dominates particle shape.

PubMed

Sahari, Ali; Traore, Mahama A; Scharf, Birgit E; Behkam, Bahareh

2014-10-01

Several attenuated and non-pathogenic bacterial species have been demonstrated to actively target diseased sites and successfully deliver plasmid DNA, proteins and other therapeutic agents into mammalian cells. These disease-targeting bacteria can be employed for targeted delivery of therapeutic and imaging cargos in the form of a bio-hybrid system. The bio-hybrid drug delivery system constructed here is comprised of motile Escherichia coli MG1655 bacteria and elliptical disk-shaped polymeric microparticles. The transport direction for these vehicles can be controlled through biased random walk of the attached bacteria in presence of chemoattractant gradients in a process known as chemotaxis. In this work, we utilize a diffusion-based microfluidic platform to establish steady linear concentration gradients of a chemoattractant and investigate the roles of chemotaxis and geometry in transport of bio-hybrid drug delivery vehicles. Our experimental results demonstrate for the first time that bacterial chemotactic response dominates the effect of body shape in extravascular transport; thus, the non-spherical system could be more favorable for drug delivery applications owing to the known benefits of using non-spherical particles for vascular transport (e.g. relatively long circulation time).

133Xe contamination found in internal bacteria filter of xenon ventilation system.

PubMed

Hackett, Michael T; Collins, Judith A; Wierzbinski, Rebecca S

2003-09-01

We report on (133)Xe contamination found in the reusable internal bacteria filter of our xenon ventilation system. Internal bacteria filters (n = 6) were evaluated after approximately 1 mo of normal use. The ventilation system was evacuated twice to eliminate (133)Xe in the system before removal of the filter. Upon removal, the filter was monitored using a survey meter with an energy-compensated probe and was imaged on a scintillation camera. The filter was monitored and imaged over several days and was stored in a fume hood. Estimated (133)Xe activity in each filter immediately after removal ranged from 132 to 2,035 kBq (3.6-55.0 micro Ci), based on imaging. Initial surface radiation levels ranged from 0.4 to 4.5 micro Sv/h (0.04-0.45 mrem/h). The (133)Xe activity did not readily leave the filter over time (i.e., time to reach half the counts of the initial decay-corrected image ranged from <6 to >72 h). The majority of the image counts (approximately 70%) were seen in 2 distinctive areas in the filter. They corresponded to sites where the manufacturer used polyurethane adhesive to attach the fiberglass filter medium to the filter housing. (133)Xe contamination within the reusable internal bacteria filter of our ventilation system was easily detected by a survey meter and imaging. Although initial activities and surface radiation levels were low, radiation safety practices would dictate that a (133)Xe-contaminated bacteria filter be stored preferably in a fume hood until it cannot be distinguished from background before autoclaving or disposal.

Endosafe(R)-Portable Test System (PTS)

NASA Technical Reports Server (NTRS)

Maule, Jake; Wainwright, Norm; Burbank, Dan

2005-01-01

The Portable Test System (PTS) is a hand-held device for monitoring the presence of potentially hazardous bacteria in the environment. It uses an immunological method derived from the horseshoe crab (Limulus polyphemus) to detect bacterial cell membranes and other molecular components of a cell. Further modifications of the PTS will allow detection of individual hazardous species of bacteria. This study was a follow-up of previous PTS and other immunological tests performed on the KC-135 during 2002-2003 (Maule et al., 2003, J. Gravit. Physiol.) and in the underwater habitat Aquarius during NEEMO 5 (Maule et al., 2005, Appl. Environ. Microbiol in prep.). The experiments described here were part of a final testing phase prior to use of the PTS on the International Space Station (ISS), scheduled for launch on 12A.1 on February 9th 2006. The specific aspects of PTS operation studied were those involving a fluid component: pumping, mixing, incubations and pipetting into the instrument. The PTS uses a stepper motor to move fluid along small channels, which may be affected by reduced gravity.

Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems.

PubMed

Marcus, Daniel N; Pinto, Ameet; Anantharaman, Karthik; Ruberg, Steven A; Kramer, Eva L; Raskin, Lutgarde; Dick, Gregory J

2017-04-01

Manganese (Mn) oxides are highly reactive minerals that influence the speciation, mobility, bioavailability and toxicity of a wide variety of organic and inorganic compounds. Although Mn(II)-oxidizing bacteria are known to catalyze the formation of Mn oxides, little is known about the organisms responsible for Mn oxidation in situ, especially in engineered environments. Mn(II)-oxidizing bacteria are important in drinking water systems, including in biofiltration and water distribution systems. Here, we used cultivation dependent and independent approaches to investigate Mn(II)-oxidizing bacteria in drinking water sources, a treatment plant and associated distribution system. We isolated 29 strains of Mn(II)-oxidizing bacteria and found that highly similar 16S rRNA gene sequences were present in all culture-independent datasets and dominant in the studied drinking water treatment plant. These results highlight a potentially important role for Mn(II)-oxidizing bacteria in drinking water systems, where biogenic Mn oxides may affect water quality in terms of aesthetic appearance, speciation of metals and oxidation of organic and inorganic compounds. Deciphering the ecology of these organisms and the factors that regulate their Mn(II)-oxidizing activity could yield important insights into how microbial communities influence the quality of drinking water. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Survival of hydrogen sulfide oxidizing bacteria on corroded concrete surfaces of sewer systems.

PubMed

Jensen, H S; Nielsen, A H; Hvitved-Jacobsen, T; Vollertsen, J

2008-01-01

The activity of hydrogen sulfide oxidizing bacteria within corroded concrete from a sewer manhole was investigated. The bacteria were exposed to hydrogen sulfide starvation for up till 18 months, upon which their hydrogen sulfide oxidizing activity was measured. It was tested whether the observed reduction in biological activity was caused by a biological lag phase or by decay of the bacteria. The results showed that the bacterial activity declined with approximately 40% pr. month during the first two months of hydrogen sulfide starvation. After 2-3 months of starvation, the activity stabilized. Even after 6 months of starvation, exposure to hydrogen sulfide for 6 hours a day on three successive days could restore the bacteriological activity to about 80% of the initial activity. After 12 months of starvation, the activity could, however, not be restored, and after 18 months the biological activity approached zero. The long-term survival aspect of concrete corroding bacteria has implications for predicting hydrogen sulfide corrosion in sewer systems subject to irregular hydrogen sulfide loadings, e.g. as they occur in temperate climates where hydrogen sulfide often is a summer-problem only.

Aptamer-based viability impedimetric sensor for bacteria.

PubMed

Labib, Mahmoud; Zamay, Anna S; Kolovskaya, Olga S; Reshetneva, Irina T; Zamay, Galina S; Kibbee, Richard J; Sattar, Syed A; Zamay, Tatiana N; Berezovski, Maxim V

2012-11-06

The development of an aptamer-based viability impedimetric sensor for bacteria (AptaVISens-B) is presented. Highly specific DNA aptamers to live Salmonella typhimurium were selected via the cell-systematic evolution of ligands by exponential enrichment (SELEX) technique. Twelve rounds of selection were performed; each comprises a positive selection step against viable S. typhimurium and a negative selection step against heat killed S. typhimurium and a mixture of related pathogens, including Salmonella enteritidis, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Citrobacter freundii to ensure the species specificity of the selected aptamers. The DNA sequence showing the highest binding affinity to the bacteria was further integrated into an impedimetric sensor via self-assembly onto a gold nanoparticle-modified screen-printed carbon electrode (GNP-SPCE). Remarkably, this aptasensor is highly selective and can successfully detect S. typhimurium down to 600 CFU mL(-1) (equivalent to 18 live cells in 30 μL of assay volume) and distinguish it from other Salmonella species, including S. enteritidis and S. choleraesuis. This report is envisaged to open a new venue for the aptamer-based viability sensing of a variety of microorganisms, particularly viable but nonculturable (VBNC) bacteria, using a rapid, economic, and label-free electrochemical platform.

Azolla-anabaena-bacteria system as a natural microcosm

NASA Astrophysics Data System (ADS)

Carrapico, Francisco J.

2002-02-01

Azolla is an aquatic fern that contains a permanent endosymbiotic prokaryotic community (cyanobacteria and bacteria) inside of the cavity in the leaf dorsal lobe of the pteridophyte. This is a unique situation and can be seen as a microcosm inside of an organism and also can be considered a good example of a living model for biological and environmental studies. These symbionts are specific of this symbiosis and lives immobilized in a mucilaginous fibrillar network, which fills part of the cavity. The symbionts works as immobilized organisms in a natural system that can be used as a model for biotechnological research and in biologically based life support systems. The nature and the complexity of this system is simultaneously a reference and a challenge for the research in the communication between the two levels of nature organization (microcosm and mesocosm), and can also be used as a reference for the design of new environmental engineered symbiotic systems that include man as a prelude to life in space.

Lytic and inhibition responses to bacteriophages among marine bacteria, with special reference to the origin of phage-host systems

NASA Astrophysics Data System (ADS)

Moebus, K.

1983-12-01

The results of phage-host cross-reaction tests reported by Moebus & Nattkemper (1981) were re-examined using serially diluted bacteriophage suspensions to elicit the actual type of reaction between the bacteria and phage lysates tested. More than 1450 phage-host systems were studied at 25 °C incubation temperature. Among the nearly 300 phage strains used, 29 were identified as temperate ones. In about 65 % of the phage-host systems bacteriophage propagation was indicated by plaque formation. The remaining systems were characterized by the “inhibition” reaction of bacteria to phage lysates indicated by homogenously reduced bacterial growth within the test area without production of progeny phages. Since crude phage lysates had to be used, it remains obscure whether agents other than infective phage particles (defective ones or bacteriocins) caused this reaction. Among 269 systems of the inhibition type which were also tested at 5° and 15 °C, 54 were observed to propagate phages at one of or both the lower temperatures. Plaques produced at 15 °C with several phage-host systems were found to yield only few progeny phages which generally could not be propagated to produce high-titer phage stocks. With one system temperature-sensitive phage mutants were isolated. The probability of inhibition reactions occurring was found to be higher with phage-host systems isolated east of the Azores than with systems derived from the western Atlantic. With systems from the last mentioned area the proportion of inhibition versus lytic responses of bacteria to phages was observed to increase with the distance between the stations where both parts of the systems were derived. The latter findings are discussed in view of the assumption that bacterial and bacteriophage populations undergo genetic changes while being transported from west to east.

Large-aperture space optical system testing based on the scanning Hartmann.

PubMed

Wei, Haisong; Yan, Feng; Chen, Xindong; Zhang, Hao; Cheng, Qiang; Xue, Donglin; Zeng, Xuefeng; Zhang, Xuejun

2017-03-10

Based on the Hartmann testing principle, this paper proposes a novel image quality testing technology which applies to a large-aperture space optical system. Compared with the traditional testing method through a large-aperture collimator, the scanning Hartmann testing technology has great advantages due to its simple structure, low cost, and ability to perform wavefront measurement of an optical system. The basic testing principle of the scanning Hartmann testing technology, data processing method, and simulation process are presented in this paper. Certain simulation results are also given to verify the feasibility of this technology. Furthermore, a measuring system is developed to conduct a wavefront measurement experiment for a 200 mm aperture optical system. The small deviation (6.3%) of root mean square (RMS) between experimental results and interferometric results indicates that the testing system can measure low-order aberration correctly, which means that the scanning Hartmann testing technology has the ability to test the imaging quality of a large-aperture space optical system.

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints.

PubMed

Liu, Gang; Zhang, Ya; van der Mark, Ed; Magic-Knezev, Aleksandra; Pinto, Ameet; van den Bogert, Bartholomeus; Liu, Wentso; van der Meer, Walter; Medema, Gertjan

2018-07-01

The general consensus is that the abundance of tap water bacteria is greatly influenced by water purification and distribution. Those bacteria that are released from biofilm in the distribution system are especially considered as the major potential risk for drinking water bio-safety. For the first time, this full-scale study has captured and identified the proportional contribution of the source water, treated water, and distribution system in shaping the tap water bacterial community based on their microbial community fingerprints using the Bayesian "SourceTracker" method. The bacterial community profiles and diversity analyses illustrated that the water purification process shaped the community of planktonic and suspended particle-associated bacteria in treated water. The bacterial communities associated with suspended particles, loose deposits, and biofilm were similar to each other, while the community of tap water planktonic bacteria varied across different locations in distribution system. The microbial source tracking results showed that there was not a detectable contribution of source water to bacterial community in the tap water and distribution system. The planktonic bacteria in the treated water was the major contributor to planktonic bacteria in the tap water (17.7-54.1%). The particle-associated bacterial community in the treated water seeded the bacterial community associated with loose deposits (24.9-32.7%) and biofilm (37.8-43.8%) in the distribution system. In return, the loose deposits and biofilm showed a significant influence on tap water planktonic and particle-associated bacteria, which were location dependent and influenced by hydraulic changes. This was revealed by the increased contribution of loose deposits to tap water planktonic bacteria (from 2.5% to 38.0%) and an increased contribution of biofilm to tap water particle-associated bacteria (from 5.9% to 19.7%) caused by possible hydraulic disturbance from proximal to distal regions

Piloting a Collaborative Web-Based System for Testing ICD-11.

PubMed

Donada, Marc; Kostanjsek, Nenad; Della Mea, Vincenzo; Celik, Can; Jakob, Robert

2017-01-01

The 11^th revision of the International Classification of Diseases (ICD-11), for the first time in ICD history, deployed web-based collaboration of experts and ICT tools. To ensure that ICD-11 is working well, it needs to be systematically field tested in different settings, across the world. This will be done by means of a number of experiments. In order to support its implementation, a web-based system (ICDfit) has been designed and developed. The present paper illustrates the current prototype of the system and its technical testing. the system has been designed according to WHO requirements, and implemented using PHP and MySQL. Then, a preliminary technical test has been designed and run in January 2016, involving 8 users. They had to carry out double coding, that is, coding case summaries with both ICD-10 and ICD-11, and answering quick questions on the coding difficulty. the 8 users coded 632 cases each, spending an average of 163 seconds per case. While we found an issue in the mechanism used to record coding times, no further issues were found. the proposed system seems to be technically adequate for supporting future ICD-11 testing.

Pilot-scale investigation of sludge reduction in aerobic digestion system with endospore-forming bacteria.

PubMed

Seo, Kyu Won; Choi, Yong-Su; Gu, Man Bock; Kwon, Eilhann E; Tsang, Yiu Fai; Rinklebe, Jörg; Park, Chanhyuk

2017-11-01

A pilot-scale investigation of membrane-based aerobic digestion system dominated by endospore-forming bacteria was evaluated as one of the potential sludge treatment processes (STP). Most of the organic matter in the sludge was removed (90.1%) by the particular bacteria in the STP, which consisted of mixed liquor suspended solid (MLSS) contact reactor (MCR), MLSS oxidation reactor (MOR), and membrane bioreactor (MBR). The sludge was accumulated in the MBR without wasting, and then the effluent in STP was fed into the first step in water resource recovery facility (WRRF). According to the analysis of microbial communities in all reactors, various Bacillus species were present in the STP, mainly due to their intrinsic resistance to the extreme conditions. As the surviving Bacillus species might consume degraded microorganisms for their growth, these endospore-forming bacteria-based STP could be suitable for the sludge reduction when they operated for a long time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Apical Extrusion of Intracanal Bacteria with Single File and Multifile Rotary Instrumentation Systems.

PubMed

Saberi, Eshaghali; Zahedani, Shahram Shahraki; Ebrahimipour, Sediqe

2017-01-01

Instrumentation techniques may cause extrusion of microorganisms and their products into the periapical region resulting inflammation and treatment failure. The aim of this ex vivo study was comparing the apical bacterial extrusion in canals prepared with single file versus multiple file rotary systems. Ninety-two human single-rooted mandibular first premolars were used. Endodontic access cavities were prepared, and root canals were contaminated with an Enterococcus faecalis ( E. faecalis ) suspension. The samples were incubated at 37°C for 30 days; the contaminated teeth were divided into four groups of 20 specimens each (1: Reciproc, 2: Mtwo, 3: Neoniti A1, 4: Safesider). Six teeth were not infected and each were prepared with one of the above instruments were considered as negative and six teeth which had been previously infected, were used as positive control groups. Extruded bacteria from the apical foramen during instrumentation were collected into vials containing 0.9% NaCl. The microbial samples were taken from the vials and incubated in brain heart agar medium for 24 h. The resulting bacterial titer, in colony-forming units per mL, was determined. The data entered into SPSS 18 software and were analyzed by Kruskal-Wallis and Mann-Whitney U-tests at 0.05 significance level. Mtwo multifile system showed significantly less bacterial extrusion than Safesider ( P = 0.015) and Neoniti A1 ( P = 0.042) but did not show significant difference with Reciproc system ( P = 0.25). All instrumentation systems extruded bacteria beyond the apical foramen. However, this study showed that Mtwo multifile rotary system extruded fewer bacteria.

Amoeba-Resisting Bacteria and Ventilator-Associated Pneumonia

PubMed Central

La Scola, Bernard; Boyadjiev, Ioanna; Greub, Gilbert; Khamis, Atieh; Martin, Claude

2003-01-01

To evaluate the role of amoeba-associated bacteria as agents of ventilator-associated pneumonia (VAP), we tested the water from an intensive care unit (ICU) every week for 6 months for such bacteria isolates; serum samples and bronchoalveolar lavage samples (BAL) were also obtained from 30 ICU patients. BAL samples were examined for amoeba-associated bacteria DNA by suicide-polymerase chain reaction, and serum samples were tested against ICU amoeba-associated bacteria. A total of 310 amoeba-associated bacteria from10 species were isolated. Twelve of 30 serum samples seroconverted to one amoeba-associated bacterium isolated in the ICU, mainly Legionella anisa and Bosea massiliensis, the most common isolates from water (p=0.021). Amoeba-associated bacteria DNA was detected in BAL samples from two patients whose samples later seroconverted. Seroconversion was significantly associated with VAP and systemic inflammatory response syndrome, especially in patients for whom no etiologic agent was found by usual microbiologic investigations. Amoeba-associated bacteria might be a cause of VAP in ICUs, especially when microbiologic investigations are negative. PMID:12890321

Rapid High-Throughput Assessment of Aerobic Bacteria in Complex Samples by Fluorescence-Based Oxygen Respirometry

PubMed Central

O'Mahony, Fiach C.; Papkovsky, Dmitri B.

2006-01-01

A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including Escherichia coli, Micrococcus luteus, and Pseudomonas fluorescens, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given. PMID:16461677

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

PubMed Central

Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-01-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS‐based diagnosis methods for bacteria identification and typing have been created, not only on well‐accepted MALDI‐TOF‐MS‐based fingerprint matches, but also on solving the insufficiencies of MALDI‐TOF‐MS‐based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS‐based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. PMID:26751976

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis.

PubMed

Topcuoglu, Nursen; Kulekci, Guven

2015-10-01

DNA microarray analysis is a computer based technology, that a reverse capture, which targets 10 periodontal bacteria (ParoCheck) is available for rapid semi-quantitative determination. The aim of this three-year retrospective study was to display the microarray analysis results for the subgingival biofilm samples taken from patient cases diagnosed with different forms of periodontitis. A total of 84 patients with generalized aggressive periodontitis (GAP,n:29), generalized chronic periodontitis (GCP, n:25), peri-implantitis (PI,n:14), localized aggressive periodontitis (LAP,n:8) and refractory chronic periodontitis (RP,n:8) were consecutively selected from the archives of the Oral Microbiological Diagnostic Laboratory. The subgingival biofilm samples were analyzed by the microarray-based identification of 10 selected species. All the tested species were detected in the samples. The red complex bacteria were the most prevalent with very high levels in all groups. Fusobacterium nucleatum was detected in all samples at high levels. The green and blue complex bacteria were less prevalent compared with red and orange complex, except Aggregatibacter actinomycetemcomitas was detected in all LAP group. Positive correlations were found within all the red complex bacteria and between red and orange complex bacteria especially in GCP and GAP groups. Parocheck enables to monitoring of periodontal pathogens in all forms of periodontal disease and can be alternative to other guiding and reliable microbiologic tests. Copyright © 2015 Elsevier Ltd. All rights reserved.

Differentiating sepsis from non-infectious systemic inflammation based on microvesicle-bacteria aggregation

NASA Astrophysics Data System (ADS)

Herrmann, I. K.; Bertazzo, S.; O'Callaghan, D. J. P.; Schlegel, A. A.; Kallepitis, C.; Antcliffe, D. B.; Gordon, A. C.; Stevens, M. M.

2015-08-01

Sepsis is a severe medical condition and a leading cause of hospital mortality. Prompt diagnosis and early treatment has a significant, positive impact on patient outcome. However, sepsis is not always easy to diagnose, especially in critically ill patients. Here, we present a conceptionally new approach for the rapid diagnostic differentiation of sepsis from non-septic intensive care unit patients. Using advanced microscopy and spectroscopy techniques, we measure infection-specific changes in the activity of nano-sized cell-derived microvesicles to bind bacteria. We report on the use of a point-of-care-compatible microfluidic chip to measure microvesicle-bacteria aggregation and demonstrate rapid (<=1.5 hour) and reliable diagnostic differentiation of bacterial infection from non-infectious inflammation in a double-blind pilot study. Our study demonstrates the potential of microvesicle activities for sepsis diagnosis and introduces microvesicle-bacteria aggregation as a potentially useful parameter for making early clinical management decisions.Sepsis is a severe medical condition and a leading cause of hospital mortality. Prompt diagnosis and early treatment has a significant, positive impact on patient outcome. However, sepsis is not always easy to diagnose, especially in critically ill patients. Here, we present a conceptionally new approach for the rapid diagnostic differentiation of sepsis from non-septic intensive care unit patients. Using advanced microscopy and spectroscopy techniques, we measure infection-specific changes in the activity of nano-sized cell-derived microvesicles to bind bacteria. We report on the use of a point-of-care-compatible microfluidic chip to measure microvesicle-bacteria aggregation and demonstrate rapid (<=1.5 hour) and reliable diagnostic differentiation of bacterial infection from non-infectious inflammation in a double-blind pilot study. Our study demonstrates the potential of microvesicle activities for sepsis diagnosis and

Quorum-Sensing Signal-Response Systems in Gram-Negative Bacteria

PubMed Central

Papenfort, Kai; Bassler, Bonnie

2016-01-01

Abstract / Preface Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy. PMID:27510864

Filamentous bacteria existence in aerobic granular reactors.

PubMed

Figueroa, M; Val del Río, A; Campos, J L; Méndez, R; Mosquera-Corral, A

2015-05-01

Filamentous bacteria are associated to biomass settling problems in wastewater treatment plants. In systems based on aerobic granular biomass they have been proposed to contribute to the initial biomass aggregation process. However, their development on mature aerobic granular systems has not been sufficiently studied. In the present research work, filamentous bacteria were studied for the first time after long-term operation (up to 300 days) of aerobic granular systems. Chloroflexi and Sphaerotilus natans have been observed in a reactor fed with synthetic wastewater. These filamentous bacteria could only come from the inoculated sludge. Thiothrix and Chloroflexi bacteria were observed in aerobic granular biomass treating wastewater from a fish canning industry. Meganema perideroedes was detected in a reactor treating wastewater from a plant processing marine products. As a conclusion, the source of filamentous bacteria in these mature aerobic granular systems fed with industrial effluents was the incoming wastewater.

Fault tolerant system based on IDDQ testing

NASA Astrophysics Data System (ADS)

Guibane, Badi; Hamdi, Belgacem; Mtibaa, Abdellatif; Bensalem, Brahim

2018-06-01

Offline test is essential to ensure good manufacturing quality. However, for permanent or transient faults that occur during the use of the integrated circuit in an application, an online integrated test is needed as well. This procedure should ensure the detection and possibly the correction or the masking of these faults. This requirement of self-correction is sometimes necessary, especially in critical applications that require high security such as automotive, space or biomedical applications. We propose a fault-tolerant design for analogue and mixed-signal design complementary metal oxide (CMOS) circuits based on the quiescent current supply (IDDQ) testing. A defect can cause an increase in current consumption. IDDQ testing technique is based on the measurement of power supply current to distinguish between functional and failed circuits. The technique has been an effective testing method for detecting physical defects such as gate-oxide shorts, floating gates (open) and bridging defects in CMOS integrated circuits. An architecture called BICS (Built In Current Sensor) is used for monitoring the supply current (IDDQ) of the connected integrated circuit. If the measured current is not within the normal range, a defect is signalled and the system switches connection from the defective to a functional integrated circuit. The fault-tolerant technique is composed essentially by a double mirror built-in current sensor, allowing the detection of abnormal current consumption and blocks allowing the connection to redundant circuits, if a defect occurs. Spices simulations are performed to valid the proposed design.

SERS based immuno-microwell arrays for multiplexed detection of foodborne pathogenic bacteria

NASA Astrophysics Data System (ADS)

Sun, Jian; Hankus, Mikella E.; Cullum, Brian M.

2009-05-01

A novel surface enhanced Raman scattering (SERS)-based immuno-microwell array has been developed for multiplexed detection of foodborne pathogenic bacteria. The immuno-microwell array was prepared by immobilizing the optical addressable immunomagnetic beads (IMB) into the microwell array on one end of a fiber optic bundle. The IMBs, magnetic beads coated with specific antibody to specific bacteria, were used for immunomagnetic separation (IMS) of corresponding bacteria. The magnetic separation by the homemade magnetic separation system was evaluated in terms of the influences of several important parameters including the beads concentration, the sample volume and the separation time. IMS separation efficiency of the model bacteria E.coli O157:H7 was 63% in 3 minutes. The microwell array was fabricated on hydrofluoric acid etched end of a fiber optic bundle containing 30,000 fiber elements. After being coated with silver, the microwell array was used as a uniform SERS substrate with the relative standard deviation of the SERS enhancement across the microwell array < 2% and the enhancement factor as high as 2.18 x 107. The antibody modified microwell array was prepared for bacteria immobilization into the microwell array, which was characterized by a sandwich immunoassay. To demonstrate the potential of multiplexed SERS detection with the immuno-microwell array, the SERS spectra of different Raman dye labeled magnetic beads as well as mixtures were measured on the mircrowell array. In bead mixture, different beads were identified by the characteristic SERS bands of the corresponding Raman label.

UFC advisor: An AI-based system for the automatic test environment

NASA Technical Reports Server (NTRS)

Lincoln, David T.; Fink, Pamela K.

1990-01-01

The Air Logistics Command within the Air Force is responsible for maintaining a wide variety of aircraft fleets and weapon systems. To maintain these fleets and systems requires specialized test equipment that provides data concerning the behavior of a particular device. The test equipment is used to 'poke and prod' the device to determine its functionality. The data represent voltages, pressures, torques, temperatures, etc. and are called testpoints. These testpoints can be defined numerically as being in or out of limits/tolerance. Some test equipment is termed 'automatic' because it is computer-controlled. Due to the fact that effective maintenance in the test arena requires a significant amount of expertise, it is an ideal area for the application of knowledge-based system technology. Such a system would take testpoint data, identify values out-of-limits, and determine potential underlying problems based on what is out-of-limits and how far. This paper discusses the application of this technology to a device called the Unified Fuel Control (UFC) which is maintained in this manner.

Does the Reciproc file remove root canal bacteria and endotoxins as effectively as multifile rotary systems?

PubMed

Marinho, A C S; Martinho, F C; Gonçalves, L M; Rabang, H R C; Gomes, B P F A

2015-06-01

To evaluate the effectiveness of Reciproc for the removal of cultivable bacteria and endotoxins from root canals in comparison with multifile rotary systems. The root canals of forty human single-rooted mandibular pre-molars were contaminated with an Escherichia coli suspension for 21 days and randomly assigned to four groups according to the instrumentation system: GI - Reciproc (VDW); GII - Mtwo (VDW); GIII - ProTaper Universal (Dentsply Maillefer); and GIV -FKG Race(™) (FKG Dentaire) (n = 10 per group). Bacterial and endotoxin samples were taken with a sterile/apyrogenic paper point before (s1) and after instrumentation (s2). Culture techniques determined the colony-forming units (CFU) and the Limulus Amebocyte Lysate assay was used for endotoxin quantification. Results were submitted to paired t-test and anova. At s1, bacteria and endotoxins were recovered in 100% of the root canals investigated (40/40). After instrumentation, all systems were associated with a highly significant reduction of the bacterial load and endotoxin levels, respectively: GI - Reciproc (99.34% and 91.69%); GII - Mtwo (99.86% and 83.11%); GIII - ProTaper (99.93% and 78.56%) and GIV - FKG Race(™) (99.99% and 82.52%) (P < 0.001). No statistical difference were found amongst the instrumentation systems regarding bacteria and endotoxin removal (P > 0.01). The reciprocating single file, Reciproc, was as effective as the multifile rotary systems for the removal of bacteria and endotoxins from root canals. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Using a data base management system for modelling SSME test history data

NASA Technical Reports Server (NTRS)

Abernethy, K.

1985-01-01

The usefulness of a data base management system (DBMS) for modelling historical test data for the complete series of static test firings for the Space Shuttle Main Engine (SSME) was assessed. From an analysis of user data base query requirements, it became clear that a relational DMBS which included a relationally complete query language would permit a model satisfying the query requirements. Representative models and sample queries are discussed. A list of environment-particular evaluation criteria for the desired DBMS was constructed; these criteria include requirements in the areas of user-interface complexity, program independence, flexibility, modifiability, and output capability. The evaluation process included the construction of several prototype data bases for user assessement. The systems studied, representing the three major DBMS conceptual models, were: MIRADS, a hierarchical system; DMS-1100, a CODASYL-based network system; ORACLE, a relational system; and DATATRIEVE, a relational-type system.

The population dynamics of bacteria, phage and RM Systems

NASA Astrophysics Data System (ADS)

Guet, Calin; Levin, Bruce; Pleska, Maros

Viruses drive and mediate bacterial evolution as parasites and vectors of horizontal gene transfer, respectively. Temperate bacteriophages, defined by the ability to lysogenize a fraction of hosts and to transmit horizontally as well as vertically in the form of prophages, frequently carry genes that increase fitness or contribute to bacterial pathogenicity. Restriction-modification (RM) systems, which are widely diverse and ubiquitous among bacteria, can prevent infections leading to lysis, but their effect on lysogeny is not clear. We show that RM systems prevent lytic and lysogenic infections to the same extent and therefore represent a molecular barrier to prophage acquisition. Surprisingly, we find that this negative effect can be overcome and even reversed at the population level, as a consequence of dynamic interactions between viruses, hosts and RM systems. Thus the population dynamics of bacteria carrying RM systems impacts bacterial genome-wide evolution. .

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria.

PubMed

Cheng, Keding; Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-04-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS-based diagnosis methods for bacteria identification and typing have been created, not only on well-accepted MALDI-TOF-MS-based fingerprint matches, but also on solving the insufficiencies of MALDI-TOF-MS-based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS-based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. © 2016 The Authors. PROTEOMICS - Clinical Applications Published by WILEY-VCH Verlag GmbH & Co. KGaA.

Laser-Based Identification of Pathogenic Bacteria

ERIC Educational Resources Information Center

Rehse, Steven J.

2009-01-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the…

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria

PubMed Central

Ibarra-Arellano, Miguel A.; Campos-González, Adrián I.; Treviño-Quintanilla, Luis G.; Tauch, Andreas; Freyre-González, Julio A.

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy (Across-bacteria systems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708

Can pulsed xenon ultraviolet light systems disinfect aerobic bacteria in the absence of manual disinfection?

PubMed

Jinadatha, Chetan; Villamaria, Frank C; Ganachari-Mallappa, Nagaraja; Brown, Donna S; Liao, I-Chia; Stock, Eileen M; Copeland, Laurel A; Zeber, John E

2015-04-01

Whereas pulsed xenon-based ultraviolet light no-touch disinfection systems are being increasingly used for room disinfection after patient discharge with manual cleaning, their effectiveness in the absence of manual disinfection has not been previously evaluated. Our study indicates that pulsed xenon-based ultraviolet light systems effectively reduce aerobic bacteria in the absence of manual disinfection. These data are important for hospitals planning to adopt this technology as adjunct to routine manual disinfection. Published by Elsevier Inc.

Fecal-indicator bacteria in streams alonga gradient of residential development

USGS Publications Warehouse

Frenzel, Steven A.; Couvillion, Charles S.

2002-01-01

Fecal-indicator bacteria were sampled at 14 stream sites in Anchorage, Alaska, USA, as part of a study to determine the effects of urbanization on water quality. Population density in the subbasins sampled ranged from zero to 1,750 persons per square kilometer. Higher concentrations of fecal-coliform, E. coli, and enterococci bacteria were measured at the most urbanized sites. Although fecal-indicator bacteria concentrations were higher in summer than in winter, seasonal differences in bacteria concentrations generally were not significant. Areas served by sewer systems had significantly higher fecal-indicator bacteria concentrations than did areas served by septic systems. The areas served by sewer systems also had storm drains that discharged directly to the streams, whereas storm sewers were not present in the areas served by septic systems. Fecal-indicator bacteria concentrations were highly variable over a two-day period of stable streamflow, which may have implications for testing of compliance to water-quality standards.

Acute toxicity testing of some herbicides-, alkaloids-, and antibiotics-metabolizing soil bacteria in the rat.

PubMed

Kaiser, A; Classen, H G; Eberspächer, J; Lingens, F

1981-01-01

Seven strains of soil bacteria with the ability to metabolize herbicides, alkaloids or antibiotics were tested in rats for acute toxicity. 1. Upon oral administration of 9.0 x 10(8) to 6.6 x 10(10) cells daily during 7 d no adverse reactions were observed. 2. Exposure by air did not lead to specific pulmonary changes. 3. Intracutaneous injection of 7.5 x 10(6) to 1.4 x 10(8) cells did not lead to adverse skin reactions. 4. Intraperitoneal injections up to 10(8) cells per animal did not kill rats although bacteria entered blood. At higher concentrations some mortality occurred partly due to unspecific stress reactions. 5. Animal data and observations on 20 humans being exposed to these strains for 2 months up to 15 years support the view that the bacteria tested are essentially harmless for health.

Detection of Mannitol Formation by Bacteria

PubMed Central

Chalfan, Y.; Levy, R.; Mateles, R. I.

1975-01-01

A test is described by means of which formation of mannitol from fructose by lactic acid bacteria can be readily detected. The test is based on removal of interference of residual fructose by dehydration with hydrochloric acid followed by thin-layer chromatography. PMID:1101827

Systems solutions by lactic acid bacteria: from paradigms to practice

PubMed Central

2011-01-01

Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications. PMID:21995776

Evaluation of conventional, protaper hand and protaper rotary instrumentation system for apical extrusion of debris, irrigants and bacteria- An in vitro randomized trial.

PubMed

Kalra, Pinky; Rao, Arathi; Suman, Ethel; Shenoy, Ramya; Suprabha, Baranya-Shrikrishna

2017-02-01

Endodontic instrumentation carries the risk of over extrusion of debris and bacteria. The technique used and the type of instrumentation influences this risk. The purpose of this study was to evaluate and compare the K-file, ProTaper hand and ProTaper rotary instrumentation systems for the amount of apically extruded debris, irrigant solution and intracanal bacteria. Experimental single blinded randomized type of in vitro study with sample of 30 single rooted teeth. Endodontic access cavities were prepared and the root canals were filled with the suspension of E. faecalis . Myers and Montogomery Model was used to collect apically extruded debris and irrigant. Canals were prepared using K files, Hand protapers and Protaper rotary files. Non Parametric test like Kruskal-Wallis and Mann-Whitney U test were applied to determine the significant differences among the group. Tests revealed statistically significant difference between the amount of debris and number of bacteria extruded by the ProTaper hand and the K-files. No statistically significant difference was observed between the amounts of irrigant extruded by the ProTaper hand and the K-file system. Statistically significant differences were observed between the amounts of bacteria and irrigant extruded by the ProTaper rotary and the Protaper hand. No statistically significant difference was observed between the amounts of debris extruded by the ProTaper hand and the K-file system. Amount of apical extrusion of irrigant solution, bacteria and debris are significantly greater with K File instruments and least with Protaper rotary instruments. Key words: Protaper, rotary, periapical extrusion.

Simple, rapid, and cost-effective modified Carba NP test for carbapenemase detection among Gram-negative bacteria

PubMed Central

Rudresh, Shoorashetty Manohara; Ravi, Giriyapur Siddappa; Sunitha, Lakshminarayanappa; Hajira, Sadiya Noor; Kalaiarasan, Ellappan; Harish, Belgode Narasimha

2017-01-01

PURPOSE: Detection of carbapenemases among Gram-negative bacteria (GNB) is important for both clinicians and infection control practitioners. The Clinical and Laboratory Standards Institute recommends Carba NP (CNP) as confirmatory test for carbapenemase production. The reagents required for CNP test are costly and hence the test cannot be performed on a routine basis. The present study evaluates modifications of CNP test for rapid detection of carbapenemases among GNB. MATERIALS AND METHODS: The GNB were screened for carbapenemase production using CNP, CarbAcineto NP (CANP), and modified CNP (mCNP) test. A multiplex polymerase chain reaction (PCR) was performed on all the carbapenem-resistant bacteria for carbapenemase genes. The results of three phenotypic tests were compared with PCR. RESULTS: A total of 765 gram negative bacteria were screened for carbapenem resistance. Carbapenem resistance was found in 144 GNB. The metallo-β-lactamases were most common carbapenemases followed by OXA-48-like enzymes. The CANP test was most sensitive (80.6%) for carbapenemases detection. The mCNP test was 62.1% sensitive for detection of carbapenemases. The mCNP, CNP, and CANP tests were equally sensitive (95%) for detection of NDM enzymes among Enterobacteriaceae. The mCNP test had poor sensitivity for detection of OXA-48-like enzymes. CONCLUSION: The mCNP test was rapid, cost-effective, and easily adoptable on routine basis. The early detection of carbapenemases using mCNP test will help in preventing the spread of multidrug-resistant organisms in the hospital settings. PMID:28966495

Simple, rapid, and cost-effective modified Carba NP test for carbapenemase detection among Gram-negative bacteria.

PubMed

Rudresh, Shoorashetty Manohara; Ravi, Giriyapur Siddappa; Sunitha, Lakshminarayanappa; Hajira, Sadiya Noor; Kalaiarasan, Ellappan; Harish, Belgode Narasimha

2017-01-01

Detection of carbapenemases among Gram-negative bacteria (GNB) is important for both clinicians and infection control practitioners. The Clinical and Laboratory Standards Institute recommends Carba NP (CNP) as confirmatory test for carbapenemase production. The reagents required for CNP test are costly and hence the test cannot be performed on a routine basis. The present study evaluates modifications of CNP test for rapid detection of carbapenemases among GNB. The GNB were screened for carbapenemase production using CNP, CarbAcineto NP (CANP), and modified CNP (mCNP) test. A multiplex polymerase chain reaction (PCR) was performed on all the carbapenem-resistant bacteria for carbapenemase genes. The results of three phenotypic tests were compared with PCR. A total of 765 gram negative bacteria were screened for carbapenem resistance. Carbapenem resistance was found in 144 GNB. The metallo-β-lactamases were most common carbapenemases followed by OXA-48-like enzymes. The CANP test was most sensitive (80.6%) for carbapenemases detection. The mCNP test was 62.1% sensitive for detection of carbapenemases. The mCNP, CNP, and CANP tests were equally sensitive (95%) for detection of NDM enzymes among Enterobacteriaceae. The mCNP test had poor sensitivity for detection of OXA-48-like enzymes. The mCNP test was rapid, cost-effective, and easily adoptable on routine basis. The early detection of carbapenemases using mCNP test will help in preventing the spread of multidrug-resistant organisms in the hospital settings.

Increase in detectable opportunistic bacteria in the oral cavity of orthodontic patients.

PubMed

Kitada, K; de Toledo, A; Oho, T

2009-05-01

This study was performed to detect the opportunistic bacteria and fungi from the oral cavities of orthodontic patients and examine the ability of the organisms to adhere to saliva-coated metallic brackets. Opportunistic bacteria and fungi were isolated from 58 patients (orthodontic group: 42; non-orthodontic group: 16) using culture methods and were identified based on their biochemical and enzymatic profiles. Seven opportunistic and four streptococcal strains were tested for their ability to adhere to saliva-coated metallic brackets. More opportunistic bacteria and fungi were detected in the orthodontic group than in the non-orthodontic group (P < 0.05). Opportunistic bacteria adhered to saliva-coated metallic brackets to the same degree as oral streptococci. The isolation frequencies of opportunistic bacteria and fungi increase during orthodontic treatment, suggesting the importance of paying special attention to oral hygiene in orthodontic patients to prevent periodontal disease and the aggravation of systemic disease in immunocompromised conditions.

A microsensor for the detection of a single pathogenic bacterium using magnetotactic bacteria-based bio-carriers: simulations and preliminary experiments.

PubMed

Denomme, Ryan C; Lu, Zhao; Martel, Sylvain

2007-01-01

The proposed Magnetotactic Bacteria (MTB) based bio-carrier has the potential to greatly improve pathogenic bacteria detection time, specificity, and sensitivity. Microbeads are attached to the MTB and are modified with a coating of an antibody or phage that is specific to the target pathogenic bacteria. Using magnetic fields, the modified MTB are swept through a solution and the target bacteria present become attached to the microbeads (due to the coating). Then, the MTB are brought to the detection region and the number of pathogenic bacteria is determined. The high swimming speed and controllability of the MTB make this method ideal for the fast detection of small concentrations of specific bacteria. This paper focuses on an impedimetric detection system that will be used to identify if a target bacterium is attached to the microbead. The proposed detection system measures changes in electrical impedance as objects (MTB, microbeads, and pathogenic bacteria) pass through a set of microelectrodes embedded in a microfluidic device. FEM simulation is used to acquire the optimized parameters for the design of such a system. Specifically, factors such as electrode/detection channel geometry, object size and position, which have direct effects on the detection sensitivity for a single bacterium or microparticle, are investigated. Polymer microbeads and the MTB system with an E. coli bacterium are considered to investigate their impedance variations. Furthermore, preliminary experimental data using a microfabricated microfluidic device connected to an impedance analyzer are presented.

Development of hybrid electric vehicle powertrain test system based on virtue instrument

NASA Astrophysics Data System (ADS)

Xu, Yanmin; Guo, Konghui; Chen, Liming

2017-05-01

Hybrid powertrain has become the standard configuration of some automobile models. The test system of hybrid vehicle powertrain was developed based on virtual instrument, using electric dynamometer to simulate the work of engines, to test the motor and control unit of the powertrain. The test conditions include starting, acceleration, and deceleration. The results show that the test system can simulate the working conditions of the hybrid electric vehicle powertrain under various conditions.

Concentration and detection of bacteria in virtual environmental samples based on non-immunomagnetic separation and quantum dots by using a laboratory-made system

NASA Astrophysics Data System (ADS)

Cheng, Zhi; Wu, Taihu; Chen, Feng; Du, Yaohua; Gu, Biao; Li, Chao; Yang, Zijian

2012-03-01

This study investigated a method that simultaneously detects three bacteria, Salmonella typhimurium, Escherichia coli, and Staphylococcus aureus via an approach that combines un-immunized magnetic nanoparticles for the enrichment and antibody-conjugated quantum dots (QDs) as fluorescence markers, by using a laboratory-made system. In the enrichment procedure, the un-immunized superparamagnetic polymer nanoparticles and the three bacteria formed "beadcell" complex. Magnetic nanoparticles with different size were used and some interferents were added into the bacteria suspension respectively to check the influence on concentration efficiency. In the immuno-fluorescence labeling procedure, QDs with different emission wavelenghs were immobilized with antibody. Antibody conjugated QDs capture the bacteria selectively and specifically so that "sandwich" complex were formed. The suspension of the labeled bacteria was trickled onto a microporous membrane. A 450nm semiconductor laser was used as a part of the laboratory-made system to excite the QDs. Three PMT detectors were utilized to detect the fluorescence intensity. These un-immunized magnetic nanoparticles can be applied in nonspecific separation and enrichment of bacteria from environmental samples, and this method, of which the detection procedures are completed within 2 h, can be applied to the cost-effective and rapid detecting of bacterial contamination.

Bare laser-synthesized Au-based nanoparticles as nondisturbing surface-enhanced Raman scattering probes for bacteria identification.

PubMed

Kögler, Martin; Ryabchikov, Yury V; Uusitalo, Sanna; Popov, Alexey; Popov, Anton; Tselikov, Gleb; Välimaa, Anna-Liisa; Al-Kattan, Ahmed; Hiltunen, Jussi; Laitinen, Riitta; Neubauer, Peter; Meglinski, Igor; Kabashin, Andrei V

2018-02-01

The ability of noble metal-based nanoparticles (NPs) (Au, Ag) to drastically enhance Raman scattering from molecules placed near metal surface, termed as surface-enhanced Raman scattering (SERS), is widely used for identification of trace amounts of biological materials in biomedical, food safety and security applications. However, conventional NPs synthesized by colloidal chemistry are typically contaminated by nonbiocompatible by-products (surfactants, anions), which can have negative impacts on many live objects under examination (cells, bacteria) and thus decrease the precision of bioidentification. In this article, we explore novel ultrapure laser-synthesized Au-based nanomaterials, including Au NPs and AuSi hybrid nanostructures, as mobile SERS probes in tasks of bacteria detection. We show that these Au-based nanomaterials can efficiently enhance Raman signals from model R6G molecules, while the enhancement factor depends on the content of Au in NP composition. Profiting from the observed enhancement and purity of laser-synthesized nanomaterials, we demonstrate successful identification of 2 types of bacteria (Listeria innocua and Escherichia coli). The obtained results promise less disturbing studies of biological systems based on good biocompatibility of contamination-free laser-synthesized nanomaterials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In vitro testing of commercial and potential probiotic lactic acid bacteria.

PubMed

Jensen, Hanne; Grimmer, Stine; Naterstad, Kristine; Axelsson, Lars

2012-02-01

Probiotics are defined as live microorganisms which when administered in adequate amounts confer a health benefit on the host. The objective of this study was to investigate the diversity of selected commercial and potential probiotic lactic acid bacteria using common in vitro screening assays such as transit tolerance in the upper human gastrointestinal tract, adhesion capacity to human intestinal cell lines and effect on epithelial barrier function. The selected bacteria include strains of Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus farciminis, Lactobacillus sakei, Lactobacillus gasseri, Lactobacillus rhamnosus, Lactobacillus reuteri and Pediococcus pentosaceus. Viable counts after simulated gastric transit tolerance showed that L. reuteri strains and P. pentosaceus tolerate gastric juice well, with no reduction of viability, whereas L. pentosus, L. farciminis and L. sakei strains lost viability over 180min. All strains tested tolerate the simulated small intestinal juice well. The bacterial adhesion capacity to human intestinal cells revealed major species and strain differences. Overall, L. plantarum MF1298 and three L. reuteri strains had a significant higher adhesion capacity compared to the other strains tested. All strains, both living and UV-inactivated, had little effect on the epithelial barrier function. However, living L. reuteri strains revealed a tendency to increase the transepithelial electrical resistance (TER) from 6 to 24h. This work demonstrates the diversity of 18 potential probiotic bacteria, with major species and strain specific effects in the in vitro screening assays applied. Overall, L. reuteri strains reveal some interesting characteristics compared to the other strains investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

New methods for isolation of keratolytic bacteria inducing intractable hoof wall cavity (Gidoh) in a horse; double screening procedures of the horn powder agar-translucency test and horn zymography

PubMed Central

KUWANO, Atsutoshi; NIWA, Hidekazu; ARAI, Katsuhiko

2017-01-01

ABSTRACT To establish a new system to isolate keratolytic bacteria from the hoof wall cavity (Gidoh) of a racehorse, we invented the horn powder agar-translucency (HoPAT) test and horn zymography (HZ). Using routine bacteriological techniques and these methods, we isolated five strains of keratolytic soil bacteria, which were then identified by means of 16S ribosomal RNA (rRNA) gene sequencing analysis. The findings from the study on the horse suggested that Brevibacterium luteolum played the main role in the local fragility of the hoof, eventually forming a Gidoh in coordination with four other strains of keratolytic bacteria. The double screening procedures of the HoPAT test and HZ were useful and easy techniques for isolating the keratolytic bacteria from the horn lesions. PMID:28400703

A new analytical platform based on field-flow fractionation and olfactory sensor to improve the detection of viable and non-viable bacteria in food.

PubMed

Roda, Barbara; Mirasoli, Mara; Zattoni, Andrea; Casale, Monica; Oliveri, Paolo; Bigi, Alessandro; Reschiglian, Pierluigi; Simoni, Patrizia; Roda, Aldo

2016-10-01

An integrated sensing system is presented for the first time, where a metal oxide semiconductor sensor-based electronic olfactory system (MOS array), employed for pathogen bacteria identification based on their volatile organic compound (VOC) characterisation, is assisted by a preliminary separative technique based on gravitational field-flow fractionation (GrFFF). In the integrated system, a preliminary step using GrFFF fractionation of a complex sample provided bacteria-enriched fractions readily available for subsequent MOS array analysis. The MOS array signals were then analysed employing a chemometric approach using principal components analysis (PCA) for a first-data exploration, followed by linear discriminant analysis (LDA) as a classification tool, using the PCA scores as input variables. The ability of the GrFFF-MOS system to distinguish between viable and non-viable cells of the same strain was demonstrated for the first time, yielding 100 % ability of correct prediction. The integrated system was also applied as a proof of concept for multianalyte purposes, for the detection of two bacterial strains (Escherichia coli O157:H7 and Yersinia enterocolitica) simultaneously present in artificially contaminated milk samples, obtaining a 100 % ability of correct prediction. Acquired results show that GrFFF band slicing before MOS array analysis can significantly increase reliability and reproducibility of pathogen bacteria identification based on their VOC production, simplifying the analytical procedure and largely eliminating sample matrix effects. The developed GrFFF-MOS integrated system can be considered a simple straightforward approach for pathogen bacteria identification directly from their food matrix. Graphical abstract An integrated sensing system is presented for pathogen bacteria identification in food, in which field-flow fractionation is exploited to prepare enriched cell fractions prior to their analysis by electronic olfactory system

Base excitation testing system using spring elements to pivotally mount wind turbine blades

DOEpatents

Cotrell, Jason; Hughes, Scott; Butterfield, Sandy; Lambert, Scott

2013-12-10

A system (1100) for fatigue testing wind turbine blades (1102) through forced or resonant excitation of the base (1104) of a blade (1102). The system (1100) includes a test stand (1112) and a restoring spring assembly (1120) mounted on the test stand (1112). The restoring spring assembly (1120) includes a primary spring element (1124) that extends outward from the test stand (1112) to a blade mounting plate (1130) configured to receive a base (1104) of blade (1102). During fatigue testing, a supported base (1104) of a blad (1102) may be pivotally mounted to the test stand (1112) via the restoring spring assembly (1120). The system (1100) may include an excitation input assembly (1140) that is interconnected with the blade mouting plate (1130) to selectively apply flapwise, edgewise, and/or pitch excitation forces. The restoring spring assemply (1120) may include at least one tuning spring member (1127) positioned adjacent to the primary spring element (1124) used to tune the spring constant or stiffness of the primary spring element (1124) in one of the excitation directions.

Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria

USDA-ARS?s Scientific Manuscript database

The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater- and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hotspot for pr...

Evolutionary Genomics of Defense Systems in Archaea and Bacteria*

PubMed Central

Koonin, Eugene V.; Makarova, Kira S.; Wolf, Yuri I.

2018-01-01

Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death. PMID:28657885

A lysozyme and magnetic bead based method of separating intact bacteria.

PubMed

Diler, Ebru; Obst, Ursula; Schmitz, Katja; Schwartz, Thomas

2011-07-01

As a response to environmental stress, bacterial cells can enter a physiological state called viable but noncultivable (VBNC). In this state, bacteria fail to grow on routine bacteriological media. Consequently, standard methods of contamination detection based on bacteria cultivation fail. Although they are not growing, the cells are still alive and are able to reactivate their metabolism. The VBNC state and low bacterial densities are big challenges for cultivation-based pathogen detection in drinking water and the food industry, for example. In this context, a new molecular-biological separation method for bacteria using point-mutated lysozymes immobilised on magnetic beads for separating bacteria is described. The immobilised mutated lysozymes on magnetic beads serve as bait for the specific capture of bacteria from complex matrices or water due to their remaining affinity for bacterial cell wall components. Beads with bacteria can be separated using magnetic racks. To avoid bacterial cell lysis by the lysozymes, the protein was mutated at amino acid position 35, leading to the exchange of the catalytic glutamate for alanine (LysE35A) and glutamine (LysE35Q). As proved by turbidity assay with reference bacteria, the muramidase activity was knocked out. The mutated constructs were expressed by the yeast Pichia pastoris and secreted into expression medium. Protein enrichment and purification were carried out by SO(3)-functionalised nanoscale cationic exchanger particles. For a proof of principle, the proteins were biotinylated and immobilised on streptavidin-functionalised, fluorescence dye-labelled magnetic beads. These constructs were used for the successful capture of Syto9-marked Microccocus luteus cells from cell suspension, as visualised by fluorescence microscopy, which confirmed the success of the strategy.

Implementing and testing a fiber-optic polarization-based intrusion detection system

NASA Astrophysics Data System (ADS)

Hajj, Rasha El; MacDonald, Gregory; Verma, Pramode; Huck, Robert

2015-09-01

We describe a layer-1-based intrusion detection system for fiber-optic-based networks. Layer-1-based intrusion detection represents a significant elevation in security as it prohibits an adversary from obtaining information in the first place (no cryptanalysis is possible). We describe the experimental setup of the intrusion detection system, which is based on monitoring the behavior of certain attributes of light both in unperturbed and perturbed optical fiber links. The system was tested with optical fiber links of various lengths and types, under different environmental conditions, and under changes in fiber geometry similar to what is experienced during tapping activity. Comparison of the results for perturbed and unperturbed links has shown that the state of polarization is more sensitive to intrusion activity than the degree of polarization or power of the received light. The testing was conducted in a simulated telecommunication network environment that included both underground and aerial links. The links were monitored for intrusion activity. Attempts to tap the link were easily detected with no apparent degradation in the visual quality of the real-time surveillance video.

Laser-Based Identification of Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Rehse, Steven J.

2009-03-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the last 10 years, however, several events have occurred that demand the attention of the general populace — including the ranks of physicists among them.

Multiplex Identification of Gram-Positive Bacteria and Resistance Determinants Directly from Positive Blood Culture Broths: Evaluation of an Automated Microarray-Based Nucleic Acid Test

PubMed Central

Buchan, Blake W.; Ginocchio, Christine C.; Manii, Ryhana; Cavagnolo, Robert; Pancholi, Preeti; Swyers, Lettie; Thomson, Richard B.; Anderson, Christopher; Kaul, Karen; Ledeboer, Nathan A.

2013-01-01

Background A multicenter study was conducted to evaluate the diagnostic accuracy (sensitivity and specificity) of the Verigene Gram-Positive Blood Culture Test (BC-GP) test to identify 12 Gram-positive bacterial gene targets and three genetic resistance determinants directly from positive blood culture broths containing Gram-positive bacteria. Methods and Findings 1,252 blood cultures containing Gram-positive bacteria were prospectively collected and tested at five clinical centers between April, 2011 and January, 2012. An additional 387 contrived blood cultures containing uncommon targets (e.g., Listeria spp., S. lugdunensis, vanB-positive Enterococci) were included to fully evaluate the performance of the BC-GP test. Sensitivity and specificity for the 12 specific genus or species targets identified by the BC-GP test ranged from 92.6%–100% and 95.4%–100%, respectively. Identification of the mecA gene in 599 cultures containing S. aureus or S. epidermidis was 98.6% sensitive and 94.3% specific compared to cefoxitin disk method. Identification of the vanA gene in 81 cultures containing Enterococcus faecium or E. faecalis was 100% sensitive and specific. Approximately 7.5% (87/1,157) of single-organism cultures contained Gram-positive bacteria not present on the BC-GP test panel. In 95 cultures containing multiple organisms the BC-GP test was in 71.6% (68/95) agreement with culture results. Retrospective analysis of 107 separate blood cultures demonstrated that identification of methicillin resistant S. aureus and vancomycin resistant Enterococcus spp. was completed an average of 41.8 to 42.4 h earlier using the BC-GP test compared to routine culture methods. The BC-GP test was unable to assign mecA to a specific organism in cultures containing more than one Staphylococcus isolate and does not identify common blood culture contaminants such as Micrococcus, Corynebacterium, and Bacillus. Conclusions The BC-GP test is a multiplex test capable of detecting most

High-throughput living cell-based optical biosensor for detection of bacterial lipopolysaccharide (LPS) using a red fluorescent protein reporter system.

PubMed

Jiang, Hui; Jiang, Donglei; Shao, Jingdong; Sun, Xiulan; Wang, Jiasheng

2016-11-14

Due to the high toxicity of bacterial lipopolysaccharide (LPS), resulting in sepsis and septic shock, two major causes of death worldwide, significant effort is directed toward the development of specific trace-level LPS detection systems. Here, we report sensitive, user-friendly, high-throughput LPS detection in a 96-well microplate using a transcriptional biosensor system, based on 293/hTLR4A-MD2-CD14 cells that are transformed by a red fluorescent protein (mCherry) gene under the transcriptional control of an NF-κB response element. The recognition of LPS activates the biosensor cell, TLR4, and the co-receptor-induced NF-κB signaling pathway, which results in the expression of mCherry fluorescent protein. The novel cell-based biosensor detects LPS with specificity at low concentration. The cell-based biosensor was evaluated by testing LPS isolated from 14 bacteria. Of the tested bacteria, 13 isolated Enterobacteraceous LPSs with hexa-acylated structures were found to increase red fluorescence and one penta-acylated LPS from Pseudomonadaceae appeared less potent. The proposed biosensor has potential for use in the LPS detection in foodstuff and biological products, as well as bacteria identification, assisting the control of foodborne diseases.

Microfluidic Transducer for Detecting Nanomechanical Movements of Bacteria

NASA Astrophysics Data System (ADS)

Kara, Vural; Ekinci, Kamil

2017-11-01

Various nanomechanical movements of bacteria are currently being explored as an indication of bacterial viability. Most notably, these movements have been observed to subside rapidly and dramatically when the bacteria are exposed to an effective antibiotic. This suggests that monitoring bacterial movements, if performed with high fidelity, can offer a path to various clinical microbiological applications, including antibiotic susceptibility tests. Here, we introduce a robust and sensitive microfluidic transduction technique for detecting the nanomechanical movements of bacteria. The technique is based on measuring the electrical fluctuations in a microchannel which the bacteria populate. These electrical fluctuations are caused by the swimming of motile, planktonic bacteria and random oscillations of surface-immobilized bacteria. The technique provides enough sensitivity to detect even the slightest movements of a single cell and lends itself to smooth integration with other microfluidic methods and devices; it may eventually be used for rapid antibiotic susceptibility testing. We acknowledge support from Boston University Office of Technology Development, Boston University College of Engineering, NIH (1R03AI126168-01) and The Wallace H. Coulter Foundation.

Evaluation of conventional, protaper hand and protaper rotary instrumentation system for apical extrusion of debris, irrigants and bacteria- An in vitro randomized trial

PubMed Central

Kalra, Pinky; Suman, Ethel; Shenoy, Ramya; Suprabha, Baranya-Shrikrishna

2017-01-01

Background Endodontic instrumentation carries the risk of over extrusion of debris and bacteria. The technique used and the type of instrumentation influences this risk. Aim The purpose of this study was to evaluate and compare the K-file, ProTaper hand and ProTaper rotary instrumentation systems for the amount of apically extruded debris, irrigant solution and intracanal bacteria. Design Experimental single blinded randomized type of in vitro study with sample of 30 single rooted teeth. Endodontic access cavities were prepared and the root canals were filled with the suspension of E. faecalis. Myers and Montogomery Model was used to collect apically extruded debris and irrigant. Canals were prepared using K files, Hand protapers and Protaper rotary files. Statistical analysis Non Parametric test like Kruskal-Wallis and Mann-Whitney U test were applied to determine the significant differences among the group. Results Tests revealed statistically significant difference between the amount of debris and number of bacteria extruded by the ProTaper hand and the K-files. No statistically significant difference was observed between the amounts of irrigant extruded by the ProTaper hand and the K-file system. Statistically significant differences were observed between the amounts of bacteria and irrigant extruded by the ProTaper rotary and the Protaper hand. No statistically significant difference was observed between the amounts of debris extruded by the ProTaper hand and the K-file system. Conclusions Amount of apical extrusion of irrigant solution, bacteria and debris are significantly greater with K File instruments and least with Protaper rotary instruments. Key words:Protaper, rotary, periapical extrusion. PMID:28210445

Bacteria and Composite Particles in the Glacier-Fed Systems of British Columbia and Alberta, Canada

NASA Astrophysics Data System (ADS)

Barrett, D. C.; Hodder, K. R.

2014-12-01

In controlled environments, bacteria and suspended sediment particles are linked via the creation of a composite structure ("bacteria-sediment associations"; BSA), with associated effects on size, density and hydrodynamics. However, the presence of these particles, and their corresponding effect on sedimentary processes is not well documented in many environments. Here, we compile field data from 20 glacier-fed systems in British Columbia and Alberta, Canada, to illustrate: 1) the presence, and (quantity) of bacteria-sediment associations; 2) the presence of in-situ composite particles and their associated settling velocities; 3) the simulated impact of bacteria-sediment associations on settling velocity via controlled manipulation in the laboratory. In general, a significant portion of the fine suspended sediment typical of these systems was associated with bacteria and/or present in a composite-form -- not as primary, individual particles. Four key findings include: 1) Along a 80 kilometre river transect, up to 40% of bacteria were associated with sediment particles; 2) Manipulation of bacteria concentration in the laboratory has revealed a positive relationship between sediment settling velocity, creation of composite particles and bacteria concentration; 3) Composite particles dominated the suspended sediment load among all 20 systems, especially for larger particles; and 4) Measurements reveal these composite particles are settling at rates significantly below that predicted by Stokes Law. The formation of composite particles is especially important in lakes where laminated sediments are used for paleoenvironmental reconstruction (varved), as bacteria can modulate the rate at which some of this sediment reaches the lake floor. These results highlight the importance of bacteria in Earth surface processes and, more specifically, the sediment dynamics within glacier-fed systems.

Molecular Diagnostic for Prospecting Polyhydroxyalkanoate-Producing Bacteria.

PubMed

Montenegro, Eduarda Morgana da Silva; Delabary, Gabriela Scholante; Silva, Marcus Adonai Castro da; Andreote, Fernando Dini; Lima, André Oliveira de Souza

2017-05-25

The use of molecular diagnostic techniques for bioprospecting and microbial diversity study purposes has gained more attention thanks to their functionality, low cost and quick results. In this context, ten degenerate primers were designed for the amplification of polyhydroxyalkanoate synthase ( phaC ) gene, which is involved in the production of polyhydroxyalkanoate (PHA)-a biodegradable, renewable biopolymer. Primers were designed based on multiple alignments of phaC gene sequences from 218 species that have their genomes already analyzed and deposited at Biocyc databank. The combination of oligos phaCF3/phaCR1 allowed the amplification of the expected product (PHA synthases families types I and IV) from reference organisms used as positive control (PHA producer). The method was also tested in a multiplex system with two combinations of initiators, using 16 colonies of marine bacteria (pre-characterized for PHA production) as a DNA template. All amplicon positive organisms ( n = 9) were also PHA producers, thus no false positives were observed. Amplified DNA was sequenced ( n = 4), allowing for the confirmation of the pha C gene identity as well its diversity among marine bacteria. Primers were also tested for screening purposes using 37 colonies from six different environments. Almost 30% of the organisms presented the target amplicon. Thus, the proposed primers are an efficient tool for screening bacteria with potential for the production of PHA as well to study PHA genetic diversity.

Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems.

PubMed

Duedu, Kwabena O; French, Christopher E

2017-04-01

Monitoring bacterial growth is an important technique required for many applications such as testing bacteria against compounds (e.g. drugs), evaluating bacterial composition in the environment (e.g. sewage and wastewater or food suspensions) and testing engineered bacteria for various functions (e.g. cellulose degradation). T?=1,^FigItem(1) ^ReloadFigure=Yesraditionally, rapid estimation of bacterial growth is performed using spectrophotometric measurement at 600nm (OD600) but this estimation does not differentiate live and dead cells or other debris. Colony counting enumerates live cells but the process is laborious and not suitable for large numbers of samples. Enumeration of live bacteria by flow cytometry is a more suitable rapid method with the use of dual staining with SYBR I Green nucleic acid gel stain and Propidium Iodide (SYBR-I/PI). Flow cytometry equipment and maintenance costs however are relatively high and this technique is unavailable in many laboratories that may require a rapid method for evaluating bacteria growth. We therefore sought to adapt and evaluate the SYBR-I/PI technique of enumerating live bacterial cells for a cheaper platform, a fluorimeter. The fluorimetry adapted SYBR-I/PI enumeration of bacteria in turbid growth media had direct correlations with OD600 (p>0.001). To enable comparison of fluorescence results across labs and instruments, a fluorescence intensity standard unit, the equivalent fluorescent DNA (EFD) was proposed, evaluated and found useful. The technique was further evaluated for its usefulness in enumerating bacteria in turbid media containing insoluble particles. Reproducible results were obtained which OD600 could not give. An alternative method based on the assessment of total protein using the Pierce Coomassie Plus (Bradford) Assay was also evaluated and compared. In all, the SYBR-I/PI method was found to be the quickest and most reliable. The protocol is potentially useful for high-throughput applications such as

A broad-host range dual-fluorescence reporter system for gene expression analysis in Gram-negative bacteria.

PubMed

Hennessy, Rosanna C; Christiansen, Line; Olsson, Stefan; Stougaard, Peter

2018-01-01

Fluorescence-based reporter systems are valuable tools for studying gene expression dynamics in living cells. Here we describe a dual-fluorescence reporter system carrying the red fluorescent marker mCherry and the blue fluorescent protein EBFP2 enabling the simultaneous analysis of two promoters in broad-host range autofluorescent Gram-negative bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid Bead-Based Antimicrobial Susceptibility Testing by Optical Diffusometry

PubMed Central

Chung, Chih-Yao; Wang, Jhih-Cheng; Chuang, Han-Sheng

2016-01-01

This study combined optical diffusometry and bead-based immunoassays to develop a novel technique for quantifying the growth of specific microorganisms and achieving rapid AST. Diffusivity rises when live bacteria attach to particles, resulting in additional energy from motile microorganisms. However, when UV-sterilized (dead) bacteria attach to particles, diffusivity declines. The experimental data are consistent with the theoretical model predicted according to the equivalent volume diameter. Using this diffusometric platform, the susceptibility of Pseudomonas aeruginosa to the antibiotic gentamicin was tested. The result suggests that the proliferation of bacteria is effectively controlled by gentamicin. This study demonstrated a sensitive (one bacterium on single particles) and time-saving (within 2 h) platform with a small sample volume (~0.5 μL) and a low initial bacteria count (50 CFU per droplet ~ 105 CFU/mL) for quantifying the growth of microorganisms depending on Brownian motion. The technique can be applied further to other bacterial strains and increase the success of treatments against infectious diseases in the near future. PMID:26863001

Safety impact of an integrated crash warning system based on field test data.

DOT National Transportation Integrated Search

2011-06-13

This paper provides the results of an analysis : conducted to assess the safety impact of an integrated : vehicle-based crash warning system based on : naturalistic driving data collected from a field : operational test. The system incorporates four ...

The isolation and identification of endophytic bacteria from mangrove (Sonneratia alba) that produces gelatinase

NASA Astrophysics Data System (ADS)

Nursyam, H.; Prihanto, A. A.; Warasari, N. I.; Saadah, M.; Masrifa, R. E.; Nabila, N. A.; Istiqfarin, N.; Siddiq, I. J.

2018-04-01

Gelatinase is an enzyme that hydrolyze gelatin into gelatin hydrolyzate. The purpose of this study was to isolate and to identify endophytic bacteria from Sonneratia alba mangrove which able to produce gelatinase enzyme. Sonneratia alba mangroves was obtained from Bajul Mati Beach, Malang Regency. The samples in this study were, stems, and leaves. Pure cultured bacteria were investigated for its capability for producing gelatinase enzyme by using gelatin media. Best producer would further be analyzed its species using microbact system. Screening process resulted in 3 positive isolates, namely code isolate of R, B, and L. R which was isolate from root of S. alba was the best producer for gelatinase. Identification process with morphology and microbact system revelaed that A. SBM is a Gram-negative bacterium that has a basil cell shape, with a diameter colony of 2.19 mm. Based on the microbact system test carried out, the bacteria is Pseudomonas aeruginosa.

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks.

PubMed

Amanidaz, Nazak; Zafarzadeh, Ali; Mahvi, Amir Hossein

2015-12-01

This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms.

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks

PubMed Central

AMANIDAZ, Nazak; ZAFARZADEH, Ali; MAHVI, Amir Hossein

2015-01-01

Background: This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. Methods: This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. Results: In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Conclusion: Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms. PMID:26811820

Testing primates with joystick-based automated apparatus - Lessons from the Language Research Center's Computerized Test System

NASA Technical Reports Server (NTRS)

Washburn, David A.; Rumbaugh, Duane M.

1992-01-01

Nonhuman primates provide useful models for studying a variety of medical, biological, and behavioral topics. Four years of joystick-based automated testing of monkeys using the Language Research Center's Computerized Test System (LRC-CTS) are examined to derive hints and principles for comparable testing with other species - including humans. The results of multiple parametric studies are reviewed, and reliability data are presented to reveal the surprises and pitfalls associated with video-task testing of performance.

The yield and decay coefficients of exoelectrogenic bacteria in bioelectrochemical systems.

PubMed

Wilson, Erica L; Kim, Younggy

2016-05-01

In conventional wastewater treatment, waste sludge management and disposal contribute the major cost for wastewater treatment. Bioelectrochemical systems, as a potential alternative for future wastewater treatment and resources recovery, are expected to produce small amounts of waste sludge because exoelectrogenic bacteria grow on anaerobic respiration and form highly populated biofilms on bioanode surfaces. While waste sludge production is governed by the yield and decay coefficient, none of previous studies have quantified these kinetic constants for exoelectrogenic bacteria. For yield coefficient estimation, we modified McCarty's free energy-based model by using the bioanode potential for the free energy of the electron acceptor reaction. The estimated true yield coefficient ranged 0.1 to 0.3 g-VSS (volatile suspended solids) g-COD(-1) (chemical oxygen demand), which is similar to that of most anaerobic microorganisms. The yield coefficient was sensitively affected by the bioanode potential and pH while the substrate and bicarbonate concentrations had relatively minor effects on the yield coefficient. In lab-scale experiments using microbial electrolysis cells, the observed yield coefficient (including the effect of cell decay) was found to be 0.020 ± 0.008 g-VSS g-COD(-1), which is an order of magnitude smaller than the theoretical estimation. Based on the difference between the theoretical and experimental results, the decay coefficient was approximated to be 0.013 ± 0.002 d(-1). These findings indicate that bioelectrochemical systems have potential for future wastewater treatment with reduced waste sludge as well as for resources recovery. Also, the found kinetic information will allow accurate estimation of wastewater treatment performance in bioelectrochemical systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Motility analysis of bacteria-based microrobot (bacteriobot) using chemical gradient microchamber.

PubMed

Park, Daechul; Park, Sung Jun; Cho, Sunghoon; Lee, Yeonkyung; Lee, Yu Kyung; Min, Jung-Joon; Park, Bang Ju; Ko, Seong Young; Park, Jong-Oh; Park, Sukho

2014-01-01

A bacteria-based microrobot (bacteriobot) was proposed and investigated as a new type of active drug delivery system because of its useful advantages, such as active tumor targeting, bacteria-mediated tumor diagnosis, and therapy. In this study, we fabricated a bacteriobot with enhanced motility by selective attachment of flagellar bacteria (Salmonella typhimurium). Through selective bovine serum albumin (BSA) pattering on hydrophobic polystyrene (PS) microbeads, many S. typhimurium could be selectively attached only on the unpatterned surface of PS microbead. For the evaluation of the chemotactic motility of the bacteriobot, we developed a microfluidic chamber which can generate a stable concentration gradient of bacterial chemotactic chemicals. Prior to the evaluation of the bacteriobot, we first evaluated the directional chemotactic motility of S. typhimurium using the proposed microfluidic chamber, which contained a bacterial chemo-attractant (L-aspartic acid) and a chemo-repellent (NiSO4 ), respectively. Compared to density of the control group in the microfluidic chamber without any chemical gradient, S. typhimurium increased by about 16% in the L-aspartic acid gradient region and decreased by about 22% in the NiSO4 gradient region. Second, we evaluated the bacteriobot's directional motility by using this microfluidic chamber. The chemotactic directional motility of the bacteriobot increased by 14% and decreased by 13% in the concentration gradients of L-aspartic acid and NiSO4 , respectively. These results confirm that the bacteriobot with selectively patterned S. typhimurium shows chemotaxis motility very similar to that of S. typhimurium. Moreover, the directional motilities of the bacteria and bacteriobot could be demonstrated quantitatively through the proposed microfluidic chamber. © 2013 Wiley Periodicals, Inc.

Antibacterial activity of sphingoid bases and fatty acids against Gram-positive and Gram-negative bacteria.

PubMed

Fischer, Carol L; Drake, David R; Dawson, Deborah V; Blanchette, Derek R; Brogden, Kim A; Wertz, Philip W

2012-03-01

There is growing evidence that the role of lipids in innate immunity is more important than previously realized. How lipids interact with bacteria to achieve a level of protection, however, is still poorly understood. To begin to address the mechanisms of antibacterial activity, we determined MICs and minimum bactericidal concentrations (MBCs) of lipids common to the skin and oral cavity--the sphingoid bases D-sphingosine, phytosphingosine, and dihydrosphingosine and the fatty acids sapienic acid and lauric acid--against four Gram-negative bacteria and seven Gram-positive bacteria. Exact Kruskal-Wallis tests of these values showed differences among lipid treatments (P < 0.0001) for each bacterial species except Serratia marcescens and Pseudomonas aeruginosa. D-sphingosine (MBC range, 0.3 to 19.6 μg/ml), dihydrosphingosine (MBC range, 0.6 to 39.1 μg/ml), and phytosphingosine (MBC range, 3.3 to 62.5 μg/ml) were active against all bacteria except S. marcescens and P. aeruginosa (MBC > 500 μg/ml). Sapienic acid (MBC range, 31.3 to 375.0 μg/ml) was active against Streptococcus sanguinis, Streptococcus mitis, and Fusobacterium nucleatum but not active against Escherichia coli, Staphylococcus aureus, S. marcescens, P. aeruginosa, Corynebacterium bovis, Corynebacterium striatum, and Corynebacterium jeikeium (MBC > 500 μg/ml). Lauric acid (MBC range, 6.8 to 375.0 μg/ml) was active against all bacteria except E. coli, S. marcescens, and P. aeruginosa (MBC > 500 μg/ml). Complete killing was achieved as early as 0.5 h for some lipids but took as long as 24 h for others. Hence, sphingoid bases and fatty acids have different antibacterial activities and may have potential for prophylactic or therapeutic intervention in infection.

Osmosensing by Bacteria: Signals and Membrane-Based Sensors

PubMed Central

Wood, Janet M.

1999-01-01

Bacteria can survive dramatic osmotic shifts. Osmoregulatory responses mitigate the passive adjustments in cell structure and the growth inhibition that may ensue. The levels of certain cytoplasmic solutes rise and fall in response to increases and decreases, respectively, in extracellular osmolality. Certain organic compounds are favored over ions as osmoregulatory solutes, although K+ fluxes are intrinsic to the osmoregulatory response for at least some organisms. Osmosensors must undergo transitions between “off” and “on” conformations in response to changes in extracellular water activity (direct osmosensing) or resulting changes in cell structure (indirect osmosensing). Those located in the cytoplasmic membranes and nucleoids of bacteria are positioned for indirect osmosensing. Cytoplasmic membrane-based osmosensors may detect changes in the periplasmic and/or cytoplasmic solvent by experiencing changes in preferential interactions with particular solvent constituents, cosolvent-induced hydration changes, and/or macromolecular crowding. Alternatively, the membrane may act as an antenna and osmosensors may detect changes in membrane structure. Cosolvents may modulate intrinsic biomembrane strain and/or topologically closed membrane systems may experience changes in mechanical strain in response to imposed osmotic shifts. The osmosensory mechanisms controlling membrane-based K+ transporters, transcriptional regulators, osmoprotectant transporters, and mechanosensitive channels intrinsic to the cytoplasmic membrane of Escherichia coli are under intensive investigation. The osmoprotectant transporter ProP and channel MscL act as osmosensors after purification and reconstitution in proteoliposomes. Evidence that sensor kinase KdpD receives multiple sensory inputs is consistent with the effects of K+ fluxes on nucleoid structure, cellular energetics, cytoplasmic ionic strength, and ion composition as well as on cytoplasmic osmolality. Thus, osmoregulatory

PATHOGENICITY OF BIOFILM BACTERIA

EPA Science Inventory

There is a paucity of information concerning any link between the microorganisms commonly found in biofilms of drinking water systems and their impacts on human health. For bacteria, culture-based techniques detect only a limited number of the total microorganisms associated wit...

Improved fermentation performance in an expanded ectopic fermentation system inoculated with thermophilic bacteria.

PubMed

Guo, Hui; Zhu, Changxiong; Geng, Bing; Liu, Xue; Ye, Jing; Tian, Yunlong; Peng, Xiawei

2015-12-01

Previous research showed that ectopic fermentation system (EFS) inoculated with thermophilic bacteria is an excellent alternative for cow wastewater treatment. In this study, the effects of thermophilic bacterial consortium on the efficiency and quality of the fermentation process in EFS were evaluated by measuring physicochemical and environmental factors and the changes in organic matter composition. In parallel, the microbial communities correlated with fermentation performance were identified. Inoculation of EFS with thermophilic bacterial consortium led to higher temperatures, increased wastewater requirements for continuous fermentation, and improved quality of the litters in terms of physicochemical factors, security test, functional group analysis, and bacterial community composition. The relationship between the transformation of organic component and the dominant bacteria species indicated that environmental factors contributed to strain growth, which subsequently promoted the fermentation process. The results highlight the great potential of EFS model for wide application in cow wastewater treatment and re-utilization as bio-fertilizer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Uniformity testing: assessment of a centralized web-based uniformity analysis system.

PubMed

Klempa, Meaghan C

2011-06-01

Uniformity testing is performed daily to ensure adequate camera performance before clinical use. The aim of this study is to assess the reliability of Beth Israel Deaconess Medical Center's locally built, centralized, Web-based uniformity analysis system by examining the differences between manufacturer and Web-based National Electrical Manufacturers Association integral uniformity calculations measured in the useful field of view (FOV) and the central FOV. Manufacturer and Web-based integral uniformity calculations measured in the useful FOV and the central FOV were recorded over a 30-d period for 4 cameras from 3 different manufacturers. These data were then statistically analyzed. The differences between the uniformity calculations were computed, in addition to the means and the SDs of these differences for each head of each camera. There was a correlation between the manufacturer and Web-based integral uniformity calculations in the useful FOV and the central FOV over the 30-d period. The average differences between the manufacturer and Web-based useful FOV calculations ranged from -0.30 to 0.099, with SD ranging from 0.092 to 0.32. For the central FOV calculations, the average differences ranged from -0.163 to 0.055, with SD ranging from 0.074 to 0.24. Most of the uniformity calculations computed by this centralized Web-based uniformity analysis system are comparable to the manufacturers' calculations, suggesting that this system is reasonably reliable and effective. This finding is important because centralized Web-based uniformity analysis systems are advantageous in that they test camera performance in the same manner regardless of the manufacturer.

Experiences with establishing and implementing learning management system and computer-based test system in medical college.

PubMed

Park, Joo Hyun; Son, Ji Young; Kim, Sun

2012-09-01

The purpose of this study was to establish an e-learning system to support learning in medical education and identify solutions for improving the system. A learning management system (LMS) and computer-based test (CBT) system were established to support e-learning for medical students. A survey of 219 first- and second-grade medical students was administered. The questionnaire included 9 forced choice questions about the usability of system and 2 open-ended questions about necessary improvements to the system. The LMS consisted of a class management, class evaluation, and class attendance system. CBT consisted of a test management, item bank, and authoring tool system. The results of the survey showed a high level of satisfaction in all system usability items except for stability. Further, the advantages of the e-learning system were ensuring information accessibility, providing constant feedback, and designing an intuitive interface. Necessary improvements to the system were stability, user control, readability, and diverse device usage. Based on the findings, suggestions for developing an e-learning system to improve usability by medical students and support learning effectively are recommended.

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

PubMed

Ibarra-Arellano, Miguel A; Campos-González, Adrián I; Treviño-Quintanilla, Luis G; Tauch, Andreas; Freyre-González, Julio A

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy ( A: cross- BA: cteria SY: stems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing

Protein secretion and membrane insertion systems in gram-negative bacteria.

PubMed

Saier, Milton H

2006-01-01

In contrast to other organisms, gram-negative bacteria have evolved numerous systems for protein export. Eight types are known that mediate export across or insertion into the cytoplasmic membrane, while eight specifically mediate export across or insertion into the outer membrane. Three of the former secretory pathway (SP) systems, type I SP (ISP, ABC), IIISP (Fla/Path) and IVSP (Conj/Vir), can export proteins across both membranes in a single energy-coupled step. A fourth generalized mechanism for exporting proteins across the two-membrane envelope in two distinct steps (which we here refer to as type II secretory pathways [IISP]) utilizes either the general secretory pathway (GSP or Sec) or the twin-arginine targeting translocase for translocation across the inner membrane, and either the main terminal branch or one of several protein-specific export systems for translocation across the outer membrane. We here survey the various well-characterized protein translocation systems found in living organisms and then focus on the systems present in gram-negative bacteria. Comparisons between these systems suggest specific biogenic, mechanistic and evolutionary similarities as well as major differences.

A new rapid method for direct antimicrobial susceptibility testing of bacteria from positive blood cultures.

PubMed

Barnini, Simona; Brucculeri, Veronica; Morici, Paola; Ghelardi, Emilia; Florio, Walter; Lupetti, Antonella

2016-08-12

Rapid identification and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections can lead to prompt appropriate antimicrobial therapy. To shorten species identification, in this study bacteria were recovered from monomicrobial blood cultures by serum separator tubes and spotted onto the target plate for direct MALDI-TOF MS identification. Proper antibiotics were selected for direct AST based on species identification. In order to obtain rapid AST results, bacteria were recovered from positive blood cultures by two different protocols: by serum separator tubes (further referred to as PR1), or after a short-term subculture in liquid medium (further referred to as PR2). The results were compared with those obtained by the method currently used in our laboratory consisting in identification by MALDI-TOF and AST by Vitek 2 or Sensititre on isolated colonies. The direct MALDI-TOF method concordantly identified with the current method 97.5 % of the Gram-negative bacteria and 96.1 % of the Gram-positive cocci contained in monomicrobial blood cultures. The direct AST by PR1 and PR2 for all isolate/antimicrobial agent combinations was concordant/correct with the current method for 87.8 and 90.5 % of Gram-negative bacteria and for 93.1 and 93.8 % of Gram-positive cocci, respectively. In particular, 100 % categorical agreement was found with levofloxacin for Enterobacteriaceae by both PR1 and PR2, and 99.0 and 100 % categorical agreement was observed with linezolid for Gram-positive cocci by PR1 and PR2, respectively. There was no significant difference in accuracy between PR1 and PR2 for Gram-negative bacteria and Gram-positive cocci. This newly described method seems promising for providing accurate AST results. Most importantly, these results would be available in a few hours from blood culture positivity, which would help clinicians to promptly confirm or streamline an effective antibiotic therapy in patients with bloodstream

A novel, multiplex, real-time PCR-based approach for the detection of the commonly occurring pathogenic fungi and bacteria.

PubMed

Horváth, Ádám; Pető, Zoltán; Urbán, Edit; Vágvölgyi, Csaba; Somogyvári, Ferenc

2013-12-23

Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified.The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections. A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons.With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube. This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.

Standoff detection: distinction of bacteria by hyperspectral laser induced fluorescence

NASA Astrophysics Data System (ADS)

Walter, Arne; Duschek, Frank; Fellner, Lea; Grünewald, Karin M.; Hausmann, Anita; Julich, Sandra; Pargmann, Carsten; Tomaso, Herbert; Handke, Jürgen

2016-05-01

Sensitive detection and rapid identification of hazardous bioorganic material with high sensitivity and specificity are essential topics for defense and security. A single method can hardly cover these requirements. While point sensors allow a highly specific identification, they only provide localized information and are comparatively slow. Laser based standoff systems allow almost real-time detection and classification of potentially hazardous material in a wide area and can provide information on how the aerosol may spread. The coupling of both methods may be a promising solution to optimize the acquisition and identification of hazardous substances. The capability of the outdoor LIF system at DLR Lampoldshausen test facility as an online classification tool has already been demonstrated. Here, we present promising data for further differentiation among bacteria. Bacteria species can express unique fluorescence spectra after excitation at 280 nm and 355 nm. Upon deactivation, the spectral features change depending on the deactivation method.

Propolis--based chitosan varnish: drug delivery, controlled release and antimicrobial activity against oral pathogen bacteria.

PubMed

Franca, Juçara R; De Luca, Mariana P; Ribeiro, Tatiana G; Castilho, Rachel O; Moreira, Allyson N; Santos, Vagner R; Faraco, André A G

2014-12-12

Dental caries is the most prevalent oral disease in several Asian and Latin American countries. It is an infectious disease and different types of bacteria are involved in the process. Synthetic antimicrobials are used against this disease; however, many of these substances cause unwarranted undesirable effects like vomiting, diarrhea and tooth staining. Propolis, a resinous substance collected by honeybees, has been used to control the oral microbiota. So, the objective of this study was to develop and characterize sustained-release propolis-based chitosan varnish useful on dental cariogenic biofilm prevention, besides the in vitro antimicrobial activity. Three formulations of propolis - based chitosan varnish (PCV) containing different concentrations (5%, 10% and 15%) were produced by dissolution of propolis with chitosan on hydro-alcoholic vehicle. Bovine teeth were used for testing adhesion of coatings and to observe the controlled release of propolis associated with varnish. It was characterized by infrared spectroscopy, scanning electron microscopy, casting time, diffusion test in vitro antimicrobial activity and controlled release. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were tested for the main microorganisms involved in the cariogenic biofilm through the microdilution test in 96-well plates. The formulations presented a tooth surface adherence and were able to form films very fast on bovine tooth surface. Also, propolis-based chitosan varnishes have shown antimicrobial activity similar to or better than chlorhexidine varnish against all oral pathogen bacteria. All microorganisms were sensitive to propolis varnish and chitosan. MIC and MBC for microorganisms of cariogenic biofilme showed better results than chlorhexidine. Propolis active components were released for more than one week. All developed formulations turn them, 5%, 10% and 15% propolis content varnish, into products suitable for clinical application on

Design of video processing and testing system based on DSP and FPGA

NASA Astrophysics Data System (ADS)

Xu, Hong; Lv, Jun; Chen, Xi'ai; Gong, Xuexia; Yang, Chen'na

2007-12-01

Based on high speed Digital Signal Processor (DSP) and Field Programmable Gate Array (FPGA), a video capture, processing and display system is presented, which is of miniaturization and low power. In this system, a triple buffering scheme was used for the capture and display, so that the application can always get a new buffer without waiting; The Digital Signal Processor has an image process ability and it can be used to test the boundary of workpiece's image. A video graduation technology is used to aim at the position which is about to be tested, also, it can enhance the system's flexibility. The character superposition technology realized by DSP is used to display the test result on the screen in character format. This system can process image information in real time, ensure test precision, and help to enhance product quality and quality management.

Clinical comparison of the effectiveness of single-file reciprocating systems and rotary systems for removal of endotoxins and cultivable bacteria from primarily infected root canals.

PubMed

Martinho, Frederico C; Gomes, Ana P M; Fernandes, Aletéia M M; Ferreira, Nádia S; Endo, Marcos S; Freitas, Lilian F; Camões, Izabel C G

2014-05-01

This clinical study was conducted to compare the effectiveness of single-file reciprocating systems and rotary systems in removing endotoxins and cultivable bacteria from primarily infected root canals. Forty-eight primarily infected root canals were selected and randomly divided into 4 groups: WaveOne (Dentsply Maillefer, Ballaigues, Switzerland) (n = 12); Reciproc (VDW, Munich, Germany) (n = 12), ProTaper (Dentsply Maillefer) (n = 12), and Mtwo (VDW) (n = 12). Samples were collected before and after chemomechanical preparation. The irrigation was performed by using 2.5% sodium hypochlorite. A chromogenic limulus amebocyte lysate assay test was used to quantify endotoxins. Culture techniques were used to determine bacterial colony-forming unit counts. In the baseline samples (ie, samples collected before chemomechanical preparation), endotoxins and cultivable bacteria were recovered from 100% of the root canal samples. No differences were found in the median percentage values of endotoxin reduction achieved with reciprocating systems (ie, WaveOne [95.15%] and Reciproc [96.21%]) and with rotary systems (ie, ProTaper [97.98%] and Mtwo [96.34%]) (P < .05). Both single-file reciprocating systems (ie, WaveOne [99.45%] and Reciproc [99.93%]) and rotary systems (ProTaper [99.85%] and Mtwo [99.41%]) were effective in reducing the cultivable bacteria (all P < .05). Moreover, the culture analysis revealed no differences in bacterial load reduction (P > .05). Both single-file reciprocating systems (ie, WaveOne and Reciproc instruments) and rotary systems (ie, ProTaper and Mtwo instruments) showed similar effectiveness in reducing endotoxins and cultivable bacteria from primarily infected root canals, but they were not able to eliminate them from all root canals analyzed. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Microtiter plate-based antibody microarrays for bacteria and toxins

USDA-ARS?s Scientific Manuscript database

Research has focused on the development of rapid biosensor-based, high-throughput, and multiplexed detection of pathogenic bacteria in foods. Specifically, antibody microarrays in 96-well microtiter plates have been generated for the purpose of selective detection of Shiga toxin-producing E. coli (...

The effect of nutrient media water purity on LIBS based identification of bacteria

USDA-ARS?s Scientific Manuscript database

Single pulse laser induced breakdown spectroscopy (LIBS) is used as the basis for discrimination between 3 genera of Gram-negative bacteria and 2 genera of gram-positive bacteria representing pathogenic threats commonly found in poultry processing rinse waters. Because LIBS-based discrimination reli...

Molecular Diagnostic for Prospecting Polyhydroxyalkanoate-Producing Bacteria

PubMed Central

Montenegro, Eduarda Morgana da Silva; Delabary, Gabriela Scholante; da Silva, Marcus Adonai Castro; Andreote, Fernando Dini; Lima, André Oliveira de Souza

2017-01-01

The use of molecular diagnostic techniques for bioprospecting and microbial diversity study purposes has gained more attention thanks to their functionality, low cost and quick results. In this context, ten degenerate primers were designed for the amplification of polyhydroxyalkanoate synthase (phaC) gene, which is involved in the production of polyhydroxyalkanoate (PHA)—a biodegradable, renewable biopolymer. Primers were designed based on multiple alignments of phaC gene sequences from 218 species that have their genomes already analyzed and deposited at Biocyc databank. The combination of oligos phaCF3/phaCR1 allowed the amplification of the expected product (PHA synthases families types I and IV) from reference organisms used as positive control (PHA producer). The method was also tested in a multiplex system with two combinations of initiators, using 16 colonies of marine bacteria (pre-characterized for PHA production) as a DNA template. All amplicon positive organisms (n = 9) were also PHA producers, thus no false positives were observed. Amplified DNA was sequenced (n = 4), allowing for the confirmation of the phaC gene identity as well its diversity among marine bacteria. Primers were also tested for screening purposes using 37 colonies from six different environments. Almost 30% of the organisms presented the target amplicon. Thus, the proposed primers are an efficient tool for screening bacteria with potential for the production of PHA as well to study PHA genetic diversity. PMID:28952531

Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria.

PubMed

Adesoji, Ayodele T; Ogunjobi, Adeniyi A; Olatoye, Isaac O; Call, Douglas R; Douglas, Douglas R

2015-06-25

Antibiotic resistance genes [ARGs] in aquatic systems have drawn increasing attention they could be transferred horizontally to pathogenic bacteria. Water treatment plants (WTPs) are intended to provide quality and widely available water to the local populace they serve. However, WTPs in developing countries may not be dependable for clean water and they could serve as points of dissemination for antibiotic resistant bacteria. Only a few studies have investigated the occurrence of ARGs among these bacteria including tetracycline resistance genes in water distribution systems in Nigeria. Multi-drug resistant (MDR) bacteria, including resistance to tetracycline, were isolated from treated and untreated water distribution systems in southwest Nigeria. MDR bacteria were resistant to >3 classes of antibiotics based on break-point assays. Isolates were characterized using partial 16S rDNA sequencing and PCR assays for six tetracycline-resistance genes. Plasmid conjugation was evaluated using E. coli strain DH5α as the recipient strain. Out of the 105 bacteria, 85 (81 %) and 20 (19 %) were Gram- negative or Gram- positive, respectively. Twenty-nine isolates carried at least one of the targeted tetracycline resistance genes including strains of Aeromonas, Alcaligenes, Bacillus, Klebsiella, Leucobacter, Morganella, Proteus and a sequence matching a previously uncultured bacteria. Tet(A) was the most prevalent (16/29) followed by tet(E) (4/29) and tet30 (2/29). Tet(O) was not detected in any of the isolates. Tet(A) was mostly found with Alcaligenes strains (9/10) and a combination of more than one resistance gene was observed only amongst Alcaligenes strains [tet(A) + tet30 (2/10), tet(A) + tet(E) (3/10), tet(E) + tet(M) (1/10), tet(E) + tet30 (1/10)]. Tet(A) was transferred by conjugation for five Alcaligenes and two E. coli isolates. This study found a high prevalence of plasmid-encoded tet(A) among Alcaligenes isolates, raising the possibility that this

Detecting bacteria and Determining Their Susceptibility to Antibiotics by Stochastic Confinement in Nanoliter Droplets using Plug-Based Microfluidics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boedicker, J.; Li, L; Kline, T

2008-01-01

This article describes plug-based microfluidic technology that enables rapid detection and drug susceptibility screening of bacteria in samples, including complex biological matrices, without pre-incubation. Unlike conventional bacterial culture and detection methods, which rely on incubation of a sample to increase the concentration of bacteria to detectable levels, this method confines individual bacteria into droplets nanoliters in volume. When single cells are confined into plugs of small volume such that the loading is less than one bacterium per plug, the detection time is proportional to plug volume. Confinement increases cell density and allows released molecules to accumulate around the cell, eliminatingmore » the pre-incubation step and reducing the time required to detect the bacteria. We refer to this approach as stochastic confinement. Using the microfluidic hybrid method, this technology was used to determine the antibiogram - or chart of antibiotic sensitivity - of methicillin-resistant Staphylococcus aureus (MRSA) to many antibiotics in a single experiment and to measure the minimal inhibitory concentration (MIC) of the drug cefoxitin (CFX) against this strain. In addition, this technology was used to distinguish between sensitive and resistant strains of S. aureus in samples of human blood plasma. High-throughput microfluidic techniques combined with single-cell measurements also enable multiple tests to be performed simultaneously on a single sample containing bacteria. This technology may provide a method of rapid and effective patient-specific treatment of bacterial infections and could be extended to a variety of applications that require multiple functional tests of bacterial samples on reduced timescales.« less

Interactions among sulfide-oxidizing bacteria

NASA Technical Reports Server (NTRS)

Poplawski, R.

1985-01-01

The responses of different phototrophic bacteria in a competitive experimental system are studied, one in which primary factors such as H2S or light limited photometabolism. Two different types of bacteria shared one limited source of sulfide under specific conditions of light. The selection of a purple and a green sulfur bacteria and the cyanobacterium was based on their physiological similarity and also on the fact that they occur together in microbial mats. They all share anoxygenic photosynthesis, and are thus probably part of an evolutionary continuum of phototrophic organisms that runs from, strictly anaerobic physiology to the ability of some cyanobacteria to shift between anoxygenic bacterial style photosynthesis and the oxygenic kind typical of eukaryotes.

A novel continuous toxicity test system using a luminously modified freshwater bacterium.

PubMed

Cho, Jang-Cheon; Park, Kyung-Je; Ihm, Hyuk-Soon; Park, Ji-Eun; Kim, Se-Young; Kang, Ilnam; Lee, Kyu-Ho; Jahng, Deokjin; Lee, Dong-Hun; Kim, Sang-Jong

2004-09-15

An automated continuous toxicity test system was developed using a recombinant bioluminescent freshwater bacterium. The groundwater-borne bacterium, Janthinobacterium lividum YH9-RC, was modified with luxAB and optimized for toxicity tests using different kinds of organic carbon compounds and heavy metals. luxAB-marked YH9-RC cells were much more sensitive (average 7.3-8.6 times) to chemicals used for toxicity detection than marine Vibrio fischeri cells used in the Microtox assay. Toxicity tests for wastewater samples using the YH9-RC-based toxicity assay showed that EC50-5 min values in an untreated raw wastewater sample (23.9 +/- 12.8%) were the lowest, while those in an effluent sample (76.7 +/- 14.9%) were the highest. Lyophilization conditions were optimized in 384-multiwell plates containing bioluminescent bacteria that were pre-incubated for 15 min in 0.16 M of trehalose prior to freeze-drying, increasing the recovery of bioluminescence and viability by 50%. Luminously modified cells exposed to continuous phenol or wastewater stream showed a rapid decrease in bioluminescence, which fell below detectable range within 1 min. An advanced toxicity test system, featuring automated real-time toxicity monitoring and alerting functions, was designed and finely tuned. This novel continuous toxicity test system can be used for real-time biomonitoring of water toxicity, and can potentially be used as a biological early warning system.

Development and Testing of a Sorbent-Based Atmosphere Revitalization System 2010/2011

NASA Technical Reports Server (NTRS)

Miller, Lee A.; Knox, James C.

2012-01-01

Spacecraft being developed for future exploration missions incorporate Environmental Control and Life Support Systems (ECLSS) that limit weight, power, and volume thus requiring systems with higher levels of efficiency while maintaining high dependability and robustness. For air revitalization, an approach that meets those goals utilizes a regenerative Vacuum-Swing Adsorption (VSA) system that removes 100% of the CO2 from the cabin atmosphere as well as 100% of the water. A Sorbent Based Atmosphere Revitalization (SBAR) system is a VSA system that utilizes standard commercial adsorbents that have been proven effective and safe in spacecraft including Skylab and the International Space Station. The SBAR system is the subject of a development, test, and evaluation program that is being conducted at NASA s Marshall Space Flight Center. While previous testing had validated that the technology is a viable option, potential improvements to system design and operation were identified. Modifications of the full-scale SBAR test articles and adsorption cycles have been implemented and have shown significant performance gains resulting in a decrease in the consumables required for a mission as well as improved mission safety. Previous testing had utilized single bed test articles, during this period the test facility was enhanced to allow testing on the full 2-bed SBAR system. The test facility simulates a spacecraft ECLSS and allows testing of the SBAR system over the full range of operational conditions using mission simulations that assess the real-time performance of the SBAR system during scenarios that include the metabolic transients associated with extravehicular activity. Although future manned missions are currently being redefined, the atmosphere revitalization requirements for the spacecraft are expected to be quite similar to the Orion and the Altair vehicles and the SBAR test program addressed validation to the defined mission requirements as well as operation

Development of remote data acquisition system based on OPC for brake test bench

NASA Astrophysics Data System (ADS)

Wang, Yiwei; Wu, Mengling; Tian, Chun; Ma, Tianhe

2017-08-01

The 1:1 train brake system test bench can be used to carry out brake-related adhesion-slid control, stability test, noise test and dynamic test. To collect data of the test bench, a data acquisition method is needed. In this paper, the remote data acquisition system of test bench is built by LabVIEW based on OPC technology. Unlike the traditional hardwire way connecting PLC acquisition module with sensors, the novel method is used to collect data and share them through the internal LAN built by Ethernet switches, which avoids the complex wiring interference in an easy, efficient and flexible way. The system has been successfully applied to the data acquisition activities of the comprehensive brake system test bench of CRRC Nanjing Puzhen Haitai Brake Equipment Co., Ltd., and the relationship test between the adhesion coefficient and the slip-ratio is realized. The speed signal, torque signal and brake disc temperature can be collected and displayed. The results show that the system is reliable, convenient, and efficient, and can meet the requirements of data acquisition.

Development of crash imminent test scenarios for Integrated Vehicle-Based Safety Systems

DOT National Transportation Integrated Search

2007-04-01

This report identifies crash imminent test scenarios based on common pre-crash scenarios for integrated vehicle-based safety systems that alert the driver of a light vehicle or a heavy truck to an impending rear-end, lane change, or run-off-road cras...

Lactic acid bacteria as oral delivery systems for biomolecules.

PubMed

Berlec, A; Ravnikar, M; Strukelj, B

2012-11-01

Lactic acid bacteria (LAB) have become increasingly studied over the last two decades as potential delivery systems for various biological molecules to the gastrointestinal tract. This article presents an overview of characteristics of LAB as delivery systems and of the applications which have already been developed. The majority of LAB strains are able to survive the intestinal passage and some are also able to persist and colonize the intestine. Several strains were in fact described as members of the human commensal flora. They can interact with their host and are able to deliver large molecular weight biomolecules across the epithelium via M-cells or dendritic cells. The most widely applied LAB species has been Lactococcus lactis; however species from genus Lactobacillus are gaining popularity and the first examples from genus Bifidobacterium are starting to emerge. Bacteria are mostly applied live and enable continuous delivery of the biomolecules. However, killed bacteria (e.g. gram-positive enhancer matrix), with bound biomolecules or as adjuvants, are also being developed. The techniques for genetic modification of LAB are well known. This review focuses on the delivery of recombinant proteins and DNA, which can cause either local or systemic effects. We divide recombinant proteins into antigens and therapeutic proteins. Delivery of antigens for the purpose of vaccination represents the most abundant application with numerous successful demonstrations of the efficacy on the animal model. Therapeutic proteins have mostly been developed for the treatment of the inflammatory bowel disease, by the delivery of anti-inflammatory cytokines, or downregulation of proinflammatory cytokines. Delivery of allergens for the modulation of allergic disorders represents the second most popular application of therapeutic proteins. The delivery of DNA by LAB was demonstrated and offers exciting opportunities, especially as a vaccine. New discoveries may eventually lead to the

Immune system responses and fitness costs associated with consumption of bacteria in larvae of Trichoplusia ni

PubMed Central

Freitak, Dalial; Wheat, Christopher W; Heckel, David G; Vogel, Heiko

2007-01-01

Background Insects helped pioneer, and persist as model organisms for, the study of specific aspects of immunity. Although they lack an adaptive immune system, insects possess an innate immune system that recognizes and destroys intruding microorganisms. Its operation under natural conditions has not been well studied, as most studies have introduced microbes to laboratory-reared insects via artificial mechanical wounding. One of the most common routes of natural exposure and infection, however, is via food; thus, the role of dietary microbial communities in herbivorous insect immune system evolution invites study. Here, we examine the immune system response and consequences of exposing a lepidopteran agricultural pest to non-infectious microorganisms via simple oral consumption. Results Immune system response was compared between Trichoplusia ni larvae reared on diets with or without non-pathogenic bacteria (Escherichia coli and Micrococcus luteus). Two major immune response-related enzymatic activities responded to diets differently – phenoloxidase activity was inhibited in the bacteria-fed larvae, whereas general antibacterial activity was enhanced. Eight proteins were highly expressed in the hemolymph of the bacteria fed larvae, among them immune response related proteins arylphorin, apolipophorin III and gloverin. Expression response among 25 putative immune response-related genes were assayed via RT-qPCR. Seven showed more than fivefold up regulation in the presence of bacterial diet, with 22 in total being differentially expressed, among them apolipophorin III, cecropin, gallerimycin, gloverin, lysozyme, and phenoloxidase inhibiting enzyme. Finally, potential life-history trade-offs were studied, with pupation time and pupal mass being negatively affected in bacteria fed larvae. Conclusion The presence of bacteria in food, even if non-pathogenic, can trigger an immune response cascade with life history tradeoffs. Trichoplusia ni larvae are able to detect

Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

PubMed Central

Ferrari, Belinda C.; Binnerup, Svend J.; Gillings, Michael

2005-01-01

Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used. PMID:16332866

A fully automated microfluidic-based electrochemical sensor for real-time bacteria detection.

PubMed

Altintas, Zeynep; Akgun, Mete; Kokturk, Guzin; Uludag, Yildiz

2018-02-15

A fully automated microfluidic-based electrochemical biosensor was designed and manufactured for pathogen detection. The quantification of Escherichia coli was investigated with standard and nanomaterial amplified immunoassays in the concentration ranges of 0.99 × 10 4 3.98 × 10 9 cfu mL -1 and 103.97 × 10 7 cfu mL -1 which resulted in detection limits of 1.99 × 10 4 cfu mL -1 and 50 cfu mL -1 , respectively. The developed methodology was then applied for E. coli quantification in water samples using nanomaterial modified assay. Same detection limit for E. coli was achieved for real sample analysis with a little decrease on the sensor signal. Cross-reactivity studies were conducted by testing Shigella, Salmonella spp., Salmonella typhimurium and Staphylococcus aureus on E. coli specific antibody surface that confirmed the high specificity of the developed immunoassays. The sensor surface could be regenerated multiple times which significantly reduces the cost of the system. Our custom-designed biosensor is capable of detecting bacteria with high sensitivity and specificity, and can serve as a promising tool for pathogen detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Clay-Bacteria Systems and Biofilm Production

NASA Astrophysics Data System (ADS)

Steiner, J.; Alimova, A.; Katz, A.; Steiner, N.; Rudolph, E.; Gottlieb, P.

2007-12-01

Soil clots and the aerosol transport of bacteria and spores are promoted by the formation of biofilms (bacteria cells in an extracellular polymeric matrix). Biofilms protect microorganisms by promoting adhesion to both organic and inorganic surfaces. Time series experiments on bacteria-clay suspensions demonstrate that biofilm growth is catalyzed by the presence of hectorite in minimal growth media for the studied species: Gram negatives (Pseudomonas syringae and Escherichia coli,) and Gram positives (Staphylococcus aureus and Bacillus subtilis). Soil organisms (P. syringae, B. subtilis) and organisms found in the human population (E. coli, S. aureus) are both used to demonstrate the general applicability of clay involvement. Fluorescent images of the biofilms are acquired by staining with propidium iodide, a component of the BacLightTM Live/Dead bacterial viability staining kit (Molecular Probes, Eugene, OR). The evolving polysaccharide-rich biofilm reacts with the clay interlayer site causing a complex substitution of the two-water hectorite interlayer with polysaccharide. The result is often a three-peak composite of the (001) x-ray diffraction maxima resulting from polysaccharide-expanded clays and an organic-driven contraction of a subset of the clays in the reaction medium. X-ray diffractograms reveal that the expanded set creates a broad maximum with clay subsets at 1.84 nm and 1.41 nm interlayer spacings as approximated by a least squares double Lorentzian fit, and a smaller shoulder at larger 2q, deriving from a contraction of the interlayer spacing. Washing with chlorox removes organic material from the contracted clay and creates a 1-water hectorite single peak in place of the double peak. The clay response can be used as an indirect indicator of biofilm in an environmental system.

Integrated vehicle-based safety systems field operational test final program report.

DOT National Transportation Integrated Search

2011-06-01

"This document presents results from the light-vehicle and heavy-truck field operational tests performed as part of the Integrated Vehicle-Based Safety Systems (IVBSS) program. The findings are the result of analyses performed by the University of Mi...

Integrated Vehicle-Based Safety Systems Field Operational Test : Final Program Report

DOT National Transportation Integrated Search

2011-06-01

This document presents results from the light-vehicle and heavy-truck field operational tests performed as part of the Integrated Vehicle-Based Safety Systems (IVBSS) program. The findings are the result of analyses performed by the University of Mic...

Design and implementation of web service-based mobile reply testing management system

NASA Astrophysics Data System (ADS)

Gao, Liang; Han, Yu-min

2013-03-01

This paper introduces the design and implementation of a reply testing management system that based-on C#, Web Service and ASP .Net. With the system, teachers can manage reply site through Windows Mobile, judges can grade onscene by visiting WAP site through GPRS. Then this paper discusses details of the implementation and key technologies of the system.

Bioprobes Based on Aptamer and Silica Fluorescent Nanoparticles for Bacteria Salmonella typhimurium Detection

NASA Astrophysics Data System (ADS)

Wang, Qiu-Yue; Kang, Yan-Jun

2016-03-01

In this study, we have developed an efficient method based on single-stranded DNA (ssDNA) aptamers along with silica fluorescence nanoparticles for bacteria Salmonella typhimurium detection. Carboxyl-modified Tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate (RuBPY)-doped silica nanoparticles (COOH-FSiNPs) were prepared using reverse microemulsion method, and the streptavidin was conjugated to the surface of the prepared COOH-FSiNPs. The bacteria S. typhimurium was incubated with a specific ssDNA biotin-labeled aptamer, and then the aptamer-bacteria conjugates were treated with the synthetic streptavidin-conjugated silica fluorescence nanoprobes (SA-FSiNPs). The results under fluorescence microscopy show that SA-FSiNPs can be applied effectively for the labeling of bacteria S. typhimurium with great photostable property. To further verify the specificity of SA-FSiNPs out of multiple bacterial conditions, variant concentrations of bacteria mixtures composed of bacteria S. typhimurium, Escherichia coli, and Bacillus subtilis were treated with SA-FSiNPs.

Luciferase-Zinc-Finger System for the Rapid Detection of Pathogenic Bacteria.

PubMed

Shi, Chu; Xu, Qing; Ge, Yue; Jiang, Ling; Huang, He

2017-08-09

Rapid and reliable detection of pathogenic bacteria is crucial for food safety control. Here, we present a novel luciferase-zinc finger system for the detection of pathogens that offers rapid and specific profiling. The system, which uses a zinc-finger protein domain to probe zinc finger recognition sites, was designed to bind the amplified conserved regions of 16S rDNA, and the obtained products were detected using a modified luciferase. The luciferase-zinc finger system not only maintained luciferase activity but also allowed the specific detection of different bacterial species, with a sensitivity as low as 10 copies and a linear range from 10 to 10 4 copies per microliter of the specific PCR product. Moreover, the system is robust and rapid, enabling the simultaneous detection of 6 species of bacteria in artificially contaminated samples with excellent accuracy. Thus, we envision that our luciferase-zinc finger system will have far-reaching applications.

Colorimetric test-systems for creatinine detection based on composite molecularly imprinted polymer membranes.

PubMed

Sergeyeva, T A; Gorbach, L A; Piletska, E V; Piletsky, S A; Brovko, O O; Honcharova, L A; Lutsyk, O D; Sergeeva, L M; Zinchenko, O A; El'skaya, A V

2013-04-03

An easy-to-use colorimetric test-system for the efficient detection of creatinine in aqueous samples was developed. The test-system is based on composite molecularly imprinted polymer (MIP) membranes with artificial receptor sites capable of creatinine recognition. A thin MIP layer was created on the surface of microfiltration polyvinylidene fluoride (PVDF) membranes using method of photo-initiated grafting polymerization. The MIP layer was obtained by co-polymerization of a functional monomer (e.g. 2-acrylamido-2-methyl-1-propanesulfonic acid, itaconic acid or methacrylic acid) with N, N'-methylenebisacrylamide as a cross-linker. The choice of the functional monomer was based on the results of computational modeling. The creatinine-selective composite MIP membranes were used for measuring creatinine in aqueous samples. Creatinine molecules were selectively adsorbed by the MIP membranes and quantified using color reaction with picrates. The intensity of MIP membranes staining was proportional to creatinine concentration in an analyzed sample. The colorimetric test-system based on the composite MIP membranes was characterized with 0.25 mM detection limit and 0.25-2.5mM linear dynamic range. Storage stability of the MIP membranes was estimated as at least 1 year at room temperature. As compared to the traditional methods of creatinine detection the developed test-system is characterized by simplicity of operation, small size and low cost. Copyright © 2013 Elsevier B.V. All rights reserved.

Revisiting the cape cod bacteria injection experiment using a stochastic modeling approach

USGS Publications Warehouse

Maxwell, R.M.; Welty, C.; Harvey, R.W.

2007-01-01

Bromide and resting-cell bacteria tracer tests conducted in a sandy aquifer at the U.S. Geological Survey Cape Cod site in 1987 were reinterpreted using a three-dimensional stochastic approach. Bacteria transport was coupled to colloid filtration theory through functional dependence of local-scale colloid transport parameters upon hydraulic conductivity and seepage velocity in a stochastic advection - dispersion/attachment - detachment model. Geostatistical information on the hydraulic conductivity (K) field that was unavailable at the time of the original test was utilized as input. Using geostatistical parameters, a groundwater flow and particle-tracking model of conservative solute transport was calibrated to the bromide-tracer breakthrough data. An optimization routine was employed over 100 realizations to adjust the mean and variance ofthe natural-logarithm of hydraulic conductivity (InK) field to achieve best fit of a simulated, average bromide breakthrough curve. A stochastic particle-tracking model for the bacteria was run without adjustments to the local-scale colloid transport parameters. Good predictions of mean bacteria breakthrough were achieved using several approaches for modeling components of the system. Simulations incorporating the recent Tufenkji and Elimelech (Environ. Sci. Technol. 2004, 38, 529-536) correlation equation for estimating single collector efficiency were compared to those using the older Rajagopalan and Tien (AIChE J. 1976, 22, 523-533) model. Both appeared to work equally well at predicting mean bacteria breakthrough using a constant mean bacteria diameter for this set of field conditions. Simulations using a distribution of bacterial cell diameters available from original field notes yielded a slight improvement in the model and data agreement compared to simulations using an average bacterial diameter. The stochastic approach based on estimates of local-scale parameters for the bacteria-transport process reasonably captured

Interpretation of coagulation test results using a web-based reporting system.

PubMed

Quesada, Andres E; Jabcuga, Christine E; Nguyen, Alex; Wahed, Amer; Nedelcu, Elena; Nguyen, Andy N D

2014-01-01

Web-based synoptic reporting has been successfully integrated into diverse fields of pathology, improving efficiency and reducing typographic errors. Coagulation is a challenging field for practicing pathologists and pathologists-in-training alike. To develop a Web-based program that can expedite the generation of a individualized interpretive report for a variety of coagulation tests. We developed a Web-based synoptic reporting system composed of 119 coagulation report templates and 38 thromboelastography (TEG) report templates covering a wide range of findings. Our institution implemented this reporting system in July 2011; it is currently used by pathology residents and attending pathologists. Feedback from the users of these reports have been overwhelmingly positive. Surveys note the time saved and reduced errors. Our easily accessible, user-friendly, Web-based synoptic reporting system for coagulation is a valuable asset to our laboratory services. Copyright© by the American Society for Clinical Pathology (ASCP).

Wind turbine blade testing system using base excitation

DOEpatents

Cotrell, Jason; Thresher, Robert; Lambert, Scott; Hughes, Scott; Johnson, Jay

2014-03-25

An apparatus (500) for fatigue testing elongate test articles (404) including wind turbine blades through forced or resonant excitation of the base (406) of the test articles (404). The apparatus (500) includes a testing platform or foundation (402). A blade support (410) is provided for retaining or supporting a base (406) of an elongate test article (404), and the blade support (410) is pivotally mounted on the testing platform (402) with at least two degrees of freedom of motion relative to the testing platform (402). An excitation input assembly (540) is interconnected with the blade support (410) and includes first and second actuators (444, 446, 541) that act to concurrently apply forces or loads to the blade support (410). The actuator forces are cyclically applied in first and second transverse directions. The test article (404) responds to shaking of its base (406) by oscillating in two, transverse directions (505, 507).

Bioenergetics of photoheterotrophic bacteria in the oceans.

PubMed

Kirchman, David L; Hanson, Thomas E

2013-04-01

Photoheterotrophic microbes, such as proteorhodopsin (PR)-based phototrophic (PRP) and aerobic anoxygenic phototrophic (AAP) bacteria, are well known to be abundant in the oceans, potentially playing unique roles in biogeochemical cycles. However, the contribution of phototrophy to the energy requirements of these bacteria has not been quantitatively examined to date. To better understand the implications of photoheterophy in the oceans, we calculated energy benefits and costs of phototrophy and compared net benefits with maintenance costs. Benefits depend on the number of photosynthetic units (PSUs), absorption cross-section area of each PSU as function of wavelength, the in situ light quality, and the energy yield per absorbed photon. For costs we considered the energy required for the synthesis of pigments, amino acids and proteins in each PSU. Our calculations indicate that AAP bacteria harvest more light energy than do PRP bacteria, but the costs of phototrophy are much higher for AAP bacteria. Still, the net energy gained by AAP bacteria is often sufficient to meet maintenance costs, while that is not the case for PRP bacteria except with high light intensities and large numbers of proteorhodopsin molecules per cell. The low costs and simplicity of PR-based phototrophy explain the high abundance of proteorhodopsin genes in the oceans. However, even for AAP bacteria, the net energy yield of phototrophy is apparently too low to influence the distribution of photoheterotrophic bacteria among various marine systems. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Space Launch System Base Heating Test: Sub-Scale Rocket Engine/Motor Design, Development and Performance Analysis

NASA Technical Reports Server (NTRS)

Mehta, Manish; Seaford, Mark; Kovarik, Brian; Dufrene, Aaron; Solly, Nathan; Kirchner, Robert; Engel, Carl D.

2014-01-01

The Space Launch System (SLS) base heating test is broken down into two test programs: (1) Pathfinder and (2) Main Test. The Pathfinder Test Program focuses on the design, development, hot-fire test and performance analyses of the 2% sub-scale SLS core-stage and booster element propulsion systems. The core-stage propulsion system is composed of four gaseous oxygen/hydrogen RS-25D model engines and the booster element is composed of two aluminum-based model solid rocket motors (SRMs). The first section of the paper discusses the motivation and test facility specifications for the test program. The second section briefly investigates the internal flow path of the design. The third section briefly shows the performance of the model RS-25D engines and SRMs for the conducted short duration hot-fire tests. Good agreement is observed based on design prediction analysis and test data. This program is a challenging research and development effort that has not been attempted in 40+ years for a NASA vehicle.

Continuing challenges for computer-based neuropsychological tests.

PubMed

Letz, Richard

2003-08-01

A number of issues critical to the development of computer-based neuropsychological testing systems that remain continuing challenges to their widespread use in occupational and environmental health are reviewed. Several computer-based neuropsychological testing systems have been developed over the last 20 years, and they have contributed substantially to the study of neurologic effects of a number of environmental exposures. However, many are no longer supported and do not run on contemporary personal computer operating systems. Issues that are continuing challenges for development of computer-based neuropsychological tests in environmental and occupational health are discussed: (1) some current technological trends that generally make test development more difficult; (2) lack of availability of usable speech recognition of the type required for computer-based testing systems; (3) implementing computer-based procedures and tasks that are improvements over, not just adaptations of, their manually-administered predecessors; (4) implementing tests of a wider range of memory functions than the limited range now available; (5) paying more attention to motivational influences that affect the reliability and validity of computer-based measurements; and (6) increasing the usability of and audience for computer-based systems. Partial solutions to some of these challenges are offered. The challenges posed by current technological trends are substantial and generally beyond the control of testing system developers. Widespread acceptance of the "tablet PC" and implementation of accurate small vocabulary, discrete, speaker-independent speech recognition would enable revolutionary improvements to computer-based testing systems, particularly for testing memory functions not covered in existing systems. Dynamic, adaptive procedures, particularly ones based on item-response theory (IRT) and computerized-adaptive testing (CAT) methods, will be implemented in new tests that will be

BASE COMPOSITION OF THE DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA

PubMed Central

Sigal, Nicole; Senez, Jacques C.; Le Gall, Jean; Sebald, Madeleine

1963-01-01

Sigal, Nicole (Laboratoire de Chimie Bactérienne du CNRS, Marseille, France), Jacques C. Senez, Jean Le Gall, and Madeleine Sebald. Base composition of the deoxyribonucleic acid of sulfate-reducing bacteria. J. Bacteriol. 85:1315–1318. 1963—The deoxyribonucleic acid constitution of several strains of sulfate-reducing bacteria has been analytically determined. The results of these studies show that this group of microorganisms includes at least four subgroups characterized by significantly different values of the adenine plus thymine to guanine plus cytosine ratio. The nonsporulated forms with polar flagellation, containing both cytochrome c3 and desulfoviridin, are divided into two subgroups. One includes the fresh-water, nonhalophilic strains with base ratio from 0.54 to 0.59, and the other includes the halophilic or halotolerant strains with base ratio from 0.74 to 0.77. The sporulated, peritrichous strains without cytochrome and desulfoviridin (“nigrificans” and “orientis”) are distinct from the above two types and differ from each other, having base ratios of 1.20 and 1.43, respectively. PMID:14047223

BASE COMPOSITION OF THE DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA.

PubMed

SIGAL, N; SENEZ, J C; LEGALL, J; SEBALD, M

1963-06-01

Sigal, Nicole (Laboratoire de Chimie Bactérienne du CNRS, Marseille, France), Jacques C. Senez, Jean Le Gall, and Madeleine Sebald. Base composition of the deoxyribonucleic acid of sulfate-reducing bacteria. J. Bacteriol. 85:1315-1318. 1963-The deoxyribonucleic acid constitution of several strains of sulfate-reducing bacteria has been analytically determined. The results of these studies show that this group of microorganisms includes at least four subgroups characterized by significantly different values of the adenine plus thymine to guanine plus cytosine ratio. The nonsporulated forms with polar flagellation, containing both cytochrome c(3) and desulfoviridin, are divided into two subgroups. One includes the fresh-water, nonhalophilic strains with base ratio from 0.54 to 0.59, and the other includes the halophilic or halotolerant strains with base ratio from 0.74 to 0.77. The sporulated, peritrichous strains without cytochrome and desulfoviridin ("nigrificans" and "orientis") are distinct from the above two types and differ from each other, having base ratios of 1.20 and 1.43, respectively.

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

2013-04-01

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

The philosophy of benchmark testing a standards-based picture archiving and communications system.

PubMed

Richardson, N E; Thomas, J A; Lyche, D K; Romlein, J; Norton, G S; Dolecek, Q E

1999-05-01

The Department of Defense issued its requirements for a Digital Imaging Network-Picture Archiving and Communications System (DIN-PACS) in a Request for Proposals (RFP) to industry in January 1997, with subsequent contracts being awarded in November 1997 to the Agfa Division of Bayer and IBM Global Government Industry. The Government's technical evaluation process consisted of evaluating a written technical proposal as well as conducting a benchmark test of each proposed system at the vendor's test facility. The purpose of benchmark testing was to evaluate the performance of the fully integrated system in a simulated operational environment. The benchmark test procedures and test equipment were developed through a joint effort between the Government, academic institutions, and private consultants. Herein the authors discuss the resources required and the methods used to benchmark test a standards-based PACS.

Label and label-free based surface-enhanced Raman scattering for pathogen bacteria detection: A review.

PubMed

Liu, Yu; Zhou, Haibo; Hu, Ziwei; Yu, Guangxia; Yang, Danting; Zhao, Jinshun

2017-08-15

Rapid, accurate detection of pathogen bacteria is a highly topical research area for the sake of food safety and public health. Surface-enhanced Raman scattering (SERS) is being considered as a powerful and attractive technique for pathogen bacteria detection, due to its sensitivity, high speed, comparatively low cost, multiplexing ability and portability. This contribution aims to give a comprehensive overview of SERS as a technique for rapid detection of pathogen bacteria based on label and label-free strategies. A brief tutorial on SERS is given first of all. Then we summarize the recent trends and developments of label and label-free based SERS applied to detection of pathogen bacteria, including the relatively complete interpretation of SERS spectra. In addition, multifunctional SERS platforms for pathogen bacteria in matrix are discussed as well. Furthermore, an outlook of the work done and a perspective on the future directions of SERS as a reliable tool for real-time pathogen bacteria detection are given. Copyright © 2017 Elsevier B.V. All rights reserved.

Antimicrobial effects of a new therapeutic liquid dentifrice formulation on oral bacteria including odorigenic species.

PubMed

Sreenivasan, P K; Furgang, D; Zhang, Y; DeVizio, W; Fine, D H

2005-03-01

The control of oral malodor is well-recognized in efforts to improve oral health. Antimicrobial formulations can mitigate oral malodor, however, procedures to assess effects on oral bacteria including those implicated in halitosis are unavailable. This investigation examined the antimicrobial effects of a new liquid triclosan/copolymer dentifrice (test) formulation that demonstrated significant inhibition of oral malodor in previous organoleptic clinical studies. Procedures compared antimicrobial effects of the test and control formulations on a range of oral micro-organisms including members implicated in halitosis, substantive antimicrobial effects of formulations with hydroxyapatite as a surrogate for human teeth and ex vivo effects on oral bacteria from human volunteers. With Actinomyces viscosus, as a model system, the test formulation demonstrated a dose-dependent effect. At these concentrations the test formulation provided significant antimicrobial effects on 13 strains of oral bacteria including those implicated in bad breath at selected posttreatment time points. Treatment of hydroxyapatite by the test dentifrice resulted in a significant and substantive antimicrobial effect vs. controls. Oral bacteria from subjects treated ex vivo with the test dentifrice resulted in significant reductions in cultivable oral bacteria and odorigenic bacteria producing hydrogen sulfide. In summary, microbiological methods adapted to study odorigenic bacteria demonstrate the significant antimicrobial effects of the test (triclosan/copolymer) dentifrice with laboratory and clinical strains of oral bacteria implicated in bad breath.

Development of bacteria-based bioassays for arsenic detection in natural waters.

PubMed

Diesel, Elizabeth; Schreiber, Madeline; van der Meer, Jan Roelof

2009-06-01

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.

Nemesis Autonomous Test System

NASA Technical Reports Server (NTRS)

Barltrop, Kevin J.; Lee, Cin-Young; Horvath, Gregory A,; Clement, Bradley J.

2012-01-01

A generalized framework has been developed for systems validation that can be applied to both traditional and autonomous systems. The framework consists of an automated test case generation and execution system called Nemesis that rapidly and thoroughly identifies flaws or vulnerabilities within a system. By applying genetic optimization and goal-seeking algorithms on the test equipment side, a "war game" is conducted between a system and its complementary nemesis. The end result of the war games is a collection of scenarios that reveals any undesirable behaviors of the system under test. The software provides a reusable framework to evolve test scenarios using genetic algorithms using an operation model of the system under test. It can automatically generate and execute test cases that reveal flaws in behaviorally complex systems. Genetic algorithms focus the exploration of tests on the set of test cases that most effectively reveals the flaws and vulnerabilities of the system under test. It leverages advances in state- and model-based engineering, which are essential in defining the behavior of autonomous systems. It also uses goal networks to describe test scenarios.

Intelligent pump test system based on virtual instrument

NASA Astrophysics Data System (ADS)

Ma, Jungong; Wang, Shifu; Wang, Zhanlin

2003-09-01

The intelligent pump system is the key component of the aircraft hydraulic system that can solve the problem, such as the temperature sharply increasing. As the performance of the intelligent pump directly determines that of the aircraft hydraulic system and seriously affects fly security and reliability. So it is important to test all kinds of performance parameters of intelligent pump during design and development, while the advanced, reliable and complete test equipments are the necessary instruments for achieving the goal. In this paper, the application of virtual instrument and computer network technology in aircraft intelligent pump test is presented. The composition of the hardware, software, hydraulic circuit in this system are designed and implemented.

Space Launch System Base Heating Test: Sub-Scale Rocket Engine/Motor Design, Development & Performance Analysis

NASA Technical Reports Server (NTRS)

Mehta, Manish; Seaford, Mark; Kovarik, Brian; Dufrene, Aaron; Solly, Nathan

2014-01-01

ATA-002 Technical Team has successfully designed, developed, tested and assessed the SLS Pathfinder propulsion systems for the Main Base Heating Test Program. Major Outcomes of the Pathfinder Test Program: Reach 90% of full-scale chamber pressure Achieved all engine/motor design parameter requirements Reach steady plume flow behavior in less than 35 msec Steady chamber pressure for 60 to 100 msec during engine/motor operation Similar model engine/motor performance to full-scale SLS system Mitigated nozzle throat and combustor thermal erosion Test data shows good agreement with numerical prediction codes Next phase of the ATA-002 Test Program Design & development of the SLS OML for the Main Base Heating Test Tweak BSRM design to optimize performance Tweak CS-REM design to increase robustness MSFC Aerosciences and CUBRC have the capability to develop sub-scale propulsion systems to meet desired performance requirements for short-duration testing.

Detection of proteins and bacteria using an array of feedback capacitance sensors.

PubMed

Mehta, Manav; Hanumanthaiah, Chandra Sekar; Betala, Pravin Ajitkumar; Zhang, Hong; Roh, SaeWeon; Buttner, William; Penrose, William R; Stetter, Joseph R; Pérez-Luna, Victor H

2007-12-15

An integrated array of micron-dimension capacitors, originally developed for biometric applications (fingerprint identification), was engineered for detection of biological agents such as proteins and bacteria. This device consists of an array of 93,184 (256 x 364) individual capacitor-based sensing elements located underneath a thin (0.8 microm) layer of glass. This glass layer can be functionalized with organosilane-based monolayers to provide groups amenable for the immobilization of bioreceptors such as antibodies, enzymes, peptides, aptamers, and nucleotides. Upon functionalization with antibodies and in conjunction with signal amplification schemes that result in perturbation of the dielectric constant around the captured antigens, this system can be used as a detector of biological agents. Two signal amplification schemes were tested in this work: one consisted of 4 microm diameter latex immunobeads and a second one was based on colloidal gold catalyzed reduction of silver. These signal amplification approaches were demonstrated and show that this system is capable of specific detection of bacteria (Escherichia coli) and proteins (ovalbumin). The present work shows proof-of-principle demonstration that a simple fingerprint detector based on feedback capacitance measurements can be implemented as a biosensor. The approach presented could be easily expanded to simultaneously test for a large number of analytes and multiple samples given that this device has a large number of detectors. The device and required instrumentation is highly portable and does not require expensive and bulky instrumentation because it relies purely on electronic detection.

Smartphone-based rapid quantification of viable bacteria by single-cell microdroplet turbidity imaging.

PubMed

Cui, Xiaonan; Ren, Lihui; Shan, Yufei; Wang, Xixian; Yang, Zhenlong; Li, Chunyu; Xu, Jian; Ma, Bo

2018-05-18

Standard plate count (SPC) has been recognized as the golden standard for the quantification of viable bacteria. However, SPC usually takes one to several days to grow individual cells into a visible colony, which greatly hampers its application in rapid bacteria enumeration. Here we present a microdroplet turbidity imaging based digital standard plate count (dSPC) method to overcome this hurdle. Instead of cultivating on agar plates, bacteria are encapsulated in monodisperse microdroplets for single-cell cultivation. Proliferation of the encapsulated bacterial cell produced a detectable change in microdroplet turbidity, which allowed, after just a few bacterial doubling cycles (i.e., a few hours), enumeration of viable bacteria by visible-light imaging. Furthermore, a dSPC platform integrating a power-free droplet generator with smartphone-based turbidity imaging was established. As proof-of-concept demonstrations, a series of Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus subtilis) samples were quantified via the smartphone dSPC accurately within 6 hours, representing a detection sensitivity of 100 CFU ml-1 and at least 3 times faster. In addition, Enterobacter sakazakii (E. sakazakii) in infant milk powder as a real sample was enumerated within 6 hours, in contrast to the 24 hours needed in traditional SPC. Results with high accuracy and reproducibility were achieved, with no difference in counts found between dSPC and SPC. By enabling label-free, rapid, portable and low-cost enumeration and cultivation of viable bacteria onsite, smartphone dSPC forms the basis for a temporally and geographically trackable network for surveying live microbes globally where every citizen with a cellphone can contribute anytime and anywhere.

Laser-induced breakdown spectroscopy (LIBS): An innovative tool for studying bacteria

NASA Astrophysics Data System (ADS)

Mohaidat, Qassem I.

Laser-induced breakdown spectroscopy (LIBS) has gained a reputation as a flexible and convenient technique for rapidly determining the elemental composition of samples with minimal or no sample preparation. In this dissertation, I will describe the benefits of using LIBS for the rapid discrimination and identification of bacteria (both pathogenic and non-pathogenic) based on the relative concentration of trace inorganic elements such as Mg, P, Ca, and Na. The speed, portability, and robustness of the technique suggest that LIBS may be applicable as a rapid point-of-care medical diagnostic technology. LIBS spectra of multiple genera of bacteria such as Escherichia, Streptococcus, Mycobacterium, and Staphylococcus were acquired and successfully analyzed using a computerized discriminant function analysis (DFA). It was shown that a LIBS-based bacterial identification might be insensitive to a wide range of biological changes that could occur in the bacterial cell due to a variety of environmental stresses that the cell may encounter. The effect of reducing the number of bacterial cells on the LIBS-based classification was also studied. These results showed that with 2500 bacteria, the identification of bacterial specimens was still possible. Importantly, it was shown that bacteria in mixed samples (more than one type of bacteria being present) were identifiable. The dominant or majority component of a two-component mixture was reliably identified as long as it comprised 70% of the mixture or more. Finally, to simulate a clinical specimen in a precursor to actual clinical tests, Staphylococcus epidermidis bacteria were collected from urine samples (to simulate a urinary tract infection specimen) and were tested via LIBS without washing. The analysis showed that these bacteria possessed exactly the same spectral fingerprint as control bacteria obtained from sterile deionized water, resulting in a 100% correct classification. This indicates that the presence of other

Effects of Bacteria on Artemia franciscana Cultured in Different Gnotobiotic Environments

PubMed Central

Marques, Antonio; Dinh, Thi; Ioakeimidis, Christos; Huys, Geert; Swings, Jean; Verstraete, Willy; Dhont, Jean; Sorgeloos, Patrick; Bossier, Peter

2005-01-01

The use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. However, application with consistent results is hampered by insufficient information on their modes of action. To investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards Artemia franciscana and, subsequently, if live bacteria have probiotic effects beyond the effects observed with dead bacteria, a model system was employed using gnotobiotic Artemia as a test organism. Nauplii were cultured in the presence of 10 bacterial strains combined with four different major axenic live feeds (two strains of Saccharomyces cerevisiae and two strains of Dunaliella tertiolecta) differing in their nutritional values. In combination with poor- and medium-quality live feeds, dead bacteria exerted a strong effect on Artemia survival but a rather weak or no effect on individual length and constituted a maximum of only 5.9% of the total ash-free dry weight supplied. These effects were reduced or even disappeared when medium- to good-quality major feed sources were used, possibly due to improvements in the health status of Artemia. Some probiotic bacteria, such as GR 8 (Cytophaga spp.), improved (not always significantly) the performance of nauplii beyond the effect observed with dead bacteria, independently of the feed supplied. The present approach can be an excellent system to study the exact mode of action of bacteria, especially if combined with challenge tests or other types of analysis (e.g., transcriptome and proteonomic analysis). PMID:16085818

Statistical Tests of System Linearity Based on the Method of Surrogate Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunter, N.; Paez, T.; Red-Horse, J.

When dealing with measured data from dynamic systems we often make the tacit assumption that the data are generated by linear dynamics. While some systematic tests for linearity and determinism are available - for example the coherence fimction, the probability density fimction, and the bispectrum - fi,u-ther tests that quanti$ the existence and the degree of nonlinearity are clearly needed. In this paper we demonstrate a statistical test for the nonlinearity exhibited by a dynamic system excited by Gaussian random noise. We perform the usual division of the input and response time series data into blocks as required by themore » Welch method of spectrum estimation and search for significant relationships between a given input fkequency and response at harmonics of the selected input frequency. We argue that systematic tests based on the recently developed statistical method of surrogate data readily detect significant nonlinear relationships. The paper elucidates the method of surrogate data. Typical results are illustrated for a linear single degree-of-freedom system and for a system with polynomial stiffness nonlinearity.« less

Lensfree in-line holographic detection of bacteria

NASA Astrophysics Data System (ADS)

Poher, V.; Allier, C. P.; Coutard, J. G.; Hervé, L.; Dinten, J. M.

2011-07-01

Due to low light scattering, bacteria are difficult to detect using lensless imaging systems. In order to detect individual bacteria, we report a method based on a thin wetting film imaging that produces a micro-lens effect on top of each bacterium when the sample dries up. The imaging using a high-end CMOS sensor is combined with an in-line holographic reconstruction to improve positive detection rate up to 95% with micron-sized beads at high density of ~103 objects/mm2. The system allows detecting from single bacterium to densely packed objects (103 bacteria/μl) within 10μl sample. As an example, E.coli, Bacillus subtilis and Bacillus thuringiensis, has been successfully detected with strong signal to noise ratio across a 24mm2 field of view.

[Growth characteristics and control of iron bacteria on cast iron in drinking water distribution systems].

PubMed

Wang, Yang; Zhang, Xiao-Jian; Chen, Yu-Qiao; Lu, Pin-Pin; Chen, Chao

2009-11-01

This study investigated the growth characteristics of iron bacteria on cast iron and relationship between suspended and attached iron bacteria. The steady-state growth of iron bacteria would need 12 d and iron bacteria level in effluents increased 1 lg. Hydraulics influence on iron bacteria level and detachment rate of steady-state attached iron bacteria was not significant. But it could affect the time of attached iron bacteria on cast-iron coupons reaching to steady state. When the chlorine residual was 0.3 mg/L, the iron bacteria growth could be controlled effectively and suspended and attached iron bacteria levels both decreased 1 lg. When the chlorine residual was more than 1.0 mg/L, it could not inactivate the iron bacteria of internal corrosion scale yet. There was little effect on inhibiting the iron bacteria growth that the chlorine residual was 0.05 mg/L in drinking water quality standard of China. The iron bacteria on coupons reached to steady state without disinfectant and then increased the chlorine residual to 1.25 mg/L, the attached iron bacteria level could decrease 2 lg to 3 lg. Under steady-state, the suspended iron bacteria levels were linearly dependent on the attached iron bacteria. The control of iron bacteria in drinking water distribution systems was advanced: maintaining the chlorine residual (0.3 mg/L), flushing the pipeline with high dosage disinfectant, adopting corrosion-resistant pipe materials and renovating the old pipe loop.

Asellus aquaticus as a Potential Carrier of Escherichia coli and Other Coliform Bacteria into Drinking Water Distribution Systems

PubMed Central

Christensen, Sarah C. B.; Arvin, Erik; Nissen, Erling; Albrechtsen, Hans-Jørgen

2013-01-01

Individuals of the water louse, Asellus aquaticus, enter drinking water distribution systems in temperate parts of the world, where they establish breeding populations. We analysed populations of surface water A. aquaticus from two ponds for associated faecal indicator bacteria and assessed the risk of A. aquaticus transporting bacteria into distribution systems. Concentrations of up to two E. coli and five total coliforms·mL−1 were measured in the water and 200 E. coli and >240 total coliforms·mL−1 in the sediments of the investigated ponds. Concentrations of A. aquaticus associated bacteria never exceeded three E. coli and six total coliforms·A. aquaticus−1. During exposure to high concentrations of coliforms, concentrations reached 350 coliforms·A. aquaticus−1. A. aquaticus associated E. coli were only detected as long as E. coli were present in the water and sediment. The calculated probability of exceeding drinking water guideline values in non-disinfected systems by intrusion of A. aquaticus was low. Only in scenarios with narrow pipes and low flows, did total coliforms exceed guideline values, implying that the probability of detection by routine monitoring is also low. The study expands the knowledge base for evaluating incidents with presence of coliform indicators in drinking water by showing that intruding A. aquaticus were not important carriers of E. coli or other coliform bacteria even when emerging from faecally contaminated waters. PMID:23455399

Asellus aquaticus as a potential carrier of Escherichia coli and other coliform bacteria into drinking water distribution systems.

PubMed

Christensen, Sarah C B; Arvin, Erik; Nissen, Erling; Albrechtsen, Hans-Jørgen

2013-03-01

Individuals of the water louse, Asellus aquaticus, enter drinking water distribution systems in temperate parts of the world, where they establish breeding populations. We analysed populations of surface water A. aquaticus from two ponds for associated faecal indicator bacteria and assessed the risk of A. aquaticus transporting bacteria into distribution systems. Concentrations of up to two E. coli and five total coliforms·mL-1 were measured in the water and 200 E. coli and >240 total coliforms·mL-1 in the sediments of the investigated ponds. Concentrations of A. aquaticus associated bacteria never exceeded three E. coli and six total coliforms·A. aquaticus-1. During exposure to high concentrations of coliforms, concentrations reached 350 coliforms·A. aquaticus-1. A. aquaticus associated E. coli were only detected as long as E. coli were present in the water and sediment. The calculated probability of exceeding drinking water guideline values in non-disinfected systems by intrusion of A. aquaticus was low. Only in scenarios with narrow pipes and low flows, did total coliforms exceed guideline values, implying that the probability of detection by routine monitoring is also low. The study expands the knowledge base for evaluating incidents with presence of coliform indicators in drinking water by showing that intruding A. aquaticus were not important carriers of E. coli or other coliform bacteria even when emerging from faecally contaminated waters.

Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria.

PubMed

Lee, Ki-Young; Lee, Bong-Jin

2016-10-22

Bacterial toxin-antitoxin (TA) systems have received increasing attention for their diverse identities, structures, and functional implications in cell cycle arrest and survival against environmental stresses such as nutrient deficiency, antibiotic treatments, and immune system attacks. In this review, we describe the biological functions and the auto-regulatory mechanisms of six different types of TA systems, among which the type II TA system has been most extensively studied. The functions of type II toxins include mRNA/tRNA cleavage, gyrase/ribosome poison, and protein phosphorylation, which can be neutralized by their cognate antitoxins. We mainly explore the similar but divergent structures of type II TA proteins from 12 important pathogenic bacteria, including various aspects of protein-protein interactions. Accumulating knowledge about the structure-function correlation of TA systems from pathogenic bacteria has facilitated a novel strategy to develop antibiotic drugs that target specific pathogens. These molecules could increase the intrinsic activity of the toxin by artificially interfering with the intermolecular network of the TA systems.

Results of data base management system parameterized performance testing related to GSFC scientific applications

NASA Technical Reports Server (NTRS)

Carchedi, C. H.; Gough, T. L.; Huston, H. A.

1983-01-01

The results of a variety of tests designed to demonstrate and evaluate the performance of several commercially available data base management system (DBMS) products compatible with the Digital Equipment Corporation VAX 11/780 computer system are summarized. The tests were performed on the INGRES, ORACLE, and SEED DBMS products employing applications that were similar to scientific applications under development by NASA. The objectives of this testing included determining the strength and weaknesses of the candidate systems, performance trade-offs of various design alternatives and the impact of some installation and environmental (computer related) influences.

A novel dissolution media for testing drug release from a nanostructured polysaccharide-based colon specific drug delivery system: an approach to alternative colon media.

PubMed

Kotla, Niranjan G; Singh, Sima; Maddiboyina, Balaji; Sunnapu, Omprakash; Webster, Thomas J

2016-01-01

The aim of this study was to develop a novel microbially triggered and animal-sparing dissolution method for testing of nanorough polysaccharide-based micron granules for colonic drug delivery. In this method, probiotic cultures of bacteria present in the colonic region were prepared and added to the dissolution media and compared with the performance of conventional dissolution methodologies (such as media with rat cecal and human fecal media). In this study, the predominant species (such as Bacteroides, Bifidobacterium, Lactobacillus species, Eubacterium and Streptococcus) were cultured in 12% w/v skimmed milk powder and 5% w/v grade "A" honey. Approximately 10(10)-10(11) colony forming units m/L of probiotic culture was added to the dissolution media to test the drug release of polysaccharide-based formulations. A USP dissolution apparatus I/II using a gradient pH dissolution method was used to evaluate drug release from formulations meant for colonic drug delivery. Drug release of guar gum/Eudragit FS30D coated 5-fluorouracil granules was assessed under gastric and small intestine conditions within a simulated colonic environment involving fermentation testing with the probiotic culture. The results with the probiotic system were comparable to those obtained from the rat cecal and human fecal-based fermentation model, thereby suggesting that a probiotic dissolution method can be successfully applied for drug release testing of any polysaccharide-based oral formulation meant for colonic delivery. As such, this study significantly adds to the nanostructured biomaterials' community by elucidating an easier assay for colonic drug delivery.

EPA Team Helps Water Systems Comply with New Bacteria Monitoring Rule

EPA Pesticide Factsheets

An EPA team issued nearly 200 Administrative Orders in support of Pennsylvania and Virginia to ensure that small public water systems followed new requirements for more frequent bacteria monitoring of their water supplies.

Antagonistic activity of isolated lactic acid bacteria from Pliek U against gram-negative bacteria Escherichia coli ATCC 25922

NASA Astrophysics Data System (ADS)

Kiti, A. A.; Jamilah, I.; Rusmarilin, H.

2017-09-01

Lactic acid bacteria (LAB) is one group of microbes that has many benefits, notably in food and health industries sector. LAB plays an important role in food fermentation and it has bacteriostatic effect against the growth of pathogenic microorganisms. The research related LAB continued to be done to increase the diversity of potential isolates derived from nature which is indigenous bacteria for biotechnological purposes. This study was aimed to isolate and characterize LAB derived from pliek u sample and to examine the potency to inhibits Escherichia coli ATCC 25922 bacteria growth. A total of 5 isolates were isolated and based on morphological and physiological characteristics of the fifth bacteria, they are allegedly belonging to the genus Bacillus. Result of antagonistic test showed that the five isolates could inhibits the growth of E. coli ATCC 25922. The highest inhibition zone is 8.5 mm was shown by isolates NQ2, while the lowest inhibition is 1.5 mm was shown by isolates NQ3.

[Correlation of bacteria in the contaminated drug and the environmental microbes in the clean room for pharmaceutical microbial test investigated by FTIR].

PubMed

Pei, Lin; Hu, Chang-qin; Ma, Shi-hong; Dai, Hui; Hang, Tai-jun

2007-11-01

The FTIR method was used to investigate the correlation of bacteria in the contaminated drug and the environmental microbes in the clean room for pharmaceutical microbial test. The similarity of bacteria in the contaminated drug and environmental microbes was compared by critical hit value method and cluster analysis method. This constructed the FTIR spectra library of clean room environmental microbe, and determined the criterion to promptly judge if the bacteria isolated from pharmaceuticals were contaminated by environment or not, hence the exactness of "one-off report" of sterile test result can be guaranteed, and can be used for the dynamic monitoring of environmental bacteria of clean room. The method is proven to be simple, accurate and rapid, and can be easily spread to the pharmaceutical microbial control.

Automated flight test management system

NASA Technical Reports Server (NTRS)

Hewett, M. D.; Tartt, D. M.; Agarwal, A.

1991-01-01

The Phase 1 development of an automated flight test management system (ATMS) as a component of a rapid prototyping flight research facility for artificial intelligence (AI) based flight concepts is discussed. The ATMS provides a flight engineer with a set of tools that assist in flight test planning, monitoring, and simulation. The system is also capable of controlling an aircraft during flight test by performing closed loop guidance functions, range management, and maneuver-quality monitoring. The ATMS is being used as a prototypical system to develop a flight research facility for AI based flight systems concepts at NASA Ames Dryden.

Quantitative evaluation of apical extrusion of intracanal bacteria using rotary ProTaper, K3XF, twisted and hand K-file system: An ex vivo study.

PubMed

Ghogre, Priyanka; Chourasia, Hemant Ramesh; Agarwal, Manish; Singh, M P; Gurav, Sandeep; Ghogre, Rahul

2015-01-01

The aim of this study was to evaluate the number of intracanal bacteria extruded apically during root canal preparation using rotary ProTaper, K3XF, twisted, and hand K-file system. Seventy extracted single-rooted human mandibular premolar teeth were used. Access cavities were prepared and the teeth were mounted in glass vials. Root canals were then contaminated with a pure culture of Enterococcus faecalis (ATCC 29212) and incubated at 37°C for 24 h. The contaminated roots were divided into four experimental groups of 15 teeth each and one control group of 10 teeth. Group 1: ProTaper; Group 2: K3XF; Group 3: Twisted file; Group 4: Hand K-file; Group 5: Control group. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples were incubated in culture media for 24 h. Colonies of bacteria were counted and the results were given as number of colony-forming units (CFU)/ml. The obtained data were analyzed using the Kruskal-Wallis one-way analysis of variance and Mann-Whitney U-tests. There was a significant difference between the rotary and hand instrumentation system related to the apically extruded intracanal bacteria. Both the rotary and hand instrumentation systems extruded intracanal bacteria through the apical foramen. K3XF file system showed least bacterial extrusion amongst all instrumentation groups.

Gradient microfluidics enables rapid bacterial growth inhibition testing.

PubMed

Li, Bing; Qiu, Yong; Glidle, Andrew; McIlvenna, David; Luo, Qian; Cooper, Jon; Shi, Han-Chang; Yin, Huabing

2014-03-18

Bacterial growth inhibition tests have become a standard measure of the adverse effects of inhibitors for a wide range of applications, such as toxicity testing in the medical and environmental sciences. However, conventional well-plate formats for these tests are laborious and provide limited information (often being restricted to an end-point assay). In this study, we have developed a microfluidic system that enables fast quantification of the effect of an inhibitor on bacteria growth and survival, within a single experiment. This format offers a unique combination of advantages, including long-term continuous flow culture, generation of concentration gradients, and single cell morphology tracking. Using Escherichia coli and the inhibitor amoxicillin as one model system, we show excellent agreement between an on-chip single cell-based assay and conventional methods to obtain quantitative measures of antibiotic inhibition (for example, minimum inhibition concentration). Furthermore, we show that our methods can provide additional information, over and above that of the standard well-plate assay, including kinetic information on growth inhibition and measurements of bacterial morphological dynamics over a wide range of inhibitor concentrations. Finally, using a second model system, we show that this chip-based systems does not require the bacteria to be labeled and is well suited for the study of naturally occurring species. We illustrate this using Nitrosomonas europaea, an environmentally important bacteria, and show that the chip system can lead to a significant reduction in the period required for growth and inhibition measurements (<4 days, compared to weeks in a culture flask).

Inactivation/reactivation of antibiotic-resistant bacteria by a novel UVA/LED/TiO2 system.

PubMed

Xiong, Pei; Hu, Jiangyong

2013-09-01

In this study, an effective photocatalytic disinfection system was established using the newly emerged high power UVA/LED lamp. Crystallizing dish coated with TiO2 was prepared by 32-times impregnation-drying processes, and served as the supporting container for water samples. This study focused on the application of this UVA/LED system for the photocatalytic disinfection of selected antibiotic-resistant bacteria, Escherichia coli ATCC 700891. The disinfection performances were studied under various light intensities and illumination modes. Results show that higher light intensity could reach more significant inactivation of E. coli ATCC 700891. With the same UV dose, log-removal of antibiotic-resistant bacteria decreased with circle time in the studied range, while increased with duty circle. A "residual disinfecting effect" was found in the following dark period for bacteria collected at different phases of photocatalytic process. Residual disinfecting effect was found not significant for bacteria with 30 min periodic illumination. While residual disinfecting effect could kill almost all bacteria after 90 min UV periodic illumination within the following 240 min dark period. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of a Physics-Based Stabilization Criterion to Flight System Thermal Testing

NASA Technical Reports Server (NTRS)

Baker, Charles; Garrison, Matthew; Cottingham, Christine; Peabody, Sharon

2010-01-01

The theory shown here can provide thermal stability criteria based on physics and a goal steady state error rather than on an arbitrary "X% Q/mC(sub P)" method. The ability to accurately predict steady-state temperatures well before thermal balance is reached could be very useful during testing. This holds true for systems where components are changing temperature at different rates, although it works better for the components closest to the sink. However, the application to these test cases shows some significant limitations: This theory quickly falls apart if the thermal control system in question is tightly coupled to a large mass not accounted for in the calculations, so it is more useful in subsystem-level testing than full orbiter tests. Tight couplings to a fluctuating sink causes noise in the steady state temperature predictions.

Biomanufacturing and self-propulsion dynamics of nanoscale bacteria-enabled autonomous delivery systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Traore, Mahama A.; Behkam, Bahareh, E-mail: behkam@vt.edu; School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia 24061

Flagellated bacteria have superb self-propulsion capabilities and are able to effectively move through highly viscous fluid and semi-solid (porous) environments. This innate aptitude has been harvested for whole-cell actuation of bio-hybrid microrobotic systems with applications in directed transport and microassembly. In this work, we present the biomanufacturing of Nanoscale Bacteria-Enabled Autonomous Delivery Systems (NanoBEADS) by controlled self-assembly and investigate the role of nanoparticle load on the dynamics of their self-propulsion in aqueous environments. Each NanoBEADS agent is comprised of spherical polystyrene nanoparticles assembled onto the body of a flagellated Escherichia coli bacterium. We demonstrate that the NanoBEADS assembly configuration ismore » strongly dependent upon the nanoparticles to bacteria ratio. Furthermore, we characterized the stochastic motion of the NanoBEADS as a function of the quantity and size of the nanoparticle load and computationally analyzed the effect of the nanoparticle load on the experienced drag force. We report that the average NanoBEADS swimming speed is reduced to 65% of the free-swimming bacteria speed (31 μm/s) at the highest possible load. NanoBEADS can be utilized as single agents or in a collaborative swarm in order to carry out specific tasks in a wide range of applications ranging from drug delivery to whole cell biosensing.« less

Testing of a Natural Language Retrieval System for a Full Text Knowledge Base.

ERIC Educational Resources Information Center

Bernstein, Lionel M.; Williamson, Robert E.

1984-01-01

The Hepatitis Knowledge Base (text of prototype information system) was used for modifying and testing "A Navigator of Natural Language Organized (Textual) Data" (ANNOD), a retrieval system which combines probabilistic, linguistic, and empirical means to rank individual paragraphs of full text for similarity to natural language queries…

A Browser-Server-Based Tele-audiology System That Supports Multiple Hearing Test Modalities

PubMed Central

Yao, Daoyuan; Givens, Gregg

2015-01-01

Abstract Introduction: Millions of global citizens suffering from hearing disorders have limited or no access to much needed hearing healthcare. Although tele-audiology presents a solution to alleviate this problem, existing remote hearing diagnosis systems support only pure-tone tests, leaving speech and other test procedures unsolved, due to the lack of software and hardware to enable communication required between audiologists and their remote patients. This article presents a comprehensive remote hearing test system that integrates the two most needed hearing test procedures: a pure-tone audiogram and a speech test. Materials and Methods: This enhanced system is composed of a Web application server, an embedded smart Internet-Bluetooth® (Bluetooth SIG, Kirkland, WA) gateway (or console device), and a Bluetooth-enabled audiometer. Several graphical user interfaces and a relational database are hosted on the application server. The console device has been designed to support the tests and auxiliary communication between the local site and the remote site. Results: The study was conducted at an audiology laboratory. Pure-tone audiogram and speech test results from volunteers tested with this tele-audiology system are comparable with results from the traditional face-to-face approach. Conclusions: This browser-server–based comprehensive tele-audiology offers a flexible platform to expand hearing services to traditionally underserved groups. PMID:25919376

A Browser-Server-Based Tele-audiology System That Supports Multiple Hearing Test Modalities.

PubMed

Yao, Jianchu Jason; Yao, Daoyuan; Givens, Gregg

2015-09-01

Millions of global citizens suffering from hearing disorders have limited or no access to much needed hearing healthcare. Although tele-audiology presents a solution to alleviate this problem, existing remote hearing diagnosis systems support only pure-tone tests, leaving speech and other test procedures unsolved, due to the lack of software and hardware to enable communication required between audiologists and their remote patients. This article presents a comprehensive remote hearing test system that integrates the two most needed hearing test procedures: a pure-tone audiogram and a speech test. This enhanced system is composed of a Web application server, an embedded smart Internet-Bluetooth(®) (Bluetooth SIG, Kirkland, WA) gateway (or console device), and a Bluetooth-enabled audiometer. Several graphical user interfaces and a relational database are hosted on the application server. The console device has been designed to support the tests and auxiliary communication between the local site and the remote site. The study was conducted at an audiology laboratory. Pure-tone audiogram and speech test results from volunteers tested with this tele-audiology system are comparable with results from the traditional face-to-face approach. This browser-server-based comprehensive tele-audiology offers a flexible platform to expand hearing services to traditionally underserved groups.

Detection and categorization of bacteria habitats using shallow linguistic analysis

PubMed Central

2015-01-01

Background Information regarding bacteria biotopes is important for several research areas including health sciences, microbiology, and food processing and preservation. One of the challenges for scientists in these domains is the huge amount of information buried in the text of electronic resources. Developing methods to automatically extract bacteria habitat relations from the text of these electronic resources is crucial for facilitating research in these areas. Methods We introduce a linguistically motivated rule-based approach for recognizing and normalizing names of bacteria habitats in biomedical text by using an ontology. Our approach is based on the shallow syntactic analysis of the text that include sentence segmentation, part-of-speech (POS) tagging, partial parsing, and lemmatization. In addition, we propose two methods for identifying bacteria habitat localization relations. The underlying assumption for the first method is that discourse changes with a new paragraph. Therefore, it operates on a paragraph-basis. The second method performs a more fine-grained analysis of the text and operates on a sentence-basis. We also develop a novel anaphora resolution method for bacteria coreferences and incorporate it with the sentence-based relation extraction approach. Results We participated in the Bacteria Biotope (BB) Task of the BioNLP Shared Task 2013. Our system (Boun) achieved the second best performance with 68% Slot Error Rate (SER) in Sub-task 1 (Entity Detection and Categorization), and ranked third with an F-score of 27% in Sub-task 2 (Localization Event Extraction). This paper reports the system that is implemented for the shared task, including the novel methods developed and the improvements obtained after the official evaluation. The extensions include the expansion of the OntoBiotope ontology using the training set for Sub-task 1, and the novel sentence-based relation extraction method incorporated with anaphora resolution for Sub-task 2. These

Bacteriophage sensitivity patterns among bacteria isolated from marine waters

NASA Astrophysics Data System (ADS)

Moebus, K.; Nattkemper, H.

1981-09-01

Phage-host cross-reaction tests were performed with 774 bacterial strains and 298 bacteriophages. The bacteria (bacteriophages) were isolated at different times from water samples collected in the Atlantic Ocean between the European continental shelf and the Sargasso Sea: 733 (258) strains; in the North Sea near Helgoland: 31 (31) strains; and in the Bay of Biscay: 10 (9) strains. Of the Atlantic Ocean bacteria 326 were found to be susceptible to one or more Atlantic Ocean bacteriophage(s). The bacteriophage sensitivity patterns of these bacteria vary considerably, placing 225 of them in two large clusters of bacteriophage-host systems. Taking all into account, 250 of the 326 Atlantic Ocean bacteria are different from each other. This high degree of variation among the bacteria distinguishes microbial populations derived from widely separated eastern and western regions of the Atlantic Ocean. It also sets apart from each other the populations derived from samples collected at successive stations some 200 miles apart, although to a lesser degree. With bacterial populations found from samples collected on the way back and forth between Europe and the Sargasso Sea a gradual change was observed from "western" phage sensitivity patterns to "eastern" ones. Sixty-nine Atlantic Ocean bacteria are sensitive to bacteriophages isolated from the North Sea and the Bay of Biscay; of these only 26 strains are also susceptible to Atlantic Ocean phages. The interpretation of the results is based on the hydrographical conditions prevailing in the northern Atlantic Ocean including the North Sea, and on the assumption that the microbial populations investigated have undergone genetic changes while being transported within water masses from west to east.

A MEMBRANE FILTER PROCEDURE FOR ASSAYING CYTOTOXIC ACTIVITY IN HETEROTROPHIC BACTERIA ISOLATED FROM DRINKING WATER

EPA Science Inventory

Cytotoxic activity assays of Gram-negative, heterotrophic bacteria are often laborious and time consuming. The objective of this study was to develop in situ procedures for testing potential cytotoxic activities of heterotrophic bacteria isolated from drinking water systems. Wate...

A microprocessor-based automation test system for the experiment of the multi-stage compressor

NASA Astrophysics Data System (ADS)

Zhang, Huisheng; Lin, Chongping

1991-08-01

An automation test system that is controlled by the microprocessor and used in the multistage compressor experiment is described. Based on the analysis of the compressor experiment performances, a complete hardware system structure is set up. It is composed of a IBM PC/XT computer, a large scale sampled data system, the moving machine with three directions, the scanners, the digital instrumentation and some output devices. A program structure of real-time software system is described. The testing results show that this test system can take the measure of many parameter magnitudes in the blade row places and on a boundary layer in different states. The automatic extent and the accuracy of experiment is increased and the experimental cost is reduced.

Methods and Guidance for Testing the Efficacy of Antimicrobials against Biofilm Bacteria on Hard, Non-Porous Surfaces

EPA Pesticide Factsheets

EPA is announcing the availability of two test methods (MB-19 and MB-20) for evaluating the efficacy of antimicrobial pesticides against two biofilm bacteria, Pseudomonas aeruginosa and Staphylococcus aureus.

Biochemical characterization of Gram-positive and Gram-negative plant-associated bacteria with micro-Raman spectroscopy.

PubMed

Paret, Mathews L; Sharma, Shiv K; Green, Lisa M; Alvarez, Anne M

2010-04-01

Raman spectra of Gram-positive and Gram-negative plant bacteria have been measured with micro-Raman spectrometers equipped with 785 and 514.5 nm lasers. The Gram-positive bacteria Microbacterium testaceum, Paenibacillus validus, and Clavibacter michiganensis subsp. michiganensis have strong carotenoid bands in the regions 1155-1157 cm(-1) and 1516-1522 cm(-1) that differentiate them from other tested Gram-negative bacteria. In the Raman spectrum of Gram-positive bacteria Bacillus megaterium excited with 785 nm laser, the Raman bands at 1157 and 1521 cm(-1) are weak in intensity compared to other Gram-positive bacteria, and these bands did not show significant resonance Raman enhancement in the spectrum recorded with 514.5 nm laser excitation. The Gram-positive bacteria could be separated from each other based on the bands associated with the in-phase C=C (v(1)) vibrations of the polyene chain of carotenoids. None of the Gram-negative bacteria tested had carotenoid bands. The bacteria in the genus Xanthomonas have a carotenoid-like pigment, xanthomonadin, identified in Xanthomonas axonopodis pv. dieffenbachiae, and it is a unique Raman marker for the bacteria. The representative bands for xanthomonadin were the C-C stretching (v(2)) vibrations of the polyene chain at 1135-1136 cm(-1) and the in-phase C=C (v(1)) vibrations of the polyene chain at 1529-1531 cm(-1), which were distinct from the carotenoid bands of other tested bacteria. The tyrosine peak in the region 1170-1175 cm(-1) was the only other marker present in Gram-negative bacteria that was absent in all tested Gram-positives. A strong-intensity exopolysaccharide-associated marker at 1551 cm(-1) is a distinguishable feature of Enterobacter cloacae. The Gram-negative Agrobacterium rhizogenes and Ralstonia solanacearum were differentiated from each other and other tested bacteria on the basis of presence or absence and relative intensities of peaks. The principal components analysis (PCA) of the spectra

Characterization Test Procedures for Intersection Collision Avoidance Systems Based on Vehicle-to-Vehicle Communications

DOT National Transportation Integrated Search

2015-12-01

Characterization test procedures have been developed to quantify the performance of intersection collision avoidance (ICA) systems based on vehicle-to-vehicle communications. These systems warn the driver of an imminent crossing-path collision at a r...

Structure, Biology, and Therapeutic Application of Toxin–Antitoxin Systems in Pathogenic Bacteria

PubMed Central

Lee, Ki-Young; Lee, Bong-Jin

2016-01-01

Bacterial toxin–antitoxin (TA) systems have received increasing attention for their diverse identities, structures, and functional implications in cell cycle arrest and survival against environmental stresses such as nutrient deficiency, antibiotic treatments, and immune system attacks. In this review, we describe the biological functions and the auto-regulatory mechanisms of six different types of TA systems, among which the type II TA system has been most extensively studied. The functions of type II toxins include mRNA/tRNA cleavage, gyrase/ribosome poison, and protein phosphorylation, which can be neutralized by their cognate antitoxins. We mainly explore the similar but divergent structures of type II TA proteins from 12 important pathogenic bacteria, including various aspects of protein–protein interactions. Accumulating knowledge about the structure–function correlation of TA systems from pathogenic bacteria has facilitated a novel strategy to develop antibiotic drugs that target specific pathogens. These molecules could increase the intrinsic activity of the toxin by artificially interfering with the intermolecular network of the TA systems. PMID:27782085

Methods for broth dilution susceptibility testing of bacteria isolated from aquatic animals; approved guideline-second edition

USDA-ARS?s Scientific Manuscript database

Antimicrobial susceptibility testing is recommended to determine which antimicrobial agents should be considered for treating a bacterial pathogen. Many bacteria that cause disease in aquatic animals require growth conditions that vary substantially from routine terrestrial pathogens. It has thus ...

Antibacterial Activities of Endophytic Bacteria Isolated from Taxus brevifolia Against Foodborne Pathogenic Bacteria.

PubMed

Islam, Nurul; Choi, Jaehyuk; Baek, Kwang-Hyun

2018-05-01

Endophytes are a potential source of novel bioactive compounds with medicinal properties. In this study, 41 endophytic bacteria (EB) were isolated from tissues of a medicinally important plant Taxus brevifolia (Pacific yew). The objective was to screen all the EB isolates for their antibacterial effects against five foodborne pathogenic bacteria: Bacillus cereus ATCC10876, Staphylococcus aureus ATCC12600, Listeria monocytogenes ATCC19115, Escherichia coli ATCC43890, and Salmonella Typhimurium ATCC19585. Among the EB isolates, T. brevifolia seed (TbS)-8, T. brevifolia fleshy part of fruit (TbFl)-10, T. brevifolia leaf (TbL)-22, TbS-29, and TbL-34 exerted significant antibacterial activity against the tested foodborne pathogens. Especially TbFl-10 showed the highest antibacterial activity against all the tested bacteria and was identified as Paenibacillus kribbensis (Pk). Furthermore, an ethyl acetate extract of Pk-TbFl-10 possessed antibacterial activities against the tested five foodborne pathogenic bacteria, with zones of inhibition from 15.71 ± 2.85 to 13.01 ± 2.12 mm. Scanning electron microscopy analysis revealed ruptured, lysed, shrunk, and swollen cells of all the tested foodborne pathogens treated with the ethyl acetate extract of Pk-TbFl-10, suggesting that a metabolite(s) of Pk-TbFl-10 penetrates the cell membrane and causes cell lysis leading to cell death. Our results indicate that Pk-TbFl-10 isolated from T. brevifolia can serve as a novel source of natural antibacterial agents against foodborne pathogenic bacteria, with potential applications in the pharmaceutical industry.

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens

PubMed Central

Zeng, Melody Y.; Cisalpino, Daniel; Varadarajan, Saranyaraajan; Hellman, Judith; Warren, H. Shaw; Cascalho, Marilia; Inohara, Naohiro; Núñez, Gabriel

2016-01-01

The gut microbiota is compartmentalized in the intestinal lumen and induces local immune responses, but it remains unknown whether the gut microbiota can induce systemic response and contribute to systemic immunity. We report that selective gut symbiotic gram-negative bacteria were able to disseminate systemically to induce immunoglobulin G (IgG) response, which primarily targeted gram-negative bacterial antigens and conferred protection against systemic infections by E. coli and Salmonella by directly coating bacteria to promote killing by phagocytes. T cells and Toll-like receptor 4 on B cells were important in the generation of microbiota-specific IgG. We identified murein lipoprotein (MLP), a highly conserved gram-negative outer membrane protein, as a major antigen that induced systemic IgG homeostatically in both mice and humans. Administration of anti-MLP IgG conferred crucial protection against systemic Salmonella infection. Thus, our findings reveal an important function for the gut microbiota in combating systemic infection through the induction of protective IgG. PMID:26944199

Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns

NASA Astrophysics Data System (ADS)

Suchwalko, Agnieszka; Buzalewicz, Igor; Podbielska, Halina

2012-01-01

In the presented paper the optical system with converging spherical wave illumination for classification of bacteria species, is proposed. It allows for compression of the observation space, observation of Fresnel patterns, diffraction pattern scaling and low level of optical aberrations, which are not possessed by other optical configurations. Obtained experimental results have shown that colonies of specific bacteria species generate unique diffraction signatures. Analysis of Fresnel diffraction patterns of bacteria colonies can be fast and reliable method for classification and recognition of bacteria species. To determine the unique features of bacteria colonies diffraction patterns the image processing analysis was proposed. Classification can be performed by analyzing the spatial structure of diffraction patterns, which can be characterized by set of concentric rings. The characteristics of such rings depends on the bacteria species. In the paper, the influence of basic features and ring partitioning number on the bacteria classification, is analyzed. It is demonstrated that Fresnel patterns can be used for classification of following species: Salmonella enteritidis, Staplyococcus aureus, Proteus mirabilis and Citrobacter freundii. Image processing is performed by free ImageJ software, for which a special macro with human interaction, was written. LDA classification, CV method, ANOVA and PCA visualizations preceded by image data extraction were conducted using the free software R.

Field Tests of “In-Situ” Remediation of Groundwater From Dissolved Mercury Utilizing Sulfate Reducing Bacteria

EPA Science Inventory

Field tests of biologically active filters have been conducted at groundwater mercury pollution site in Pavlodar, Kazakhstan. The biofilters represented cultures of sulfate-reducing bacteria (SRB) immobilized on claydite imbedded in wells drilled down to basalt clay layer (14-17 ...

Testing nano-silver food packaging to evaluate silver migration and food spoilage bacteria on chicken meat.

PubMed

Gallocchio, Federica; Cibin, Veronica; Biancotto, Giancarlo; Roccato, Anna; Muzzolon, Orietta; Carmen, Losasso; Simone, Belluco; Manodori, Laura; Fabrizi, Alberto; Patuzzi, Ilaria; Ricci, Antonia

2016-06-01

Migration of nanomaterials from food containers into food is a matter of concern because of the potential risk for exposed consumers. The aims of this study were to evaluate silver migration from a commercially available food packaging containing silver nanoparticles into a real food matrix (chicken meat) under plausible domestic storage conditions and to test the contribution of such packaging to limit food spoilage bacteria proliferation. Chemical analysis revealed the absence of silver in chicken meatballs under the experimental conditions in compliance with current European Union legislation, which establishes a maximum level of 0.010 mg kg(-1) for the migration of non-authorised substances through a functional barrier (Commission Regulation (EU) No. 10/2011). On the other hand, microbiological tests (total microbial count, Pseudomonas spp. and Enterobacteriaceae) showed no relevant difference in the tested bacteria levels between meatballs stored in silver-nanoparticle plastic bags or control bags. This study shows the importance of testing food packaging not only to verify potential silver migration as an indicator of potential nanoparticle migration, but also to evaluate the benefits in terms of food preservation so as to avoid unjustified usage of silver nanoparticles and possible negative impacts on the environment.

Phage & phosphatase: a novel phage-based probe for rapid, multi-platform detection of bacteria.

PubMed

Alcaine, S D; Pacitto, D; Sela, D A; Nugen, S R

2015-11-21

Genetic engineering of bacteriophages allows for the development of rapid, highly specific, and easily manufactured probes for the detection of bacterial pathogens. A challenge for novel probes is the ease of their adoption in real world laboratories. We have engineered the bacteriophage T7, which targets Escherichia coli, to carry the alkaline phosphatase gene, phoA. This inclusion results in phoA overexpression following phage infection of E. coli. Alkaline phosphatase is commonly used in a wide range of diagnostics, and thus a signal produced by our phage-based probe could be detected using common laboratory equipment. Our work demonstrates the successful: (i) modification of T7 phage to carry phoA; (ii) overexpression of alkaline phosphatase in E. coli; and (iii) detection of this T7-induced alkaline phosphatase activity using commercially available colorimetric and chemilumiscent methods. Furthermore, we demonstrate the application of our phage-based probe to rapidly detect low levels of bacteria and discern the antibiotic resistance of E. coli isolates. Using our bioengineered phage-based probe we were able to detect 10(3) CFU per mL of E. coli in 6 hours using a chemiluminescent substrate and 10(4) CFU per mL within 7.5 hours using a colorimetric substrate. We also show the application of this phage-based probe for antibiotic resistance testing. We were able to determine whether an E. coli isolate was resistant to ampicillin within 4.5 hours using chemiluminescent substrate and within 6 hours using a colorimetric substrate. This phage-based scheme could be readily adopted in labs without significant capital investments and can be translated to other phage-bacteria pairs for further detection.

Microbiological methods for the water recovery systems test, revision 1.1

NASA Technical Reports Server (NTRS)

Rhoads, Tim; Kilgore, M. V., Jr.; Mikell, A. T., Jr.

1990-01-01

Current microbiological parameters specified to verify microbiological quality of Space Station Freedom water quality include the enumeration of total bacteria, anaerobes, aerobes, yeasts and molds, enteric bacteria, gram positives, gram negatives, and E. coli. In addition, other parameters have been identified as necessary to support the Water Recovery Test activities to be conducted at the NASA/MSFC later this year. These other parameters include aerotolerant eutrophic mesophiles, legionellae, and an additional method for heterotrophic bacteria. If inter-laboratory data are to be compared to evaluate quality, analytical methods must be eliminated as a variable. Therefore, each participating laboratory must utilize the same analytical methods and procedures. Without this standardization, data can be neither compared nor validated between laboratories. Multiple laboratory participation represents a conservative approach to insure quality and completeness of data. Invariably, sample loss will occur in transport and analyses. Natural variance is a reality on any test of this magnitude and is further enhanced because biological entities, capable of growth and death, are specific parameters of interest. The large variation due to the participation of human test subjects has been noted with previous testing. The resultant data might be dismissed as 'out of control' unless intra-laboratory control is included as part of the method or if participating laboratories are not available for verification. The purpose of this document is to provide standardized laboratory procedures for the enumeration of certain microorganisms in water and wastewater specific to the water recovery systems test. The document consists of ten separate cultural methods and one direct count procedure. It is not intended nor is it implied to be a complete microbiological methods manual.

A clinical decision support system for diagnosis of Allergic Rhinitis based on intradermal skin tests.

PubMed

Jabez Christopher, J; Khanna Nehemiah, H; Kannan, A

2015-10-01

Allergic Rhinitis is a universal common disease, especially in populated cities and urban areas. Diagnosis and treatment of Allergic Rhinitis will improve the quality of life of allergic patients. Though skin tests remain the gold standard test for diagnosis of allergic disorders, clinical experts are required for accurate interpretation of test outcomes. This work presents a clinical decision support system (CDSS) to assist junior clinicians in the diagnosis of Allergic Rhinitis. Intradermal Skin tests were performed on patients who had plausible allergic symptoms. Based on patient׳s history, 40 clinically relevant allergens were tested. 872 patients who had allergic symptoms were considered for this study. The rule based classification approach and the clinical test results were used to develop and validate the CDSS. Clinical relevance of the CDSS was compared with the Score for Allergic Rhinitis (SFAR). Tests were conducted for junior clinicians to assess their diagnostic capability in the absence of an expert. The class based Association rule generation approach provides a concise set of rules that is further validated by clinical experts. The interpretations of the experts are considered as the gold standard. The CDSS diagnoses the presence or absence of rhinitis with an accuracy of 88.31%. The allergy specialist and the junior clinicians prefer the rule based approach for its comprehendible knowledge model. The Clinical Decision Support Systems with rule based classification approach assists junior doctors and clinicians in the diagnosis of Allergic Rhinitis to make reliable decisions based on the reports of intradermal skin tests. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lactic acid bacteria found in fermented fish in Thailand.

PubMed

Tanasupawat, Somboon; Okada, Sanae; Komagata, Kazuo

1998-06-01

Forty-seven strains of homofermentative rod-shaped and 5 heterofermentative sphere-shaped lactic acid bacteria were isolated from 4 kinds of fermented fish (pla-ra, pla-chom, kung-chom, and hoi-dong) in Thailand. These bacteria were separated into four groups by phenotypic and chemotaxonomic characteristics, including fluorometric DNA-DNA hybridization. Five strains (Group I) contained meso-diaminopimelic acid in the cell wall. Four strains were identified as Lactobacillus pentosus, and one strain was L. plantarum. Tested strains of this group produced DL-lactic acid. The rest of the rod-shaped bacteria, 23 strains (Group II) and 19 strains (Group III), lacked meso-diaminopimelic acid in the cell wall and were identified as L. farciminis and Lactobacillus species, respectively. The tested strains of these groups produced L-lactic acid. The amount of cellular fatty acids of C16:0 and C18:1, and the DNA base compositions were significant for differentiating the strains in Groups II and III. Five strains of cocci in chains (Group IV) produced gas from glucose. The tested strains of this group produced d-lactic acid. They were identified as a Leuconostoc species. The distribution of these bacteria in fermented fish in Thailand is discussed.

Rapid, highly sensitive detection of Gram-negative bacteria with lipopolysaccharide based disposable aptasensor.

PubMed

Zhang, Jian; Oueslati, Rania; Cheng, Cheng; Zhao, Ling; Chen, Jiangang; Almeida, Raul; Wu, Jayne

2018-07-30

Gram-negative bacteria are one of the most common microorganisms in the environment. Their differential detection and recognition from Gram-positive bacteria has been attracting much attention over the years. Using Escherichia coli (E. coli) as a model, we demonstrated on-site detection of Gram-negative bacteria by an AC electrokinetics-based capacitive sensing method using commercial microelectrodes functionalized with an aptamer specific to lipopolysaccharides. Dielectrophoresis effect was utilized to enrich viable bacteria to the microelectrodes rapidly, achieving a detection limit of 10 2 cells/mL within a 30 s' response time. The sensor showed a negligible response to Staphylococcus aureus (S. aureus), a Gram-positive species. The developed sensor showed significant advantages in sensitivity, selectivity, cost, operation simplicity, and response time. Therefore, this sensing method has shown great application potential for environmental monitoring, food safety, and real-time diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

[Immobilization of introduced bacteria and degradation of pyrene and benzo(alpha) pyrene in soil by immobilized bacteria].

PubMed

Wang, Xin; Li, Peijun; Song, Shouzhi; Zhong, Yong; Zhang, Hui; Verkhozina, E V

2006-11-01

In this study, introduced bacteria were applied in the bioremediation of pyrene and benzo (alpha) pyrene in organic pollutants-contaminated soils, aimed to test whether it was feasible to introduce bacteria to environmental engineering. Three introduced bacteria were immobilized separately or together to degrade the pyrene and benzo (alpha) pyrene in soil, taking dissociated bacteria as the control, and comparing with three indigenous bacteria. The results showed that immobilized introduced bacteria, either single or mixed, had higher degradation efficiency than dissociated bacteria. Compared with indigenous bacteria, some introduced bacteria had predominance to some degree. The introduced bacteria-mixture had better degradation efficiency after being immobilized. The degradation rate of pyrene and benzo(alpha) pyrene after treated with immobilized bacteria-( B61-B67)-mixture for 96 hours was 43.49% and 38.55%, respectively.

Effectiveness of a computerized alert system based on re-testing intervals for limiting the inappropriateness of laboratory test requests.

PubMed

Lippi, Giuseppe; Brambilla, Marco; Bonelli, Patrizia; Aloe, Rosalia; Balestrino, Antonio; Nardelli, Anna; Ceda, Gian Paolo; Fabi, Massimo

2015-11-01

There is consolidated evidence that the burden of inappropriate laboratory test requests is very high, up to 70%. We describe here the function of a computerized alert system linked to the order entry, designed to limit the number of potentially inappropriate laboratory test requests. A computerized alert system based on re-testing intervals and entailing the generation of pop-up alerts when preset criteria of appropriateness for 15 laboratory tests were violated was implemented in two clinical wards of the University Hospital of Parma. The effectiveness of the system for limiting potentially inappropriate tests was monitored for 6months. Overall, 765/3539 (22%) test requests violated the preset criteria of appropriateness and generated the appearance of electronic alert. After alert appearance, 591 requests were annulled (17% of total tests requested and 77% of tests alerted, respectively). The total number of test requests violating the preset criteria of inappropriateness constantly decreased over time (26% in the first three months of implementation versus 17% in the following period; p<0.001). The total financial saving of test withdrawn was 3387 Euros (12.8% of the total test cost) throughout the study period. The results of this study suggest that a computerized alert system may be effective to limit the inappropriateness of laboratory test requests, generating significant economic saving and educating physicians to a more efficient use of laboratory resources. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Machine Reading for Extraction of Bacteria and Habitat Taxonomies

PubMed Central

Kordjamshidi, Parisa; Massa, Wouter; Provoost, Thomas; Moens, Marie-Francine

2015-01-01

There is a vast amount of scientific literature available from various resources such as the internet. Automating the extraction of knowledge from these resources is very helpful for biologists to easily access this information. This paper presents a system to extract the bacteria and their habitats, as well as the relations between them. We investigate to what extent current techniques are suited for this task and test a variety of models in this regard. We detect entities in a biological text and map the habitats into a given taxonomy. Our model uses a linear chain Conditional Random Field (CRF). For the prediction of relations between the entities, a model based on logistic regression is built. Designing a system upon these techniques, we explore several improvements for both the generation and selection of good candidates. One contribution to this lies in the extended exibility of our ontology mapper that uses an advanced boundary detection and assigns the taxonomy elements to the detected habitats. Furthermore, we discover value in the combination of several distinct candidate generation rules. Using these techniques, we show results that are significantly improving upon the state of art for the BioNLP Bacteria Biotopes task. PMID:27077141

Built-In Data-Flow Integration Testing in Large-Scale Component-Based Systems

NASA Astrophysics Data System (ADS)

Piel, Éric; Gonzalez-Sanchez, Alberto; Gross, Hans-Gerhard

Modern large-scale component-based applications and service ecosystems are built following a number of different component models and architectural styles, such as the data-flow architectural style. In this style, each building block receives data from a previous one in the flow and sends output data to other components. This organisation expresses information flows adequately, and also favours decoupling between the components, leading to easier maintenance and quicker evolution of the system. Integration testing is a major means to ensure the quality of large systems. Their size and complexity, together with the fact that they are developed and maintained by several stake holders, make Built-In Testing (BIT) an attractive approach to manage their integration testing. However, so far no technique has been proposed that combines BIT and data-flow integration testing. We have introduced the notion of a virtual component in order to realize such a combination. It permits to define the behaviour of several components assembled to process a flow of data, using BIT. Test-cases are defined in a way that they are simple to write and flexible to adapt. We present two implementations of our proposed virtual component integration testing technique, and we extend our previous proposal to detect and handle errors in the definition by the user. The evaluation of the virtual component testing approach suggests that more issues can be detected in systems with data-flows than through other integration testing approaches.

Development and Testing of an Ultracapacitor Based Uninterruptible Power Supply (UPS) System

NASA Technical Reports Server (NTRS)

Eichenberg, Dennis J.

2010-01-01

The NASA Glenn Research Center (GRC) initiated the development and testing of an ultracapacitor based uninterruptible power supply (UPS) system as a means to provide backup power for the many critical NASA applications. A UPS system typically utilizes batteries for energy storage. The battery is the most vulnerable part of the UPS system, requiring regular maintenance and replacement. Battery performance is also extremely temperature dependent. Ultracapacitors are ideal for UPS systems where long life, maintenance free operation, and excellent low temperature performance is essential. State of the art symmetric ultracapacitors were used for these tests. The ultracapacitors were interconnected in an innovative configuration to minimize interconnection impedance, and to provide voltage balancing. Ultracapacitors can be charged extremely rapidly and supply high current, which are essential characteristics for an effective UPS system. Charging ultracapacitors is significantly less complex than charging batteries since there is no chemical reaction occurring while charging ultracapacitors. The report concludes that the implementation of symmetric ultracapacitors in a UPS system can provide significant improvements in power system performance and reliability.

Multidrug-Resistance and Toxic Metal Tolerance of Medically Important Bacteria Isolated from an Aquaculture System

PubMed Central

Resende, Juliana Alves; Silva, Vânia L.; Fontes, Cláudia Oliveira; Souza-Filho, Job Alves; de Oliveira, Tamara Lopes Rocha; Coelho, Cíntia Marques; César, Dionéia Evangelista; Diniz, Cláudio Galuppo

2012-01-01

The use of antimicrobials and toxic metals should be considered carefully in aquaculture and surrounding environments. We aimed to evaluate medically relevant bacteria in an aquaculture system and their susceptibility to antimicrobials and toxic metals. Selective cultures for enterobacteria (ENT), non-fermenting Gram-negative rods (NFR) and Gram-positive cocci (GPC) were obtained from water samples collected in two different year seasons. The isolated bacteria were biochemically identified and antimicrobial and toxic metal susceptibility patterns were determined. Overall, 407 representative strains were recovered. In general, bacteria isolated from fish ponds showed higher multiple antibiotic resistance indices when compared to those isolated from a water-fed canal. Resistance to penicillin and azithromycin was observed more frequently in the GPC group, whereas resistance to ampicillin and ampicillin/sulbactam or gentamicin was observed more frequently in the ENT and NFR groups, respectively. All the isolated bacteria were tolerant to nickel, zinc, chromium and copper at high levels (≥1,024 μg mL−1), whereas tolerance to cadmium and mercury varied among the isolated bacteria (2–1,024 μg mL−1). Multidrug-resistant bacteria were more frequent and diverse in fish ponds than in the water-fed canal. A positive correlation was observed between antimicrobial resistance and metal tolerance. The data point out the need for water treatment associated with the aquaculture system. PMID:22972388

Genetic tools for the investigation of Roseobacter clade bacteria

PubMed Central

2009-01-01

Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria. PMID:20021642

Spatial Control of Bacteria Using Screen Printing

PubMed Central

Moon, Soonhee; Fritz, Ian L.; Singer, Zakary S.

2016-01-01

Abstract Synthetic biology has led to advances in both our understanding and engineering of genetic circuits that affect spatial and temporal behaviors in living cells. A growing array of native and synthetic circuits such as oscillators, pattern generators, and cell–cell communication systems has been studied, which exhibit spatiotemporal properties. To better understand the design principles of these genetic circuits, there is a need for versatile and precise methods for patterning cell populations in various configurations. In this study, we develop a screen printing methodology to pattern bacteria on agar, glass, and paper surfaces. Initially, we tested three biocompatible resuspension media with appropriate rheological properties for screen printing. Using microscopy, we characterized the resolution and bleed of bacteria screen prints on agar and glass surfaces, obtaining resolutions as low as 188 μm. Next, we engineered bacterial strains producing visible chromoproteins analogous to the cyan, magenta, and yellow subtractive color system for the creation of multicolored bacteria images. Using this system, we printed distinct populations in overlapping or interlocking designs on both paper and agar substrates. These proof-of-principle experiments demonstrated how the screen printing method could be used to study microbial community interactions and pattern formation of biofilms at submillimeter length scales. Overall, our approach allows for rapid and precise prototyping of patterned bacteria species that will be useful in the understanding and engineering of spatiotemporal behaviors in microbial communities. PMID:29577061

Nitrite oxidizing bacteria for water treatment in coastal aquaculture system

NASA Astrophysics Data System (ADS)

Noorak, S.; Rakkhiaw, S.; Limjirakhajornt, K.; Uppabullung, A.; Keawtawee, T.; Sangnoi, Y.

2018-04-01

This research aimed to isolate and characterize nitrite oxidizing bacteria and to study their capability for water quality improvement. Fourteen strains of bacteria with nitrite-oxidizing character were isolated after 21 days of enrichment in Pep-Beef-NOB medium contained NaNO2. Two strains, SF-1 and SF-5, showed highest nitrite removal rate for 42.42% and 37.2%, respectively. These strains were determined an efficiency of open-system wastewater treatment for 14 days. The results showed that control, SF-1 and SF-5 had remove ammonia from day 1 to day 6. At the end of the study, ammonia was removed by the control, SF-1 and SF-5 for 81.27%, 70.1% and 69.82%, respectively. Nitrite concentration was lowest at day 8 with removal rate of 98.73%, 98.3% and 97.24% from control, SF-1 and SF-5, respectively. However, nitrite concentration in control experiment was increased again at day 11 whereas in SF-1 and SF-5 were increased at day 13. Chemical Oxygen Demand (COD) was decreased by 77.78%, 73.50% and 78.63% in the control, SF-1 and SF-5, respectively. Biological Oxygen Demand (BOD) in the control, SF-1 and SF-5 were reduced by 85.92%, 79.53% and 82.09%, respectively. Based on 16S rRNA gene, SF-1 and SF-5 were identified as Bacillus vietnamensis and B. firmus, respectively.

Evaluation of the In Vitro Pyrogen Test System Based on Proinflammatory Cytokine Release from Human Monocytes: Comparison with a Human Whole Blood Culture Test System and with the Rabbit Pyrogen Test

PubMed Central

Nakagawa, Yukari; Maeda, Hideko; Murai, Toshimi

2002-01-01

The reliability of an in vitro pyrogen test system based on proinflammatory cytokine release from human monocytic cells was assessed by comparison with a test system based on a human whole blood culture as well as with the conventional rabbit pyrogen test. The human cells used as the pyrogen indicator cells were newly selected by subcloning of a human monocytic cell line, Mono-Mac-6. The selected cells, named MM6-CA8, responded to various pyrogens, including endotoxin, peptidoglycan (PG), Staphylococcus aureus Cowan 1 (SAC), and poly(I ·  C), with a high sensitivity and produced proinflammatory cytokines, such as interleukin 1 (IL-1), IL-6, and tumor necrosis factor alpha. Among these cytokines, IL-6 was produced most sensitively in response to traces of the pyrogens and detected in the largest quantities in the culture medium. The cytokine-producing responses of MM6-CA8 cells correlated significantly with the responses of cultured human whole blood, which represents an ex vivo culture test system reproducing pyrogen-induced cytokine production in the human body. In terms of cytokine inducibility, the pyrogens were ranked in the order endotoxin > PG > poly (I · C) > SAC in both culture systems, a ranking which almost agreed with the ranking of their pyrogenicity as assessed by the rabbit pyrogen test. These results suggest that the in vitro responsiveness of MM6-CA8 cells to various pyrogens is highly relevant for human pyrogenic reactions. Therefore, the in vitro test system is useful and reliable for detecting the presence of materials that are pyrogenic for humans. PMID:11986265

RNA-Based Methods Increase the Detection of Fecal Bacteria and Fecal Identifiers in Environmental Waters

EPA Science Inventory

We evaluated the use of qPCR RNA-based methods in the detection of fecal bacteria in environmental waters. We showed that RNA methods can increase the detection of fecal bacteria in multiple water matrices. The data suggest that this is a viable alternative for the detection of a...

Estimating Herd Immunity to Amphibian Chytridiomycosis in Madagascar Based on the Defensive Function of Amphibian Skin Bacteria

PubMed Central

Bletz, Molly C.; Myers, Jillian; Woodhams, Douglas C.; Rabemananjara, Falitiana C. E.; Rakotonirina, Angela; Weldon, Che; Edmonds, Devin; Vences, Miguel; Harris, Reid N.

2017-01-01

For decades, Amphibians have been globally threatened by the still expanding infectious disease, chytridiomycosis. Madagascar is an amphibian biodiversity hotspot where Batrachochytrium dendrobatidis (Bd) has only recently been detected. While no Bd-associated population declines have been reported, the risk of declines is high when invasive virulent lineages become involved. Cutaneous bacteria contribute to host innate immunity by providing defense against pathogens for numerous animals, including amphibians. Little is known, however, about the cutaneous bacterial residents of Malagasy amphibians and the functional capacity they have against Bd. We cultured 3179 skin bacterial isolates from over 90 frog species across Madagascar, identified them via Sanger sequencing of approximately 700 bp of the 16S rRNA gene, and characterized their functional capacity against Bd. A subset of isolates was also tested against multiple Bd genotypes. In addition, we applied the concept of herd immunity to estimate Bd-associated risk for amphibian communities across Madagascar based on bacterial antifungal activity. We found that multiple bacterial isolates (39% of all isolates) cultured from the skin of Malagasy frogs were able to inhibit Bd. Mean inhibition was weakly correlated with bacterial phylogeny, and certain taxonomic groups appear to have a high proportion of inhibitory isolates, such as the Enterobacteriaceae, Pseudomonadaceae, and Xanthamonadaceae (84, 80, and 75% respectively). Functional capacity of bacteria against Bd varied among Bd genotypes; however, there were some bacteria that showed broad spectrum inhibition against all tested Bd genotypes, suggesting that these bacteria would be good candidates for probiotic therapies. We estimated Bd-associated risk for sampled amphibian communities based on the concept of herd immunity. Multiple amphibian communities, including those in the amphibian diversity hotspots, Andasibe and Ranomafana, were estimated to be below

Development of a chemiluminescent and bioluminescent system for the detection of bacteria in wastewater effluent

NASA Technical Reports Server (NTRS)

Thomas, R. R.

1975-01-01

Automated chemiluminescent and bioluminescent sensors were developed for continuous monitoring of microbial levels in wastewater effluent. Development of the chemiluminescent system included optimization of reagent concentrations as well as two new techniques which will allow for increased sensitivity and specificity. The optimal reagent concentrations are 0.0025 M luminol and 0.0125 M sodium perborate in 0.75N sodium hydroxide before addition of sample. The methods developed to increase specificity include (1) extraction of porphyrins from bacteria collected in a filter using 0.1N NaOH - 50 percent Ethanol, and (2) use of the specific reaction rate characteristics for the different luminol catalysts. Since reaction times are different for each catalyst, the reaction can be made specific for bacteria by measuring only the light emission from the particular reaction time zone specific for bacteria. Developments of the bioluminescent firefly luciferase system were in the area of flow system design.

TTCN-3 Based Conformance Testing of Mobile Broadcast Business Management System in 3G Networks

NASA Astrophysics Data System (ADS)

Wang, Zhiliang; Yin, Xia; Xiang, Yang; Zhu, Ruiping; Gao, Shirui; Wu, Xin; Liu, Shijian; Gao, Song; Zhou, Li; Li, Peng

Mobile broadcast service is one of the emerging most important new services in 3G networks. To better operate and manage mobile broadcast services, mobile broadcast business management system (MBBMS) should be designed and developed. Such a system, with its distributed nature, complicated XML data and security mechanism, faces many challenges in testing technology. In this paper, we study the conformance testing methodology of MBBMS, and design and implement a MBBMS protocol conformance testing tool based on TTCN-3, a standardized test description language that can be used in black-box testing of reactive and distributed system. In this methodology and testing tool, we present a semi-automatic XML test data generation method of TTCN-3 test suite and use HMSC model to help the design of test suite. In addition, we also propose an integrated testing method for hierarchical MBBMS security architecture. This testing tool has been used in industrial level’s testing.

Integrated vehicle-based safety systems (IVBSS) : heavy truck extended pilot test summary report.

DOT National Transportation Integrated Search

2009-05-01

This report describes the findings and recommendations from the heavy-truck (HT) extended pilot test (EPT) conducted by University of Michigan Transportation Research Institute (UMTRI) and its partners under the Integrated Vehicle-Based Safety System...

Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts.

PubMed

Wilson, Deborah A; Young, Stephen; Timm, Karen; Novak-Weekley, Susan; Marlowe, Elizabeth M; Madisen, Neil; Lillie, Jennifer L; Ledeboer, Nathan A; Smith, Rebecca; Hyke, Josh; Griego-Fullbright, Christen; Jim, Patricia; Granato, Paul A; Faron, Matthew L; Cumpio, Joven; Buchan, Blake W; Procop, Gary W

2017-06-01

A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts. In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed. Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively). The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization. © American Society for Clinical Pathology, 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Description and field test of an in situ coliform monitoring system

NASA Technical Reports Server (NTRS)

Grana, D. C.; Wilkins, J. R.

1979-01-01

A prototype in situ system for monitoring the levels of fecal coliforms in shallow water bodies was developed and evaluated. This system was based on the known relationship between the concentration of the coliform bacteria and the amount of hydrogen they produce during growth in a complex organic media. The prototype system consists of a sampler platform, which sits on the bottom; a surface buoy, which transmits sampler-generated data; and a shore station, which receives, displays the data, and controls the sampler. The concept of remote monitoring of fecal coliform concentrations by utilizing a system based on the electrochemical method was verified during the evaluation of the prototype.

Simulation-based Testing of Control Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozmen, Ozgur; Nutaro, James J.; Sanyal, Jibonananda

It is impossible to adequately test complex software by examining its operation in a physical prototype of the system monitored. Adequate test coverage can require millions of test cases, and the cost of equipment prototypes combined with the real-time constraints of testing with them makes it infeasible to sample more than a small number of these tests. Model based testing seeks to avoid this problem by allowing for large numbers of relatively inexpensive virtual prototypes that operate in simulation time at a speed limited only by the available computing resources. In this report, we describe how a computer system emulatormore » can be used as part of a model based testing environment; specifically, we show that a complete software stack including operating system and application software - can be deployed within a simulated environment, and that these simulations can proceed as fast as possible. To illustrate this approach to model based testing, we describe how it is being used to test several building control systems that act to coordinate air conditioning loads for the purpose of reducing peak demand. These tests involve the use of ADEVS (A Discrete Event System Simulator) and QEMU (Quick Emulator) to host the operational software within the simulation, and a building model developed with the MODELICA programming language using Buildings Library and packaged as an FMU (Functional Mock-up Unit) that serves as the virtual test environment.« less

Bacteria as a new model system for aging studies: investigations using light microscopy.

PubMed

Ackermann, Martin

2008-04-01

Aging-the decline in an individual's condition over time-is at the center of an active research field in medicine and biology. Some very basic questions have, however, remained unresolved, the most fundamental being: do all organisms age? Or are there organisms that would continue to live forever if not killed by external forces? For a long time it was believed that aging only affected organisms such as animals, plants, and fungi. Bacteria, in contrast, were assumed to be potentially immortal and until recently this assertion remained untested. We used phase-contrast microscopy (on an Olympus BX61) to follow individual bacterial cells over many divisions to prove that some bacteria show a distinction between an aging mother cell and a rejuvenated daughter, and that these bacteria thus age. This indicates that aging is a more fundamental property of organisms than was previously assumed. Bacteria can now be used as very simple model system for investigating why and how organisms age.

Toward Genome-Based Metabolic Engineering in Bacteria.

PubMed

Oesterle, Sabine; Wuethrich, Irene; Panke, Sven

2017-01-01

Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry. Copyright © 2017 Elsevier Inc. All rights reserved.

EXSPRT: An Expert Systems Approach to Computer-Based Adaptive Testing.

ERIC Educational Resources Information Center

Frick, Theodore W.; And Others

Expert systems can be used to aid decision making. A computerized adaptive test (CAT) is one kind of expert system, although it is not commonly recognized as such. A new approach, termed EXSPRT, was devised that combines expert systems reasoning and sequential probability ratio test stopping rules. EXSPRT-R uses random selection of test items,…

Environmental Systems Test Stand

NASA Astrophysics Data System (ADS)

Barta, D.; Young, J.; Ewert, M.; Lee, S.; Wells, P.; Fortson, R.; Castillo, J.

A test stand has been developed for the evaluation of prototype lighting, environmental control and crop cultivation technologies for plant production within an advanced life support system. Design of the test stand was based on preliminary designs of the center growth bay of the Biomass Production Chamber, one of several modules of the Bioregenerative Planetary Life Support Systems Test Complex (BIO- Plex). It consists of two controlled-environment shelves, each with 4.7 m2 of area for crop growth (150 cm width, 315 cm length). There are two chilled water loops, one for operation at conventional temperatures (5-10C) for air temperature and humidity control and one for operation at higher temperatures (15-50C) for waste heat acquisition and heating. Modular light boxes, utilizing either air-cooled or water- jacketed HPS lamps, have been developed. This modular design will allow for easy replacement of new lighting technologies within the light banks. An advanced data acquisition and control system has been developed utilizing localized, networked- based data acquisition modules and programmed with object-based control software.

Integrated vehicle-based safety systems : heavy-truck field operational test key findings report.

DOT National Transportation Integrated Search

2010-08-01

This document presents key findings from the heavy-truck field operational test conducted as : part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of : analyses performed by the University of Michigan Transporta...

Integrated vehicle-based safety systems light-vehicle field operational test key findings report.

DOT National Transportation Integrated Search

2011-01-01

This document presents key findings from the light-vehicle field operational test conducted as part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of analyses performed by the University of Michigan Transportati...

Integrated vehicle-based safety systems light-vehicle field operational test key findings report.

DOT National Transportation Integrated Search

2011-01-01

"This document presents key findings from the light-vehicle field operational test conducted as part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of analyses performed by the University of Michigan Transportat...

On-target digestion of collected bacteria for MALDI mass spectrometry.

PubMed

Dugas, Alton J; Murray, Kermit K

2008-10-03

An on-target protein digestion system was developed for the identification of microorganisms in collected bioaerosols using off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Bacteria analysis techniques based on MALDI-MS were adapted for use with an orthogonal MALDI quadrupole-time-of-flight mass spectrometer. Bioaerosols were generated using a pneumatic nebulizer and infused into a chamber for sampling. An Andersen N6 single-stage impactor was used to collect the bioaerosols on a MALDI target. On-target digestion was carried out inside temporary mini-wells placed over the impacted samples. The wells served as miniature reactors for proteolysis. Collected test aerosol particles containing the protein cytochrome c and E. coli bacteria were proteolyzed in situ using trypsin or cyanogen bromide. A total of 19 unique proteins were identified for E. coli. Using the TOF-MS spectra of the digested samples, peptide mass mapping was performed using the MASCOT search engine and an iterative search technique.

Discrete bacteria foraging optimization algorithm for graph based problems - a transition from continuous to discrete

NASA Astrophysics Data System (ADS)

Sur, Chiranjib; Shukla, Anupam

2018-03-01

Bacteria Foraging Optimisation Algorithm is a collective behaviour-based meta-heuristics searching depending on the social influence of the bacteria co-agents in the search space of the problem. The algorithm faces tremendous hindrance in terms of its application for discrete problems and graph-based problems due to biased mathematical modelling and dynamic structure of the algorithm. This had been the key factor to revive and introduce the discrete form called Discrete Bacteria Foraging Optimisation (DBFO) Algorithm for discrete problems which exceeds the number of continuous domain problems represented by mathematical and numerical equations in real life. In this work, we have mainly simulated a graph-based road multi-objective optimisation problem and have discussed the prospect of its utilisation in other similar optimisation problems and graph-based problems. The various solution representations that can be handled by this DBFO has also been discussed. The implications and dynamics of the various parameters used in the DBFO are illustrated from the point view of the problems and has been a combination of both exploration and exploitation. The result of DBFO has been compared with Ant Colony Optimisation and Intelligent Water Drops Algorithms. Important features of DBFO are that the bacteria agents do not depend on the local heuristic information but estimates new exploration schemes depending upon the previous experience and covered path analysis. This makes the algorithm better in combination generation for graph-based problems and combination generation for NP hard problems.

Bacteria in atmospheric waters: Detection, characteristics and implications

NASA Astrophysics Data System (ADS)

Hu, Wei; Niu, Hongya; Murata, Kotaro; Wu, Zhijun; Hu, Min; Kojima, Tomoko; Zhang, Daizhou

2018-04-01

In this review paper, we synthesize the current knowledges about bacteria in atmospheric waters, e.g., cloud, fog, rain, and snow, most of which were obtained very recently. First, we briefly describe the importance of bacteria in atmospheric waters, i.e., the essentiality of studying bacteria in atmospheric waters in understanding aerosol-cloud-precipitation-climate interactions in the Earth system. Next, approaches to collect atmospheric water samples for the detection of bacteria and methods to identify the bacteria are summarized and compared. Then the available data on the abundance, viability and community composition of bacteria in atmospheric waters are summarized. The average bacterial concentration in cloud water was usually on the order 104-105 cells mL-1, while that in precipitation on the order 103-104 cells mL-1. Most of the bacteria were viable or metabolically active. Their community composition was highly diverse and differed at various sites. Factors potentially influencing the bacteria, e.g., air pollution levels and sources, meteorological conditions, seasonal effect, and physicochemical properties of atmospheric waters, are described. After that, the implications of bacteria present in atmospheric waters, including their effect on nucleation in clouds, atmospheric chemistry, ecosystems and public health, are briefly discussed. Finally, based on the current knowledges on bacteria in atmospheric waters, which in fact remains largely unknown, we give perspectives that should be paid attention to in future studies.

Design and implementation of a general and automatic test platform base on NI PXI system

NASA Astrophysics Data System (ADS)

Shi, Long

2018-05-01

Aiming at some difficulties of test equipment such as the short product life, poor generality and high development cost, a general and automatic test platform base on NI PXI system is designed in this paper, which is able to meet most test requirements of circuit boards. The test platform is devided into 5 layers, every layer is introduced in detail except for the "Equipment Under Test" layer. An output board of a track-side equipment, which is an important part of high speed train control system, is taken as an example to make the functional circuit test by the test platform. The results show that the test platform is easy to realize add-on functions development, automatic test, wide compatibility and strong generality.

Chip-based in situ hybridization for identification of bacteria from the human microbiome.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Light, Yooli Kim; Meagher, Robert J.; Singh, Anup K.

2010-11-01

The emerging field of metagenomics seeks to assess the genetic diversity of complex mixed populations of bacteria, such as those found at different sites within the human body. A single person's mouth typically harbors up to 100 bacterial species, while surveys of many people have found more than 700 different species, of which {approx}50% have never been cultivated. In typical metagenomics studies, the cells themselves are destroyed in the process of gathering sequence information, and thus the connection between genotype and phenotype is lost. A great deal of sequence information may be generated, but it is impossible to assign anymore » given sequence to a specific cell. We seek non-destructive, culture-independent means of gathering sequence information from selected individual cells from mixed populations. As a first step, we have developed a microfluidic device for concentrating and specifically labeling bacteria from a mixed population. Bacteria are electrophoretically concentrated against a photopolymerized membrane element, and then incubated with a specific fluorescent label, which can include antibodies as well as specific or non-specific nucleic acid stains. Unbound stain is washed away, and the labeled bacteria are released from the membrane. The stained cells can then be observed via epifluorescence microscopy, or counted via flow cytometry. We have tested our device with three representative bacteria from the human microbiome: E. coli (gut, Gram-negative), Lactobacillus acidophilus (mouth, Gram-positive), and Streptococcus mutans (mouth, Gram-positive), with results comparable to off-chip labeling techniques.« less

EHR based Genetic Testing Knowledge Base (iGTKB) Development

PubMed Central

2015-01-01

Background The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to fill this gap is to develop an intelligent genetic test recommendation system that not only can provide a comprehensive view of genetic tests as education resources, but also can recommend the most appropriate genetic tests to patients based on clinical evidence. In this study, we developed an EHR based Genetic Testing Knowledge Base for Individualized Medicine (iGTKB). Methods We extracted genetic testing information and patient medical records from EHR systems at Mayo Clinic. Clinical features have been semi-automatically annotated from the clinical notes by applying a Natural Language Processing (NLP) tool, MedTagger suite. To prioritize clinical features for each genetic test, we compared odds ratio across four population groups. Genetic tests, genetic disorders and clinical features with their odds ratios have been applied to establish iGTKB, which is to be integrated into the Genetic Testing Ontology (GTO). Results Overall, there are five genetic tests operated with sample size greater than 100 in 2013 at Mayo Clinic. A total of 1,450 patients who was tested by one of the five genetic tests have been selected. We assembled 243 clinical features from the Human Phenotype Ontology (HPO) for these five genetic tests. There are 60 clinical features with at least one mention in clinical notes of patients taking the test. Twenty-eight clinical features with high odds ratio (greater than 1) have been selected as dominant features and deposited into iGTKB with their associated information about genetic tests and genetic disorders. Conclusions In this study, we developed an EHR based genetic testing knowledge base, iGTKB. iGTKB will be integrated into the GTO by providing relevant

EHR based Genetic Testing Knowledge Base (iGTKB) Development.

PubMed

Zhu, Qian; Liu, Hongfang; Chute, Christopher G; Ferber, Matthew

2015-01-01

The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to fill this gap is to develop an intelligent genetic test recommendation system that not only can provide a comprehensive view of genetic tests as education resources, but also can recommend the most appropriate genetic tests to patients based on clinical evidence. In this study, we developed an EHR based Genetic Testing Knowledge Base for Individualized Medicine (iGTKB). We extracted genetic testing information and patient medical records from EHR systems at Mayo Clinic. Clinical features have been semi-automatically annotated from the clinical notes by applying a Natural Language Processing (NLP) tool, MedTagger suite. To prioritize clinical features for each genetic test, we compared odds ratio across four population groups. Genetic tests, genetic disorders and clinical features with their odds ratios have been applied to establish iGTKB, which is to be integrated into the Genetic Testing Ontology (GTO). Overall, there are five genetic tests operated with sample size greater than 100 in 2013 at Mayo Clinic. A total of 1,450 patients who was tested by one of the five genetic tests have been selected. We assembled 243 clinical features from the Human Phenotype Ontology (HPO) for these five genetic tests. There are 60 clinical features with at least one mention in clinical notes of patients taking the test. Twenty-eight clinical features with high odds ratio (greater than 1) have been selected as dominant features and deposited into iGTKB with their associated information about genetic tests and genetic disorders. In this study, we developed an EHR based genetic testing knowledge base, iGTKB. iGTKB will be integrated into the GTO by providing relevant clinical evidence, and ultimately to

Differentiating the growth phases of single bacteria using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Strola, S. A.; Marcoux, P. R.; Schultz, E.; Perenon, R.; Simon, A.-C.; Espagnon, I.; Allier, C. P.; Dinten, J.-M.

2014-03-01

In this paper we present a longitudinal study of bacteria metabolism performed with a novel Raman spectrometer system. Longitudinal study is possible with our Raman setup since the overall procedure to localize a single bacterium and collect a Raman spectrum lasts only 1 minute. Localization and detection of single bacteria are performed by means of lensfree imaging, whereas Raman signal (from 600 to 3200 cm-1) is collected into a prototype spectrometer that allows high light throughput (HTVS technology, Tornado Spectral System). Accomplishing time-lapse Raman spectrometry during growth of bacteria, we observed variation in the net intensities for some band groups, e.g. amides and proteins. The obtained results on two different bacteria species, i.e. Escherichia coli and Bacillus subtilis clearly indicate that growth affects the Raman chemical signature. We performed a first analysis to check spectral differences and similarities. It allows distinguishing between lag, exponential and stationary growth phases. And the assignment of interest bands to vibration modes of covalent bonds enables the monitoring of metabolic changes in bacteria caused by growth and aging. Following the spectra analysis, a SVM (support vector machine) classification of the different growth phases is presented. In sum this longitudinal study by means of a compact and low-cost Raman setup is a proof of principle for routine analysis of bacteria, in a real-time and non-destructive way. Real-time Raman studies on metabolism and viability of bacteria pave the way for future antibiotic susceptibility testing.

Division-Based, Growth Rate Diversity in Bacteria

PubMed Central

Gangwe Nana, Ghislain Y.; Ripoll, Camille; Cabin-Flaman, Armelle; Gibouin, David; Delaune, Anthony; Janniere, Laurent; Grancher, Gerard; Chagny, Gaelle; Loutelier-Bourhis, Corinne; Lentzen, Esther; Grysan, Patrick; Audinot, Jean-Nicolas; Norris, Vic

2018-01-01

To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance. PMID:29867792

Antibiotic Production by Anaerobic Bacteria1

PubMed Central

Sturgen, Nancy O.; Casida, L. E.

1962-01-01

Soils from aerobic and anaerobic sources were investigated for the possible presence of bacteria which produce antibiotics under anaerobic conditions of growth. The screening techniques devised for this study yielded 157 soil bacteria which, during anaerobic growth, produced antibiotic activity against aerobic test bacteria. Studies on choice of media, presence of oxygen, and changes in antibiotic activity during growth indicated that representative strains of these bacteria produced mixtures of antibiotics. The activity was heat labile. PMID:13918037

Heavy metal toxicity to bacteria - are the existing growth media accurate enough to determine heavy metal toxicity?

PubMed

Rathnayake, I V N; Megharaj, Mallavarapu; Krishnamurti, G S R; Bolan, Nanthi S; Naidu, Ravi

2013-01-01

A new minimal medium was formulated considering the limitations of the existing media for testing heavy metal sensitivity to bacteria. Toxicity of cadmium and copper to three bacteria was investigated in the new medium and compared with three other media commonly used to study the effect of the toxic metals. Based on speciation data arrived at using ion-selective electrodes, the available free-metal concentration in solution was highest in the MES-buffered medium. This finding was strongly supported by the estimated EC(50) values for the metals tested based on the toxicity bioassays. The free-ionic cadmium and copper concentrations in the medium provide more accurate determination of metal concentrations that affects the bacteria, than with most of other existing media. This will avoid doubts on other media and misleading conclusions relevant to the toxicity of heavy metals to bacteria and provides a better option for the study of metal-bacteria interactions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System.

PubMed

Pinto, Ameet J; Marcus, Daniel N; Ijaz, Umer Zeeshan; Bautista-de Lose Santos, Quyen Melina; Dick, Gregory J; Raskin, Lutgarde

2016-01-01

We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation

Design, Fabrication, and Shakeout Testing of ATALANTE Dissolver Off-Gas Sorbent-Based Capture System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Jr, Joseph Franklin; Jubin, Robert Thomas; Jordan, Jacob A.

A sorbent-based capture system designed for integration into the existing dissolver off-gas (DOG) treatment system at the ATelier Alpha et Laboratoires pour ANalyses, Transuraniens et Etudes de retraitement (ATALANTE) facility has been successfully designed and fabricated and has undergone shakeout testing. Discussions with personnel from the ATALANTE facility provided guidance that was used for the design. All components for this system were specified, procured, and received on site at Oak Ridge National Laboratory (ORNL). The system was then fabricated and tested at ORNL to verify operation. Shakeout testing resulted in a simplified system. This system should be easily installed intomore » the existing facility and should be straightforward to operate during future experimental testing. All parts were selected to be compatible with ATALANTE power supplies, space requirements, and the existing DOG treatment system. Additionally, the system was demonstrated to meet all of four design requirements. These include (1) a dissolver off-gas flow rate of ≤100 L/h (1.67 L/min), (2) an external temperature of ≤50°C for all system components placed in the hot cell, (3) a sorbent bed temperature of ~150°C, and (4) a gas temperature of ~150°C upon entry into the sorbent bed. The system will be ready for shipment and installation in the existing DOG treatment system at ATALANTE in FY 2016.« less

Number of viable bacteria and presumptive antibiotic residues in milk fed to calves on commercial dairies.

PubMed

Selim, S A; Cullor, J S

1997-10-15

To assess the number of bacteria and presumptive antibiotic residues in milk fed to calves and to identify those bacteria and the antibiotic susceptibility of selected bacterial strains. Cross-sectional prospective study. 189 samples obtained from 12 local dairies. Samples of waste milk and milk-based fluids (eg, milk replacer, colostrum, bulk-tank milk) were obtained. Cumulative number of viable bacteria was determined. Bacteria were cultured aerobically, and antibiotic susceptibility testing of selected strains was performed. Presumptive antibiotic residues were detected by use of test kits. Geometric mean of the cumulative number of bacteria for waste milk samples was significantly higher than for other types of milk or milk-based products. Streptococcus sp (84/165 samples) and Enterobacteriaceae (83/165 samples) were the predominant bacteria identified, followed by Staphylococcus sp (68/165 samples). Escherichia coli was the gram-negative species most commonly isolated (52/165 samples; 32%); however, none were strain O157. Salmonella sp or Mycoplasma sp were not isolated. Of 189 samples, 119 (63%) were positive when tested for beta-lactams or tetracycline by use of 2 commercially available assays. In vitro, some bacteria were resistant to commonly used antibiotics. Waste milk that has not been effectively treated (eg, pasteurization) to reduce microbial load prior to use as calf feed should be used with caution, because it may contain a high number of bacteria that may be pathogenic to cattle and human beings. Antibiotic residues that would constitute violative amounts and existence of multiple antibiotic resistant bacterial strains are concerns in calf health management and dairy food safety.

Inhibition of various gram-positive and gram- negative bacteria growth on selenium nanoparticle coated paper towels

PubMed Central

Wang, Qi; Larese-Casanova, Philip; Webster, Thomas J

2015-01-01

There are wide spread bacterial contamination issues on various paper products, such as paper towels hanging in sink splash zones or those used to clean surfaces, filter papers used in water and air purifying systems, and wrappings used in the food industry; such contamination may lead to the potential spread of bacteria and consequent severe health concerns. In this study, selenium nanoparticles were coated on normal paper towel surfaces through a quick precipitation method, introducing antibacterial properties to the paper towels in a healthy way. Their effectiveness at preventing biofilm formation was tested in bacterial assays involving Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus epidermidis. The results showed significant and continuous bacteria inhibition with about a 90% reduction from 24 to 72 hours for gram-positive bacteria including S. aureus and S. epidermidis. The selenium coated paper towels also showed significant inhibition of gram-negative bacteria like P. aeruginosa and E. coli growth at about 57% and 84%, respectively, after 72 hours of treatment. Therefore, this study established a promising selenium-based antibacterial strategy to prevent bacterial growth on paper products, which may lead to the avoidance of bacteria spreading and consequent severe health concerns. PMID:25926733

Inhibition of various gram-positive and gram-negative bacteria growth on selenium nanoparticle coated paper towels.

PubMed

Wang, Qi; Larese-Casanova, Philip; Webster, Thomas J

2015-01-01

There are wide spread bacterial contamination issues on various paper products, such as paper towels hanging in sink splash zones or those used to clean surfaces, filter papers used in water and air purifying systems, and wrappings used in the food industry; such contamination may lead to the potential spread of bacteria and consequent severe health concerns. In this study, selenium nanoparticles were coated on normal paper towel surfaces through a quick precipitation method, introducing antibacterial properties to the paper towels in a healthy way. Their effectiveness at preventing biofilm formation was tested in bacterial assays involving Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus epidermidis. The results showed significant and continuous bacteria inhibition with about a 90% reduction from 24 to 72 hours for gram-positive bacteria including S. aureus and S. epidermidis. The selenium coated paper towels also showed significant inhibition of gram-negative bacteria like P. aeruginosa and E. coli growth at about 57% and 84%, respectively, after 72 hours of treatment. Therefore, this study established a promising selenium-based antibacterial strategy to prevent bacterial growth on paper products, which may lead to the avoidance of bacteria spreading and consequent severe health concerns.

Antimicrobial Activities of Bacteria Associated with the Brown Alga Padina pavonica

PubMed Central

Ismail, Amel; Ktari, Leila; Ahmed, Mehboob; Bolhuis, Henk; Boudabbous, Abdellatif; Stal, Lucas J.; Cretoiu, Mariana Silvia; El Bour, Monia

2016-01-01

Macroalgae belonging to the genus Padina are known to produce antibacterial compounds that may inhibit growth of human- and animal pathogens. Hitherto, it was unclear whether this antibacterial activity is produced by the macroalga itself or by secondary metabolite producing epiphytic bacteria. Here we report antibacterial activities of epiphytic bacteria isolated from Padina pavonica (Peacocks tail) located on northern coast of Tunisia. Eighteen isolates were obtained in pure culture and tested for antimicrobial activities. Based on the 16S rRNA gene sequences the isolates were closely related to Proteobacteria (12 isolates; 2 Alpha- and 10 Gammaproteobacteria), Firmicutes (4 isolates) and Actinobacteria (2 isolates). The antimicrobial activity was assessed as inhibition of growth of 12 species of pathogenic bacteria (Aeromonas salmonicida, A. hydrophila, Enterobacter xiangfangensis, Enterococcus faecium, Escherichia coli, Micrococcus sp., Salmonella typhimurium, Staphylococcus aureus, Streptococcus sp., Vibrio alginoliticus, V. proteolyticus, V. vulnificus) and one pathogenic yeast (Candida albicans). Among the Firmicutes, isolate P8, which is closely related to Bacillus pumilus, displayed the largest spectrum of growth inhibition of the pathogenic bacteria tested. The results emphasize the potential use of P. pavonica associated antagonistic bacteria as producers of novel antibacterial compounds. PMID:27462308

Ethernet-based test stand for a CAN network

NASA Astrophysics Data System (ADS)

Ziebinski, Adam; Cupek, Rafal; Drewniak, Marek

2017-11-01

This paper presents a test stand for the CAN-based systems that are used in automotive systems. The authors propose applying an Ethernet-based test system that supports the virtualisation of a CAN network. The proposed solution has many advantages compared to classical test beds that are based on dedicated CAN-PC interfaces: it allows the physical constraints associated with the number of interfaces that can be simultaneously connected to a tested system to be avoided, which enables the test time for parallel tests to be shortened; the high speed of Ethernet transmission allows for more frequent sampling of the messages that are transmitted by a CAN network (as the authors show in the experiment results section) and the cost of the proposed solution is much lower than the traditional lab-based dedicated CAN interfaces for PCs.

In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems--a potential broad application on bioremediation.

PubMed

Huang, Yili; Zeng, Yanhua; Yu, Zhiliang; Zhang, Jing; Feng, Hao; Lin, Xiuchun

2013-11-01

Phylogenetic overlaps between aromatics-degrading bacteria and acyl-homoserine-lactone (AHL) or autoinducer (AI) based quorum-sensing (QS) bacteria were evident in literatures; however, the diversity of bacteria with both activities had never been finely described. In-silico searching in NCBI genome database revealed that more than 11% of investigated population harbored both aromatic ring-hydroxylating-dioxygenase (RHD) gene and AHL/AI-synthetase gene. These bacteria were distributed in 10 orders, 15 families, 42 genus and 78 species. Horizontal transfers of both genes were common among them. Using enrichment and culture dependent method, 6 Sphingomonadales and 4 Rhizobiales with phenanthrene- or pyrene-degrading ability and AHL-production were isolated from marine, wetland and soil samples. Thin-layer-chromatography and gas-chromatography-mass-spectrum revealed that these Sphingomonads produced various AHL molecules. This is the first report of highly diverse bacteria that harbored both aromatics-degrading and QS systems. QS regulation may have broad impacts on aromatics biodegradation, and would be a new angle for developing bioremediation technology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of bacteriophages in post-harvest control of human pathogenic and food spoiling bacteria.

PubMed

Pérez Pulido, Rubén; Grande Burgos, Maria José; Gálvez, Antonio; Lucas López, Rosario

2016-10-01

Bacteriophages have attracted great attention for application in food biopreservation. Lytic bacteriophages specific for human pathogenic bacteria can be isolated from natural sources such as animal feces or industrial wastes where the target bacteria inhabit. Lytic bacteriophages have been tested in different food systems for inactivation of main food-borne pathogens including Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Salmonella enterica, Shigella spp., Campylobacter jejuni and Cronobacter sakazkii, and also for control of spoilage bacteria. Application of lytic bacteriophages could selectively control host populations of concern without interfering with the remaining food microbiota. Bacteriophages could also be applied for inactivation of bacteria attached to food contact surfaces or grown as biofilms. Bacteriophages may receive a generally recognized as safe status based on their lack of toxicity and other detrimental effects to human health. Phage preparations specific for L. monocytogenes, E. coli O157:H7 and S. enterica serotypes have been commercialized and approved for application in foods or as part of surface decontamination protocols. Phage endolysins have a broader host specificity compared to lytic bacteriophages. Cloned endolysins could be used as natural preservatives, singly or in combination with other antimicrobials such as bacteriocins.

Characterization of lactic acid bacteria from local cow´s milk kefir

NASA Astrophysics Data System (ADS)

Ismail, YS; Yulvizar, C.; Mazhitov, B.

2018-03-01

One of products from milk fermentation is kefir. It is made by adding kefir grains which are composed of lactic acid bacteria and yeast into milk. The lactic acid bacteria are a group of bacteria that produce antimicrobial substances and able to inhibit the growth of pathogenic bacteria. In this research, the lactic acid bacteria were isolated from Aceh local cow`s milk kefir to determine the genus of the isolates. The methods used in the characterization of lactic acid bacteria are colony morphology, cell morphology, and biochemical tests which includes a catalase test; 5%, 6.5%, and 10% salt endurance tests; 37°C and 14°C temperature endurance tests, SIM test, TSIA test, MR-VP test, and O/F test. Of the four isolates found from the cow’s milk kefir, two isolates were confirmed as lactic acid bacteria (isolates SK-1 and SK-4). Both isolates are Gram positive bacteria, and have negative catalase activity. From the observations of colony morphology, cell morphology, and biochemical tests, it was found that the genus of SK-1 is Lactobacillus and the genus of SK-4 is Enterococcus.

Polydiacetylene-Based Liposomes: An "Optical Tongue" for Bacteria Detection and Identification

ERIC Educational Resources Information Center

West, Matthew R.; Hanks, Timothy W.; Watson, Rhett T.

2009-01-01

Food- and water-borne bacteria are a major health concern worldwide. Current detection methods are time-consuming and require sophisticated equipment that is not always readily available. However, new techniques based on nanotechnology are under development that will result in a new generation of sensors. In this experiment, liposomes are…

Living bacteria in silica gels

NASA Astrophysics Data System (ADS)

Nassif, Nadine; Bouvet, Odile; Noelle Rager, Marie; Roux, Cécile; Coradin, Thibaud; Livage, Jacques

2002-09-01

The encapsulation of enzymes within silica gels has been extensively studied during the past decade for the design of biosensors and bioreactors. Yeast spores and bacteria have also been recently immobilized within silica gels where they retain their enzymatic activity, but the problem of the long-term viability of whole cells in an inorganic matrix has never been fully addressed. It is a real challenge for the development of sol-gel processes. Generic tests have been performed to check the viability of Escherichia coli bacteria in silica gels. Surprisingly, more bacteria remain culturable in the gel than in an aqueous suspension. The metabolic activity of the bacteria towards glycolysis decreases slowly, but half of the bacteria are still viable after one month. When confined within a mineral environment, bacteria do not form colonies. The exchange of chemical signals between isolated bacteria rather than aggregates can then be studied, a point that could be very important for 'quorum sensing'.

Aptamer-based hydrogel barcodes for the capture and detection of multiple types of pathogenic bacteria.

PubMed

Xu, Yueshuang; Wang, Huan; Luan, Chengxin; Liu, Yuxiao; Chen, Baoan; Zhao, Yuanjin

2018-02-15

Rapid and sensitive diagnosing hematological infections based on the separation and detection of pathogenic bacteria in the patient's blood is a significant challenge. To address this, we herein present a new barcodes technology that can simultaneously capture and detect multiple types of pathogenic bacteria from a complex sample. The barcodes are poly (ethylene glycol) (PEG) hydrogel inverse opal particles with characteristic reflection peak codes that remain stable during bacteria capture on their surfaces. As the spherical surface of the particles has ordered porous nanostructure, the barcodes can provide not only more surface area for probe immobilization and reaction, but also a nanopatterned platform for highly efficient bioreactions. In addition, the PEG hydrogel scaffold could decrease the non-specificity adsorption by its anti-adhesive effect, and the decorated aptamer probes in the scaffolds could increase the sensitivity, reliability, and specificity of the bacteria capture and detection. Moreover, the tagged magnetic nanoparticles in the PEG scaffold could impart the barcodes with controllable movement under magnetic fields, which can be used to significantly increase the reaction speed and simplify the processing of the bioassays. Based on the describe barcodes, it was demonstrated that the bacteria could be captured and identified even at low bacterial concentrations (100 CFU mL -1 ) within 2.5h, which is effectively shortened in comparison with the "gold standard" in clinic. These features make the barcodes ideal for capturing and detecting multiple bacteria from clinical samples for hematological infection diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

Development and Validation of a Portable Hearing Self-Testing System Based on a Notebook Personal Computer.

PubMed

Liu, Yan; Yang, Dong; Xiong, Fen; Yu, Lan; Ji, Fei; Wang, Qiu-Ju

2015-09-01

Hearing loss affects more than 27 million people in mainland China. It would be helpful to develop a portable and self-testing audiometer for the timely detection of hearing loss so that the optimal clinical therapeutic schedule can be determined. The objective of this study was to develop a software-based hearing self-testing system. The software-based self-testing system consisted of a notebook computer, an external sound card, and a pair of 10-Ω insert earphones. The system could be used to test the hearing thresholds by individuals themselves in an interactive manner using software. The reliability and validity of the system at octave frequencies of 0.25 Hz to 8.0 kHz were analyzed in three series of experiments. Thirty-seven normal-hearing particpants (74 ears) were enrolled in experiment 1. Forty individuals (80 ears) with sensorineural hearing loss (SNHL) participated in experiment 2. Thirteen normal-hearing participants (26 ears) and 37 participants (74 ears) with SNHL were enrolled in experiment 3. Each participant was enrolled in only one of the three experiments. In all experiments, pure-tone audiometry in a sound insulation room (standard test) was regarded as the gold standard. SPSS for Windows, version 17.0, was used for statistical analysis. The paired t-test was used to compare the hearing thresholds between the standard test and software-based self-testing (self-test) in experiments 1 and 2. In experiment 3 (main study), one-way analysis of variance and post hoc comparisons were used to compare the hearing thresholds among the standard test and two rounds of the self-test. Linear correlation analysis was carried out for the self-tests performed twice. The concordance was analyzed between the standard test and the self-test using the kappa method. p < 0.05 was considered statistically significant. Experiments 1 and 2: The hearing thresholds determined by the two methods were not significantly different at frequencies of 250, 500, or 8000 Hz (p > 0

SSME Post Test Diagnostic System: Systems Section

NASA Technical Reports Server (NTRS)

Bickmore, Timothy

1995-01-01

An assessment of engine and component health is routinely made after each test firing or flight firing of a Space Shuttle Main Engine (SSME). Currently, this health assessment is done by teams of engineers who manually review sensor data, performance data, and engine and component operating histories. Based on review of information from these various sources, an evaluation is made as to the health of each component of the SSME and the preparedness of the engine for another test or flight. The objective of this project - the SSME Post Test Diagnostic System (PTDS) - is to develop a computer program which automates the analysis of test data from the SSME in order to detect and diagnose anomalies. This report primarily covers work on the Systems Section of the PTDS, which automates the analyses performed by the systems/performance group at the Propulsion Branch of NASA Marshall Space Flight Center (MSFC). This group is responsible for assessing the overall health and performance of the engine, and detecting and diagnosing anomalies which involve multiple components (other groups are responsible for analyzing the behavior of specific components). The PTDS utilizes several advanced software technologies to perform its analyses. Raw test data is analyzed using signal processing routines which detect features in the data, such as spikes, shifts, peaks, and drifts. Component analyses are performed by expert systems, which use 'rules-of-thumb' obtained from interviews with the MSFC data analysts to detect and diagnose anomalies. The systems analysis is performed using case-based reasoning. Results of all analyses are stored in a relational database and displayed via an X-window-based graphical user interface which provides ranked lists of anomalies and observations by engine component, along with supporting data plots for each.

Apical extrusion of intracanal bacteria following use of two engine-driven instrumentation techniques.

PubMed

Er, K; Sümer, Z; Akpinar, K E

2005-12-01

To evaluate the number of bacteria extruded apically from extracted teeth ex vivo after canal instrumentation using the two engine-driven techniques utilizing nickel-titanium instruments (ProTaper and System GT). Forty extracted single-rooted human mandibular premolar teeth were used. Access cavities were prepared and root canals were then contaminated with a suspension of Enterococcus faecalis and dried. The contaminated roots were divided into two experimental groups of 15 teeth each and one control group of 10 teeth. Group 1, ProTaper group: the root canals were instrumented using ProTaper instruments. Group 2, System GT group: the root canals were instrumented using System GT instruments. Group 3, control group: no instrumentation was attempted. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples from the vials were incubated in culture media for 24 h. Colonies of bacteria were counted and the results were given as number of colony-forming units. The data obtained were analysed using the Kruskal-Wallis one-way analysis of variance and Mann-Whitney U-tests, with alpha = 0.05 as the level for statistical significance. There was no significant difference as to the number of extruded bacteria between the ProTaper and System GT engine-driven systems (P > 0.05). Both engine-driven nickel-titanium systems extruded bacteria through the apical foramen.

Vancomycin-resistant gene identification from live bacteria on an integrated microfluidic system by using low temperature lysis and loop-mediated isothermal amplification

PubMed Central

Chang, Wen-Hsin; Yu, Ju-ching; Yang, Sung-Yi; Lin, Yi-Cheng; Wang, Chih-Hung; You, Huey-Ling; Wu, Jiunn-Jong; Lee, Gwo-Bin

2017-01-01

Vancomycin-resistant Enterococcus (VRE) is a kind of enterococci, which shows resistance toward antibiotics. It may last for a long period of time and meanwhile transmit the vancomycin-resistant gene (vanA) to other bacteria. In the United States alone, the resistant rate of Enterococcus to vancomycin increased from a mere 0.3% to a whopping 40% in the past two decades. Therefore, timely diagnosis and control of VRE is of great need so that clinicians can prevent patients from becoming infected. Nowadays, VRE is diagnosed by antibiotic susceptibility test or molecular diagnosis assays such as matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and polymerase chain reaction. However, the existing diagnostic methods have some drawbacks, for example, time-consumption, no genetic information, or high false-positive rate. This study reports an integrated microfluidic system, which can automatically identify the vancomycin resistant gene (vanA) from live bacteria in clinical samples. A new approach using ethidium monoazide, nucleic acid specific probes, low temperature chemical lysis, and loop-mediated isothermal amplification (LAMP) has been presented. The experimental results showed that the developed system can detect the vanA gene from live Enterococcus in joint fluid samples with detection limit as low as 10 colony formation units/reaction within 1 h. This is the first time that an integrated microfluidic system has been demonstrated to detect vanA gene from live bacteria by using the LAMP approach. With its high sensitivity and accuracy, the proposed system may be useful to monitor antibiotic resistance genes from live bacteria in clinical samples in the near future. PMID:28798845

Best practices for implementing, testing and using a cloud-based communication system in a disaster situation.

PubMed

Makowski, Dale

2016-01-01

This paper sets out the basics for approaching the selection and implementation of a cloud-based communication system to support a business continuity programme, including: • consideration for how a cloud-based communication system can enhance a business continuity programme; • descriptions of some of the more popular features of a cloud-based communication system; • options to evaluate when selecting a cloud-based communication system; • considerations for how to design a system to be most effective for an organisation; • best practices for how to conduct the initial load of data to a cloud-based communication system; • best practices for how to conduct an initial validation of the data loaded to a cloud-based communication system; • considerations for how to keep contact information in the cloud-based communication system current and accurate; • best practices for conducting ongoing system testing; • considerations for how to conduct user training; • review of other potential uses of a cloud-based communication system; and • review of other tools and features many cloud-based communication systems may offer.

Testing the usability of two automated home-based patient-management systems.

PubMed

Farzanfar, Ramesh; Finkelstein, Joseph; Friedman, Robert H

2004-04-01

To explore to what extent observation and semistructured in-depth interviews provide effective tools for usability testing of two automated home-based systems aimed at monitoring patients' health status at home and improving self-care. Telephone-Linked Care for Diet Adherence in Dyslipidemia (TLC-DietAid) used computer telephony to interact with users and Home Asthma Telemonitoring System (HAT System) used a combination of Personal Digital Assistant (palmtops) and the Internet for similar purposes. Both systems were evaluated in two separate pilot studies. Our pilot studies uncovered "medium-specific" and "content-specific" issues that addressed either the process of the interaction or its content. The results demonstrated that patient-users tended to evaluate each system on the basis of how it fit into everyday life and corresponded to personal preferences. The methodology also allowed the system designers to understand users' concerns and the context of adoption in order to introduce necessary changes to the design to address such concerns.

Effects of bovine milk lactoperoxidase system on some bacteria.

PubMed

Cankaya, M; Sişecioğlu, M; Bariş, O; Güllüce, M; Ozdemir, H

2010-01-01

Bovine lactoperoxidase (LPO) was purified from skimmed milk using amberlite CG-50-H+ resin, CM sephadex C-50 ion-exchange chromatography, and sephadex G-100 gel filtration chromatography. Lactoperoxidase was purified 20.45-fold with a yield of 28.8%. Purity of enzyme checked by sodium dodecyl sulphate-polyacrylamide gel electrophoresis method and a single band was observed. Km was 0.25 mM at 20 degrees C, Vmax value was 7.95 micromol/ml min at 20 degrees C (pH 6.0). Antibacterial study was done by disk diffusion method of Kir-by-Bauer using Mueller-Hinton agar medium with slight modification. Bovine LPO showed high antibacterial activity in 100 mM thiocyanate-100 mM H2O2 medium for some bacteria (Brevibacillus centrosaurus, B. choshinensis, B. lyticum, Cedecea davisae, Chryseobacterium indoltheticum, Clavibacter michiganense pv. insidiosum, Kocuria erythromyxa, K. kristinae, K. rosea, K. varians, Paenibacillus validus, Pseudomonas syringae pv. populans, Ralstonia pickettii, Rhodococcus wratislaviensis, Serratia fonticola, Streptomyces violaceusniger, Vibrio cholerae-nonO1) respectively, and compared with well known antibacterial substances (levofloxacin, netilmicin). LPO system has inhibition effects on all type bacteria and concentration is really important such as LPO-100 mM thiocyanate-100 mM H2O2 system was proposed as an effective agent against many factors causing several diseases.

[Development of molecular detection of food-borne pathogenic bacteria using miniaturized microfluidic devices].

PubMed

Iván, Kristóf; Maráz, Anna

2015-12-20

Detection and identification of food-borne pathogenic bacteria are key points for the assurance of microbiological food safety. Traditional culture-based methods are more and more replaced by or supplemented with nucleic acid based molecular techniques, targeting specific (preferably virulence) genes in the genomes. Internationally validated DNA amplification - most frequently real-time polymerase chain reaction - methods are applied by the food microbiological testing laboratories for routine analysis, which will result not only in shortening the time for results but they also improve the performance characteristics (e.g. sensitivity, specificity) of the methods. Beside numerous advantages of the polymerase chain reaction based techniques for routine microbiological analysis certain drawbacks have to be mentioned, such as the high cost of the equipment and reagents, as well as the risk of contamination of the laboratory environment by the polymerase chain reaction amplicons, which require construction of an isolated laboratory system. Lab-on-a-chip systems can integrate most of these laboratory processes within a miniaturized device that delivers the same specificity and reliability as the standard protocols. The benefits of miniaturized devices are: simple - often automated - use, small overall size, portability, sterility due to single use possibility. These miniaturized rapid diagnostic tests are being researched and developed at the best research centers around the globe implementing various sample preparation and molecular DNA amplification methods on-chip. In parallel, the aim of the authors' research is to develop microfluidic Lab-on-a-chip devices for the detection and identification of food-borne pathogenic bacteria.

Rapid and automated enumeration of viable bacteria in compost using a micro-colony auto counting system.

PubMed

Wang, Xiaodan; Yamaguchi, Nobuyasu; Someya, Takashi; Nasu, Masao

2007-10-01

The micro-colony method was used to enumerate viable bacteria in composts. Cells were vacuum-filtered onto polycarbonate filters and incubated for 18 h on LB medium at 37 degrees C. Bacteria on the filters were stained with SYBR Green II, and enumerated using a newly developed micro-colony auto counting system which can automatically count micro-colonies on half the area of the filter within 90 s. A large number of bacteria in samples retained physiological activity and formed micro-colonies within 18 h, whereas most could not form large colonies on conventional media within 1 week. The results showed that this convenient technique can enumerate viable bacteria in compost rapidly for its efficient quality control.

A study on the selection of indigenous leaching-bacteria for effective bioleaching

NASA Astrophysics Data System (ADS)

Oh, S. J.; Cho, K. H.; Kim, B. J.; Choi, N. C.; Park, C. Y.

2012-04-01

Bioleaching technology, which is based on the ability of microorganisms to transform solid compounds into soluble and extractable valuable elements that can be recovered, has been rapidly developed in recent decades for its advantages, which include mild reaction condition, low energy consumption, simple process, low environmental impact and being suitable for low grade mine tailings and residues. The bacteria activities (survival, adaptation of toxically environments etc.) in the bioleaching technology play a key role in the solubilization of metals. The purpose of this study was to selection of optimal leaching-bacteria through changed pH and redox potential on bio-oxidation in batch experiments for successful bioleaching technology. Twenty three indigenous bacteria used throughout this study, leaching-bacteria were obtained from various geochemical conditions; bacteria inhabitation type (acid mine drainage, mine wastes leachate and sulfur hot springs) and base-metal type (sulfur, sulfide, iron and coal). Bio-oxidation experiment result was showed that 9 cycles (1 cycle - 28days) after the leaching-bacteria were inoculated to a leaching medium, pH was observed decreasing and redox potential increased. In the bacteria inhabitation type, bio-oxidation of sulfur hot springs bacteria was greater than other types (acid mine drainage and mine wastes leachate). In addition, bio-oxidation on base-metal type was appeared sulfur was greater than other types (sulfide, iron and coal). This study informs basic knowledge when bacteria apply to eco-/economic resources utilization studies including the biomining and the recycling of mine waste system.

Microfluidic Capillaric Circuit for Rapid and Facile Bacteria Detection.

PubMed

Olanrewaju, Ayokunle Oluwafemi; Ng, Andy; DeCorwin-Martin, Philippe; Robillard, Alessandra; Juncker, David

2017-06-20

Urinary tract infections (UTI) are one of the most common bacterial infections and would greatly benefit from a rapid point-of-care diagnostic test. Although significant progress has been made in developing microfluidic systems for nucleic acid and whole bacteria immunoassay tests, their practical application is limited by complex protocols, bulky peripherals, and slow operation. Here we present a microfluidic capillaric circuit (CC) optimized for rapid and automated detection of bacteria in urine. Molds for CCs were constructed using previously established design rules, then 3D-printed and replicated into poly(dimethylsiloxane). CCs autonomously and sequentially performed all liquid delivery steps required for the assay. For efficient bacteria capture, on-the-spot packing of antibody-functionalized microbeads was completed in <20 s followed by autonomous sequential delivery of 100 μL of bacteria sample, biotinylated detection antibodies, fluorescent streptavidin conjugate, and wash buffer for a total volume ≈115 μL. The assay was completed in <7 min. Fluorescence images of the microbead column revealed captured bacteria as bright spots that were easily counted manually or using an automated script for user-independent assay readout. The limit of detection of E. coli in synthetic urine was 1.2 × 10 2 colony-forming-units per mL (CFU/mL), which is well below the clinical diagnostic criterion (>10 5 CFU/mL) for UTI. The self-powered, peripheral-free CC presented here has potential for use in rapid point-of-care UTI screening.

Engineering solutions to improve the removal of fecal indicator bacteria by bioinfiltration systems during intermittent flow of stormwater.

PubMed

Mohanty, Sanjay K; Torkelson, Andrew A; Dodd, Hanna; Nelson, Kara L; Boehm, Alexandria B

2013-10-01

Bioinfiltration systems facilitate the infiltration of urban stormwater into soil and reduce high flow events and flooding. Stormwater carries a myriad of pollutants including fecal indicator bacteria (FIB). Significant knowledge gaps exist about the ability of bioinfiltration systems to remove and retain FIB. The present study investigates the ability of model, simplified bioinfiltration systems containing quartz sand and iron oxide-coated quartz sand (IOCS) to remove two FIB (Enterococcus faecalis and Escherichia coli) suspended in synthetic stormwater with and without natural organic matter (NOM) as well as the potential for accumulated FIB to be remobilized during intermittent flow. The experiments were conducted in two phases: (1) the saturated columns packed with either sand or IOCS were contaminated by injecting stormwater with bacteria followed by injection of sterile stormwater and (2) the contaminated columns were subjected to intermittent infiltration of sterile stormwater preceded by a pause during which columns were either kept saturated or drained by gravity. During intermittent flow, fewer bacteria were released from the saturated column compared to the column drained by gravity: 12% of attached E. coli and 3% of attached Ent. faecalis were mobilized from the drained sand column compared to 3% of attached E. coli and 2% attached Ent. faecalis mobilized from the saturated sand column. Dry and wet cycles introduce moving air-water interfaces that can scour bacteria from grain surfaces. During intermittent flows, less than 0.2% of attached bacteria were mobilized from IOCS, which bound both bacteria irreversibly in the absence of NOM. Addition of NOM, however, increased bacterial mobilization from IOCS: 50% of attached E. coli and 8% of attached Ent. faecalis were released from IOCS columns during draining and rewetting. Results indicate that using geomedia such as IOCS that promote irreversible attachment of bacteria, and maintaining saturated

Evaluation of Polymerase Chain Reaction for Detecting Coliform Bacteria in Drinking Water Sources.

PubMed

Isfahani, Bahram Nasr; Fazeli, Hossein; Babaie, Zeinab; Poursina, Farkhondeh; Moghim, Sharareh; Rouzbahani, Meisam

2017-01-01

Coliform bacteria are used as indicator organisms for detecting fecal pollution in water. Traditional methods including microbial culture tests in lactose-containing media and enzyme-based tests for the detection of β-galactosidase; however, these methods are time-consuming and less specific. The aim of this study was to evaluate polymerase chain reaction (PCR) for detecting coliform. Totally, 100 of water samples from Isfahan drinking water source were collected. Coliform bacteria and Escherichia coli were detected in drinking water using LacZ and LamB genes in PCR method performed in comparison with biochemical tests for all samples. Using phenotyping, 80 coliform isolates were found. The results of the biochemical tests illustrated 78.7% coliform bacteria and 21.2% E. coli . PCR results for LacZ and LamB genes were 67.5% and 17.5%, respectively. The PCR method was shown to be an effective, sensitive, and rapid method for detecting coliform and E. coli in drinking water from the Isfahan drinking water sources.

Effect of Feeding Palm Oil By-Products Based Diets on Total Bacteria, Cellulolytic Bacteria and Methanogenic Archaea in the Rumen of Goats

PubMed Central

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats. PMID:24756125

Effect of feeding palm oil by-products based diets on total bacteria, cellulolytic bacteria and methanogenic archaea in the rumen of goats.

PubMed

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats.

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

PubMed

Dvořák, Pavel; Nikel, Pablo I; Damborský, Jiří; de Lorenzo, Víctor

2017-11-15

Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms-specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow. Copyright © 2017 Elsevier Inc. All rights reserved.

Phylogenetic assessment of heterotrophic bacteria from a water distribution system using 16S rDNA sequencing.

PubMed

Tokajian, Sima T; Hashwa, Fuad A; Hancock, Ian C; Zalloua, Pierre A

2005-04-01

Determination of a heterotrophic plate count (HPC) for drinking-water samples alone is not enough to assess possible health hazards associated with sudden changes in the bacterial count. Speciation is very crucial to determine whether the population includes pathogens and (or) opportunistic pathogens. Most of the isolates recovered from drinking water samples could not be allocated to a specific phylogenetic branch based on the use of conventional diagnostic methods. The present study had to use phylogenetic analysis, which was simplified by determining and using the first 500-bp sequence of the 16S rDNA, to successfully identify the type and species of bacteria found in the samples. Gram-positive bacteria alpha-, beta-, and gamma-Proteobacteria were found to be the major groups representing the heterotrophic bacteria in drinking water. The study also revealed that the presence of sphingomonads in drinking water supplies may be much more common than has been reported so far and thus further studies are merited. The intermittent mode of supply, mainly characterized by water stagnation and flow interruption associated possibly with biofilm detachment, raised the possibility that the studied bacterial populations in such systems represented organisms coming from 2 different niches, the biofilm and the water column.

CRISPR-based screening of genomic island excision events in bacteria.

PubMed

Selle, Kurt; Klaenhammer, Todd R; Barrangou, Rodolphe

2015-06-30

Genomic analysis of Streptococcus thermophilus revealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats-CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs, in silico prediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. Targeting lacZ within the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac(-) survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling.

Killer Pigments in Bacteria: An Ecological Nightmare.

ERIC Educational Resources Information Center

Benathen, Isaiah A.; Saccardi, Marion

2000-01-01

Describes an alternative to teaching ecology by using bacteria to test competitor survival. Students observe a time-dependent selective killing of other unrelated bacteria by Pseudomonas aeruginosa. (SAH)

Characterization of airborne bacteria at an underground subway station.

PubMed

Dybwad, Marius; Granum, Per Einar; Bruheim, Per; Blatny, Janet Martha

2012-03-01

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence- and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization-time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence- and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers.

Characterization of Airborne Bacteria at an Underground Subway Station

PubMed Central

Dybwad, Marius; Granum, Per Einar; Bruheim, Per

2012-01-01

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence- and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization–time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence- and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers. PMID:22247150

Portable Health Algorithms Test System

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.; Wong, Edmond; Fulton, Christopher E.; Sowers, Thomas S.; Maul, William A.

2010-01-01

A document discusses the Portable Health Algorithms Test (PHALT) System, which has been designed as a means for evolving the maturity and credibility of algorithms developed to assess the health of aerospace systems. Comprising an integrated hardware-software environment, the PHALT system allows systems health management algorithms to be developed in a graphical programming environment, to be tested and refined using system simulation or test data playback, and to be evaluated in a real-time hardware-in-the-loop mode with a live test article. The integrated hardware and software development environment provides a seamless transition from algorithm development to real-time implementation. The portability of the hardware makes it quick and easy to transport between test facilities. This hard ware/software architecture is flexible enough to support a variety of diagnostic applications and test hardware, and the GUI-based rapid prototyping capability is sufficient to support development execution, and testing of custom diagnostic algorithms. The PHALT operating system supports execution of diagnostic algorithms under real-time constraints. PHALT can perform real-time capture and playback of test rig data with the ability to augment/ modify the data stream (e.g. inject simulated faults). It performs algorithm testing using a variety of data input sources, including real-time data acquisition, test data playback, and system simulations, and also provides system feedback to evaluate closed-loop diagnostic response and mitigation control.

End-Use Load and Conservation Assessment Program : Co-Instrumentation Test of Two Microcomputer-Based Energy Monitoring Systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fishbaugher, M. J.

1985-05-01

The decreasing cost of microcomputers along with improvements in power metering circuitry have changed the way in which electrical energy use is monitored. Although utilities still rely on kilowatt-hour (kWh) meters for billing purposes, a microcomputer-based monitoring system is used when greater temporal and end-use resolution is desired. Because these types of monitoring systems will be used increasingly in large-scale conservation and end-use studies, it is important that their performance be analyzed to determine their accuracy. A co-instrumentation test was devised in which two such microcomputer-based monitoring systems made simultaneous measurements of electrical end-uses in two commercial buildings. The analysismore » of the co-instrumentation data aids in the evaluation of microcomputer-based monitoring systems used for end-use measurements. Separate and independent data loggers were used to measure the same loads simultaneously. In addition to these two systems, a utility billing meter measured the total energy use in each building during the co-instrumentation test. The utility's meters provided a relatively accurate standard by which the performance of both loggers could be judged. The comparison between the SCL and PNL microcomputer-based loggers has shown that power measurement techniques directly affect system performance. The co-instrumentation test has shown that there are certain standards that a monitoring system must meet if it is to perform well. First, it is essential to calibrate a microcomputer-based logger against a known standard load before the system is installed. Second, a microcomputer-based system must have some way of accounting for power factors. Recent advances in power metering circuitry have made it relatively easy to apply these power factors automatically in real time.« less

BioNLP Shared Task--The Bacteria Track.

PubMed

Bossy, Robert; Jourde, Julien; Manine, Alain-Pierre; Veber, Philippe; Alphonse, Erick; van de Guchte, Maarten; Bessières, Philippe; Nédellec, Claire

2012-06-26

We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions. Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system. The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found common trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.

Application and validation of the TTI based chill chain management system SMAS (Safety Monitoring and Assurance System) on shelf life optimization of vacuum packed chilled tuna.

PubMed

Tsironi, Theofania; Gogou, Eleni; Velliou, Eirini; Taoukis, Petros S

2008-11-30

The objective of the study was to establish a validated kinetic model for growth of spoilage bacteria on vacuum packed tuna slices in the temperature range of 0 to 15 degrees C and to evaluate the applicability of the TTI (Time Temperature Integrators) based SMAS (Safety Monitoring and Assurance System) system to improve tuna product quality at the time of consumption in comparison to the conventional First In First Out (FIFO) approach. The overall measurements of total flora and lactic acid bacteria (LAB) on the tuna samples used in a laboratory simulated field test were in close agreement with the predictions of the developed kinetic model. The spoilage profile of the TTI bearing products, handled with SMAS, was improved. Three out of the thirty products that were handled randomly, according to the FIFO approach, were already spoiled at the time of consumption (logN(LAB)>6.5) compared to no spoiled products when handled with the SMAS approach.

A novel automated rat catalepsy bar test system based on a RISC microcontroller.

PubMed

Alvarez-Cervera, Fernando J; Villanueva-Toledo, Jairo; Moo-Puc, Rosa E; Heredia-López, Francisco J; Alvarez-Cervera, Margarita; Pineda, Juan C; Góngora-Alfaro, José L

2005-07-15

Catalepsy tests performed in rodents treated with drugs that interfere with dopaminergic transmission have been widely used for the screening of drugs with therapeutic potential in the treatment of Parkinson's disease. The basic method for measuring catalepsy intensity is the "standard" bar test. We present here an easy to use microcontroller-based automatic system for recording bar test experiments. The design is simple, compact, and has a low cost. Recording intervals and total experimental time can be programmed within a wide range of values. The resulting catalepsy times are stored, and up to five simultaneous experiments can be recorded. A standard personal computer interface is included. The automated system also permits the elimination of human error associated with factors such as fatigue, distraction, and data transcription, occurring during manual recording. Furthermore, a uniform criterion for timing the cataleptic condition can be achieved. Correlation values between the results obtained with the automated system and those reported by two independent observers ranged between 0.88 and 0.99 (P<0.0001; three treatments, nine animals, 144 catalepsy time measurements).

Assessment of anti-oxidant activity of plant extracts using microbial test systems.

PubMed

Oktyabrsky, O; Vysochina, G; Muzyka, N; Samoilova, Z; Kukushkina, T; Smirnova, G

2009-04-01

To evaluate the anti-oxidant properties of extracts from 20 medicinal herbs growing in western Siberia using microbial test systems and different in vitro methods. In vivo anti-oxidant activity of extracts was evaluated for their capacity to protect bacteria, Escherichia coli, against bacteriostatic and bactericidal effects of H(2)O(2) and menadione, and action on anti-oxidant gene expression. In vitro anti-oxidant activity has been examined by a number of methods including: the 1,1-diphenyl-2-picrylhydrazyl radical (DPPH(*))-scavenging assay, chelating activity and capacity to protect plasmid DNA against oxidative damage. In addition, total polyphenol content was determined. The extracts of Fragaria vesca, Rosa majalis, Pentaphylloides fruticosa, Alchemilla vulgaris and Pulmonaria mollis possessed the highest levels of anti-oxidant activity in vivo and in vitro. The protective properties were more closely related to the DPPH(*) radical-scavenging activity, tannin content and action on anti-oxidant gene expression than to other parameters. The extracts of medicinal plants may have anti-oxidant effects on bacteria simultaneously through several different pathways, including direct inhibition of reactive oxygen species, iron chelation and anti-oxidant genes induction. Using microbial test systems, we revealed herbs that may be used as potential sources of natural anti-oxidants.

Integrated vehicle-based safety systems heavy truck field operational test, methodology and results report.

DOT National Transportation Integrated Search

2010-12-01

"This document presents the methodology and results from the heavy-truck field operational test conducted as part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of analyses performed by the University of Michiga...

Integrated vehicle-based safety systems light-vehicle field operational test, methodology and results report.

DOT National Transportation Integrated Search

2010-12-01

"This document presents the methodology and results from the light-vehicle field operational test conducted as part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of analyses performed by the University of Michi...

Cytogenotoxicity screening of source water, wastewater and treated water of drinking water treatment plants using two in vivo test systems: Allium cepa root based and Nile tilapia erythrocyte based tests.

PubMed

Hemachandra, Chamini K; Pathiratne, Asoka

2017-01-01

Biological effect directed in vivo tests with model organisms are useful in assessing potential health risks associated with chemical contaminations in surface waters. This study examined the applicability of two in vivo test systems viz. plant, Allium cepa root based tests and fish, Oreochromis niloticus erythrocyte based tests for screening cytogenotoxic potential of raw source water, water treatment waste (effluents) and treated water of drinking water treatment plants (DWTPs) using two DWTPs associated with a major river in Sri Lanka. Measured physico-chemical parameters of the raw water, effluents and treated water samples complied with the respective Sri Lankan standards. In the in vivo tests, raw water induced statistically significant root growth retardation, mitodepression and chromosomal abnormalities in the root meristem of the plant and micronuclei/nuclear buds evolution and genetic damage (as reflected by comet scores) in the erythrocytes of the fish compared to the aged tap water controls signifying greater genotoxicity of the source water especially in the dry period. The effluents provoked relatively high cytogenotoxic effects on both test systems but the toxicity in most cases was considerably reduced to the raw water level with the effluent dilution (1:8). In vivo tests indicated reduction of cytogenotoxic potential in the tested drinking water samples. The results support the potential applications of practically feasible in vivo biological test systems such as A. cepa root based tests and the fish erythrocyte based tests as complementary tools for screening cytogenotoxicity potential of the source water and water treatment waste reaching downstream of aquatic ecosystems and for evaluating cytogenotoxicity eliminating efficacy of the DWTPs in different seasons in view of human and ecological safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

Long-term preservation of anammox bacteria.

PubMed

Rothrock, Michael J; Vanotti, Matias B; Szögi, Ariel A; Gonzalez, Maria Cruz Garcia; Fujii, Takao

2011-10-01

Deposit of useful microorganisms in culture collections requires long-term preservation and successful reactivation techniques. The goal of this study was to develop a simple preservation protocol for the long-term storage and reactivation of the anammox biomass. To achieve this, anammox biomass was frozen or lyophilized at two different freezing temperatures (-60°C and in liquid nitrogen (-200°C)) in skim milk media (with and without glycerol), and the reactivation of anammox activity was monitored after a 4-month storage period. Of the different preservation treatments tested, only anammox biomass preserved via freezing in liquid nitrogen followed by lyophilization in skim milk media without glycerol achieved stoichiometric ratios for the anammox reaction similar to the biomass in both the parent bioreactor and in the freshly harvested control treatment. A freezing temperature of -60°C alone, or in conjunction with lyophilization, resulted in the partial recovery of the anammox bacteria, with an equal mixture of anammox and nitrifying bacteria in the reactivated biomass. To our knowledge, this is the first report of the successful reactivation of anammox biomass preserved via sub-zero freezing and/or lyophilization. The simple preservation protocol developed from this study could be beneficial to accelerate the integration of anammox-based processes into current treatment systems through a highly efficient starting anammox biomass.

Integrated Component-based Data Acquisition Systems for Aerospace Test Facilities

NASA Technical Reports Server (NTRS)

Ross, Richard W.

2001-01-01

The Multi-Instrument Integrated Data Acquisition System (MIIDAS), developed by the NASA Langley Research Center, uses commercial off the shelf (COTS) products, integrated with custom software, to provide a broad range of capabilities at a low cost throughout the system s entire life cycle. MIIDAS combines data acquisition capabilities with online and post-test data reduction computations. COTS products lower purchase and maintenance costs by reducing the level of effort required to meet system requirements. Object-oriented methods are used to enhance modularity, encourage reusability, and to promote adaptability, reducing software development costs. Using only COTS products and custom software supported on multiple platforms reduces the cost of porting the system to other platforms. The post-test data reduction capabilities of MIIDAS have been installed at four aerospace testing facilities at NASA Langley Research Center. The systems installed at these facilities provide a common user interface, reducing the training time required for personnel that work across multiple facilities. The techniques employed by MIIDAS enable NASA to build a system with a lower initial purchase price and reduced sustaining maintenance costs. With MIIDAS, NASA has built a highly flexible next generation data acquisition and reduction system for aerospace test facilities that meets customer expectations.

Modeling the Population Dynamics of Antibiotic-Resistant Bacteria:. AN Agent-Based Approach

NASA Astrophysics Data System (ADS)

Murphy, James T.; Walshe, Ray; Devocelle, Marc

The response of bacterial populations to antibiotic treatment is often a function of a diverse range of interacting factors. In order to develop strategies to minimize the spread of antibiotic resistance in pathogenic bacteria, a sound theoretical understanding of the systems of interactions taking place within a colony must be developed. The agent-based approach to modeling bacterial populations is a useful tool for relating data obtained at the molecular and cellular level with the overall population dynamics. Here we demonstrate an agent-based model, called Micro-Gen, which has been developed to simulate the growth and development of bacterial colonies in culture. The model also incorporates biochemical rules and parameters describing the kinetic interactions of bacterial cells with antibiotic molecules. Simulations were carried out to replicate the development of methicillin-resistant S. aureus (MRSA) colonies growing in the presence of antibiotics. The model was explored to see how the properties of the system emerge from the interactions of the individual bacterial agents in order to achieve a better mechanistic understanding of the population dynamics taking place. Micro-Gen provides a good theoretical framework for investigating the effects of local environmental conditions and cellular properties on the response of bacterial populations to antibiotic exposure in the context of a simulated environment.

A suite of phantom-based test methods for assessing image quality of photoacoustic tomography systems

NASA Astrophysics Data System (ADS)

Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Pfefer, T. Joshua

2017-03-01

As Photoacoustic Tomography (PAT) matures and undergoes clinical translation, objective performance test methods are needed to facilitate device development, regulatory clearance and clinical quality assurance. For mature medical imaging modalities such as CT, MRI, and ultrasound, tissue-mimicking phantoms are frequently incorporated into consensus standards for performance testing. A well-validated set of phantom-based test methods is needed for evaluating performance characteristics of PAT systems. To this end, we have constructed phantoms using a custom tissue-mimicking material based on PVC plastisol with tunable, biologically-relevant optical and acoustic properties. Each phantom is designed to enable quantitative assessment of one or more image quality characteristics including 3D spatial resolution, spatial measurement accuracy, ultrasound/PAT co-registration, uniformity, penetration depth, geometric distortion, sensitivity, and linearity. Phantoms contained targets including high-intensity point source targets and dye-filled tubes. This suite of phantoms was used to measure the dependence of performance of a custom PAT system (equipped with four interchangeable linear array transducers of varying design) on design parameters (e.g., center frequency, bandwidth, element geometry). Phantoms also allowed comparison of image artifacts, including surface-generated clutter and bandlimited sensing artifacts. Results showed that transducer design parameters create strong variations in performance including a trade-off between resolution and penetration depth, which could be quantified with our method. This study demonstrates the utility of phantom-based image quality testing in device performance assessment, which may guide development of consensus standards for PAT systems.

Viable bacteria associated with red blood cells and plasma in freshly drawn blood donations.

PubMed

Damgaard, Christian; Magnussen, Karin; Enevold, Christian; Nilsson, Martin; Tolker-Nielsen, Tim; Holmstrup, Palle; Nielsen, Claus Henrik

2015-01-01

Infection remains a leading cause of post-transfusion mortality and morbidity. Bacterial contamination is, however, detected in less than 0.1% of blood units tested. The aim of the study was to identify viable bacteria in standard blood-pack units, with particular focus on bacteria from the oral cavity, and to determine the distribution of bacteria revealed in plasma and in the red blood cell (RBC)-fraction. Cross-sectional study. Blood were separated into plasma and RBC-suspensions, which were incubated anaerobically or aerobically for 7 days on trypticase soy blood agar (TSA) or blue lactose plates. For identification colony PCR was performed using primers targeting 16S rDNA. Blood donors attending Capital Region Blood Bank, Copenhagen University Hospital, Rigshospitalet, Hvidovre, Denmark, October 29th to December 10th 2013. 60 donors (≥50 years old), self-reported medically healthy. Bacterial growth was observed on plates inoculated with plasma or RBCs from 62% of the blood donations. Growth was evident in 21 (35%) of 60 RBC-fractions and in 32 (53%) of 60 plasma-fractions versus 8 of 60 negative controls (p = 0.005 and p = 2.6x10-6, respectively). Propionibacterium acnes was found in 23% of the donations, and Staphylococcus epidermidis in 38%. The majority of bacteria identified in the present study were either facultative anaerobic (59.5%) or anaerobic (27.8%) species, which are not likely to be detected during current routine screening. Viable bacteria are present in blood from donors self-reported as medically healthy, indicating that conventional test systems employed by blood banks insufficiently detect bacteria in plasma. Further investigation is needed to determine whether routine testing for anaerobic bacteria and testing of RBC-fractions for adherent bacteria should be recommended.

Series quartz crystal sensor for remote bacteria population monitoring in raw milk via the Internet.

PubMed

Chang, Ku-Shang; Jang, Hung-Der; Lee, Ching-Fu; Lee, Yuan-Guey; Yuan, Chiun-Jye; Lee, Sheng-Hsien

2006-02-15

A remote monitoring system based on a piezoelectric quartz crystal (SPQC) sensor was developed for the determination of the bacteria population in raw milk. The system employs the Windows XP server operating system, and its programs for data acquisition, display and transmission were developed using the LabVIEW 7.1 programming language. The circuit design consists of a circuit with a piezoelectric quartz crystal (SPQC) and a pair of electrodes. This system can provide dynamic data monitoring on a web-page via the Internet. Immersion of the electrodes in a cell culture with bacteria inoculums resulted in a change of frequency caused by the impedance change due to microbial metabolism and the adherence of bacteria on the surface of the electrodes. The calibration curve of detection times against density of bacteria showed a linear correlation coefficient (R(2) = 0.9165) over the range of 70-10(6) CFU ml(-1). The sensor could acquire sufficient data rapidly (within 4 h) and thus enabled real-time monitoring of bacteria growth via the Internet. This system has potential application in the detection of bacteria concentration of milk at dairy farms.

Inactivation of biofilm bacteria.

PubMed Central

LeChevallier, M W; Cawthon, C D; Lee, R G

1988-01-01

The current project was developed to examine inactivation of biofilm bacteria and to characterize the interaction of biocides with pipe surfaces. Unattached bacteria were quite susceptible to the variety of disinfectants tested. Viable bacterial counts were reduced 99% by exposure to 0.08 mg of hypochlorous acid (pH 7.0) per liter (1 to 2 degrees C) for 1 min. For monochloramine, 94 mg/liter was required to kill 99% of the bacteria within 1 min. These results were consistent with those found by other investigators. Biofilm bacteria grown on the surfaces of granular activated carbon particles, metal coupons, or glass microscope slides were 150 to more than 3,000 times more resistant to hypochlorous acid (free chlorine, pH 7.0) than were unattached cells. In contrast, resistance of biofilm bacteria to monochloramine disinfection ranged from 2- to 100-fold more than that of unattached cells. The results suggested that, relative to inactivation of unattached bacteria, monochloramine was better able to penetrate and kill biofilm bacteria than free chlorine. For free chlorine, the data indicated that transport of the disinfectant into the biofilm was a major rate-limiting factor. Because of this phenomenon, increasing the level of free chlorine did not increase disinfection efficiency. Experiments where equal weights of disinfectants were used suggested that the greater penetrating power of monochloramine compensated for its limited disinfection activity. These studies showed that monochloramine was as effective as free chlorine for inactivation of biofilm bacteria. The research provides important insights into strategies for control of biofilm bacteria. Images PMID:2849380

Performance Evaluation of the Verigene Gram-Positive and Gram-Negative Blood Culture Test for Direct Identification of Bacteria and Their Resistance Determinants from Positive Blood Cultures in Hong Kong

PubMed Central

Siu, Gilman K. H.; Chen, Jonathan H. K.; Ng, T. K.; Lee, Rodney A.; Fung, Kitty S. C.; To, Sabrina W. C.; Wong, Barry K. C.; Cheung, Sherman; Wong, Ivan W. F.; Tam, Marble M. P.; Lee, Swing S. W.; Yam, W. C.

2015-01-01

Background A multicenter study was conducted to evaluate the diagnostic performance and the time to identifcation of the Verigene Blood Culture Test, the BC-GP and BC-GN assays, to identify both Gram-positive and Gram-negative bacteria and their drug resistance determinants directly from positive blood cultures collected in Hong Kong. Methods and Results A total of 364 blood cultures were prospectively collected from four public hospitals, in which 114 and 250 cultures yielded Gram-positive and Gram-negative bacteria, and were tested with the BC-GP and BC-GN assay respectively. The overall identification agreement for Gram-positive and Gram-negative bacteria were 89.6% and 90.5% in monomicrobial cultures and 62.5% and 53.6% in polymicrobial cultures, respectively. The sensitivities for most genus/species achieved at least 80% except Enterococcus spp. (60%), K.oxytoca (0%), K.pneumoniae (69.2%), whereas the specificities for all targets ranged from 98.9% to 100%. Of note, 50% (7/14) cultures containing K.pneumoniae that were missed by the BC-GN assay were subsequently identified as K.variicola. Approximately 5.5% (20/364) cultures contained non-target organisms, of which Aeromonas spp. accounted for 25% and are of particular concern. For drug resistance determination, the Verigene test showed 100% sensitivity for identification of MRSA, VRE and carbapenem resistant Acinetobacter, and 84.4% for ESBL-producing Enterobacteriaceae based on the positive detection of mecA, vanA, bla OXA and bla CTXM respectively. Conclusion Overall, the Verigene test provided acceptable accuracy for identification of bacteria and resistance markers with a range of turnaround time 40.5 to 99.2 h faster than conventional methods in our region. PMID:26431434

[Application of anaerobic bacteria detection in oral and maxillofacial infection].

PubMed

Bao, Zhen-ying; Lin, Qin; Meng, Yan-hong; He, Chun; Su, Jia-zeng; Peng, Xin

2016-02-18

To investigate the distribution and drug resistance of anaerobic bacteria in the patients with oral and maxillofacial infection. Aerobic and anaerobic bacteria cultures from 61 specimens of pus from the patients with oral and maxillofacial infection in the Department of Oral and Maxillofacial Surgery, Peking University School of Stomatology were identified. The culture type was evaluated by API 20A kit and drug resistance test was performed by Etest method. The clinical data and antibacterial agents for the treatment of the 61 cases were collected, and the final outcomes were recorded. The bacteria cultures were isolated from all the specimens, with aerobic bacteria only in 6 cases (9.8%), anaerobic bacteria only in 7 cases (11.5%), and both aerobic and anaerobic bacteria in 48 cases (78.7%). There were 55 infected cases (90.2%) with anaerobic bacteria, and 81 anaerobic bacteria stains were isolated. The highest bacteria isolation rate of Gram positive anaerobic bacteria could be found in Peptostreptococcus, Bifidobacterium and Pemphigus propionibacterium. No cefoxitin, amoxicillin/carat acid resistant strain was detected in the above three Gram positive anaerobic bacteria. The highest bacteria isolation rate of Gram negative anaerobic bacteria could be detected in Porphyromonas and Prevotella. No metronidazole, cefoxitin, amoxicillin/carat acid resistant strain was found in the two Gram negative anaerobic bacteria. In the study, 48 patients with oral and maxillofacial infection were treated according to the results of drug resistance testing, and the clinical cure rate was 81.3%. Mixed aerobic and anaerobic bacteria cultures are very common in most oral and maxillofacial infection patients. Anaerobic bacteria culture and drug resistance testing play an important role in clinical treatment.

Fluorescence-based multi-parameter approach to characterize dynamics of organic carbon, faecal bacteria and particles at alpine karst springs.

PubMed

Frank, Simon; Goeppert, Nadine; Goldscheider, Nico

2018-02-15

Karst springs, especially in alpine regions, are important for drinking water supply but also vulnerable to contamination, especially after rainfall events. This high variability of water quality requires rapid quantification of contamination parameters. Here, we used a fluorescence-based multi-parameter approach to characterize the dynamics of organic carbon, faecal bacteria, and particles at three alpine karst springs. We used excitation emission matrices (EEMs) to identify fluorescent dissolved organic material (FDOM). At the first system, peak A fluorescence and total organic carbon (TOC) were strongly correlated (Spearman's r s of 0.949), indicating that a large part of the organic matter is related to humic-like substances. Protein-like fluorescence and cultivation-based determination of coliform bacteria also had a significant correlation with r s =0.734, indicating that protein-like fluorescence is directly related to faecal pollution. At the second system, which has two spring outlets, the absolute values of all measured water-quality parameters were lower; there was a significant correlation between TOC and humic-like fluorescence (r s =0.588-0.689) but coliform bacteria and protein-like fluorescence at these two springs were not correlated. Additionally, there was a strong correlation (r s =0.571-0.647) between small particle fractions (1.0 and 2.0μm), a secondary turbidity peak and bacteria. At one of these springs, discharge was constant despite the reaction of all other parameters to the rainfall event. Our results demonstrated that i) all three springs showed fast and marked responses of all investigated water-quality parameters after rain events; ii) a constant discharge does not necessarily mean constant water quality; iii) at high contamination levels, protein-like fluorescence is a good indicator of bacterial contamination, while at low contamination levels no correlation between protein-like fluorescence and bacterial values was detected; and

Existence and control of Legionella bacteria in building water systems: A review.

PubMed

Springston, John P; Yocavitch, Liana

2017-02-01

Legionellae are waterborne bacteria which are capable of causing potentially fatal Legionnaires' disease (LD), as well as Pontiac Fever. Public concern about Legionella exploded following the 1976 outbreak at the American Legion conference in Philadelphia, where 221 attendees contracted pneumonia and 34 died. Since that time, a variety of different control methods and strategies have been developed and implemented in an effort to eradicate Legionella from building water systems. Despite these efforts, the incidence of LD has been steadily increasing in the U.S. for more than a decade. Public health and occupational hygiene professionals have maintained an active debate regarding best practices for management and control of Legionella. Professional opinion remains divided with respect to the relative merits of performing routine sampling for Legionella, vs. the passive, reactive approach that has been largely embraced by public health officials and facility owners. Given the potential risks and ramifications associated with waiting to assess systems for Legionella until after disease has been identified and confirmed, a proactive approach of periodic testing for Legionella, along with proper water treatment, is the best approach to avoiding large-scale disease outbreaks.

Simultaneous aptasensor for multiplex pathogenic bacteria detection based on multicolor upconversion nanoparticles labels.

PubMed

Wu, Shijia; Duan, Nuo; Shi, Zhao; Fang, Congcong; Wang, Zhouping

2014-03-18

A highly sensitive and specific multiplex method for the simultaneous detection of three pathogenic bacteria was fabricated using multicolor upconversion nanoparticles (UCNPs) as luminescence labels coupled with aptamers as the molecular recognition elements. Multicolor UCNPs were synthesized via doping with various rare-earth ions to obtain well-separated emission peaks. The aptamer sequences were selected using the systematic evolution of ligands by exponential enrichment (SELEX) strategy for Staphylococcus aureus, Vibrio parahemolyticus, and Salmonella typhimurium. When applied in this method, aptamers can be used for the specific recognition of the bacteria from complex mixtures, including those found in real food matrixes. Aptamers and multicolor UCNPs were employed to selectively capture and simultaneously quantify the three target bacteria on the basis of the independent peaks. Under optimal conditions, the correlation between the concentration of three bacteria and the luminescence signal was found to be linear from 50-10(6) cfu mL(-1). Improved by the magnetic separation and concentration effect of Fe3O4 magnetic nanoparticles, the limits of detection of the developed method were found to be 25, 10, and 15 cfu mL(-1) for S. aureus, V. parahemolyticus, and S. typhimurium, respectively. The capability of the bioassay in real food samples was also investigated, and the results were consistent with experimental results obtained from plate-counting methods. This proposed method for the detection of various pathogenic bacteria based on multicolor UCNPs has great potential in the application of food safety and multiplex nanosensors.

Evaluation of a commercial latex test for Clostridium difficile for reactivity with C. difficile and cross-reactions with other bacteria.

PubMed Central

Miles, B L; Siders, J A; Allen, S D

1988-01-01

Seventy-eight species of bacteria (739 isolates) were tested for reactivity with a commercial latex test for Clostridium difficile. All noncytotoxic as well as cytotoxic strains of C. difficile reacted positively. Immuno-specific cross-reactions were found only with C. sporogenes, proteolytic C. botulinum, and Peptostreptococcus anaerobius. PMID:3235677

A smartphone-based system for the automated management of point-of-care test results in hospitals.

PubMed

Jang, Dasom; Shin, Soo-Yong; Seo, Dong-Woo; Joo, Segyeong; Huh, Soo-Jin

2015-04-01

Managing test results is an important issue in hospitals because of the increasing use of point-of-care testing (POCT). Here, we propose a smartphone-based system for automatically managing POCT test results. We developed the system to provide convenience to the medical staffs. The system recognizes the patient identification or prescription number of the test by reading barcodes and provides a countdown to indicate when the results will be ready. When the countdown in finished, a picture of the test result is transferred to the electronic medical record server using the Health Level 7 protocol. Human immunodeficiency virus (HIV) kits were selected in this research because HIV is a life-threatening infectious virus, especially for the medical staff who treat undiagnosed patients. The performance of the system was verified from a survey of the users. The performance of the system was tested at the emergency room (ER) for 10 months using commercially available POCT kits for detecting HIV. The survey showed that, in total, 80% and 0% of users reported positive or negative feedback, respectively. The staff also reported that the system reduced total processing time by approximately 32 min, in addition to reducing workload. The developed automated management system was successfully tested at an ER for 10 months. The survey results show that the system is effective and that medical staff members who used the system are satisfied with using the system at the ER.

Integrated test system of infrared and laser data based on USB 3.0

NASA Astrophysics Data System (ADS)

Fu, Hui Quan; Tang, Lin Bo; Zhang, Chao; Zhao, Bao Jun; Li, Mao Wen

2017-07-01

Based on USB3.0, this paper presents the design method of an integrated test system for both infrared image data and laser signal data processing module. The core of the design is FPGA logic control, the design uses dual-chip DDR3 SDRAM to achieve high-speed laser data cache, and receive parallel LVDS image data through serial-to-parallel conversion chip, and it achieves high-speed data communication between the system and host computer through the USB3.0 bus. The experimental results show that the developed PC software realizes the real-time display of 14-bit LVDS original image after 14-to-8 bit conversion and JPEG2000 compressed image after decompression in software, and can realize the real-time display of the acquired laser signal data. The correctness of the test system design is verified, indicating that the interface link is normal.

Raman microspectrometer combined with scattering microscopy and lensless imaging for bacteria identification

NASA Astrophysics Data System (ADS)

Strola, S. A.; Schultz, E.; Allier, C. P.; DesRoches, B.; Lemmonier, J.; Dinten, J.-M.

2013-03-01

In this paper, we report on a compact prototype capable both of lensfree imaging, Raman spectrometry and scattering microscopy from bacteria samples. This instrument allows high-throughput real-time characterization without the need of markers, making it potentially suitable to field label-free biomedical and environmental applications. Samples are illuminated from above with a focused-collimated 532nm laser beam and can be x-y-z scanned. The bacteria detection is based on emerging lensfree imaging technology able to localize cells of interest over a large field-of-view of 24mm2. Raman signal and scattered light are then collected by separate measurement arms simultaneously. In the first arm the emission light is fed by a fiber into a prototype spectrometer, developed by Tornado Spectral System based on Tornado's High Throughput Virtual Slit (HTVS) novel technology. The enhanced light throughput in the spectral region of interest (500-1800 cm-1) reduces Raman acquisition time down to few seconds, thus facilitating experimental protocols and avoiding the bacteria deterioration induced by laser thermal heating. Scattered light impinging in the second arm is collected onto a charge-coupled-device. The reconstructed image allows studying the single bacteria diffraction pattern and their specific structural features. The characterization and identification of different bacteria have been performed to validate and optimize the acquisition system and the component setup. The results obtained demonstrate the benefits of these three techniques combination by providing the precise bacteria localization, their chemical composition and a morphology description. The procedure for a rapid identification of particular pathogen bacteria in a sample is illustrated.

The aerobic activity of metronidazole against anaerobic bacteria.

PubMed

Dione, Niokhor; Khelaifia, Saber; Lagier, Jean-Christophe; Raoult, Didier

2015-05-01

Recently, the aerobic growth of strictly anaerobic bacteria was demonstrated using antioxidants. Metronidazole is frequently used to treat infections caused by anaerobic bacteria; however, to date its antibacterial activity was only tested in anaerobic conditions. Here we aerobically tested using antioxidants the in vitro activities of metronidazole, gentamicin, doxycycline and imipenem against 10 common anaerobic and aerobic bacteria. In vitro susceptibility testing was performed by the disk diffusion method, and minimum inhibitory concentrations (MICs) were determined by Etest. Aerobic culture of the bacteria was performed at 37°C using Schaedler agar medium supplemented with 1mg/mL ascorbic acid and 0.1mg/mL glutathione; the pH was adjusted to 7.2 by 10M KOH. Growth of anaerobic bacteria cultured aerobically using antioxidants was inhibited by metronidazole after 72h of incubation at 37°C, with a mean inhibition diameter of 37.76mm and an MIC of 1μg/mL; however, strains remained non-sensitive to gentamicin. No growth inhibition of aerobic bacteria was observed after 24h of incubation at 37°C with metronidazole; however, inhibition was observed with doxycycline and imipenem used as controls. These results indicate that bacterial sensitivity to metronidazole is not related to the oxygen tension but is a result of the sensitivity of the micro-organism. In future, both culture and antibiotic susceptibility testing of strictly anaerobic bacteria will be performed in an aerobic atmosphere using antioxidants in clinical microbiology laboratories. Copyright © 2015 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Smart monitoring system based on adaptive current control for superconducting cable test.

PubMed

Arpaia, Pasquale; Ballarino, Amalia; Daponte, Vincenzo; Montenero, Giuseppe; Svelto, Cesare

2014-12-01

A smart monitoring system for superconducting cable test is proposed with an adaptive current control of a superconducting transformer secondary. The design, based on Fuzzy Gain Scheduling, allows the controller parameters to adapt continuously, and finely, to the working variations arising from transformer nonlinear dynamics. The control system is integrated in a fully digital control loop, with all the related benefits, i.e., high noise rejection, ease of implementation/modification, and so on. In particular, an accurate model of the system, controlled by a Fuzzy Gain Scheduler of the superconducting transformer, was achieved by an experimental campaign through the working domain at several current ramp rates. The model performance was characterized by simulation, under all the main operating conditions, in order to guide the controller design. Finally, the proposed monitoring system was experimentally validated at European Organization for Nuclear Research (CERN) in comparison to the state-of-the-art control system [P. Arpaia, L. Bottura, G. Montenero, and S. Le Naour, "Performance improvement of a measurement station for superconducting cable test," Rev. Sci. Instrum. 83, 095111 (2012)] of the Facility for the Research on Superconducting Cables, achieving a significant performance improvement: a reduction in the system overshoot by 50%, with a related attenuation of the corresponding dynamic residual error (both absolute and RMS) up to 52%.

[Significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection].

PubMed

Zou, X H; Zhu, Y P; Ren, G Q; Li, G C; Zhang, J; Zou, L J; Feng, Z B; Li, B H

2017-02-20

Objective: To evaluate the significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection. Methods: Eighteen patients with diabetic foot ulcer conforming to the study criteria were hospitalized in Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology from July 2014 to July 2015. Diabetic foot ulcer wounds were classified according to the University of Texas diabetic foot classification (hereinafter referred to as Texas grade) system, and general condition of patients with wounds in different Texas grade was compared. Exudate and tissue of wounds were obtained, and filter paper method and biopsy method were adopted to detect the bacteria of wounds of patients respectively. Filter paper method was regarded as the evaluation method, and biopsy method was regarded as the control method. The relevance, difference, and consistency of the detection results of two methods were tested. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of filter paper method in bacteria detection were calculated. Receiver operating characteristic (ROC) curve was drawn based on the specificity and sensitivity of filter paper method in bacteria detection of 18 patients to predict the detection effect of the method. Data were processed with one-way analysis of variance and Fisher's exact test. In patients tested positive for bacteria by biopsy method, the correlation between bacteria number detected by biopsy method and that by filter paper method was analyzed with Pearson correlation analysis. Results: (1) There were no statistically significant differences among patients with wounds in Texas grade 1, 2, and 3 in age, duration of diabetes, duration of wound, wound area, ankle brachial index, glycosylated hemoglobin, fasting blood sugar, blood platelet count, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, serum creatinine, and

A mathematical model for expected time to extinction of pathogenic bacteria through antibiotic

NASA Astrophysics Data System (ADS)

Ghosh, M. K.; Nandi, S.; Roy, P. K.

2016-04-01

Application of antibiotics in human system to prevent bacterial diseases like Gastritis, Ulcers, Meningitis, Pneumonia and Gonorrhea are indispensable. Antibiotics saved innumerable lives and continue to be a strong support for therapeutic application against pathogenic bacteria. In human system, bacterial diseases occur when pathogenic bacteria gets into the body and begin to reproduce and crowd out healthy bacteria. In this process, immature bacteria releases enzyme which is essential for bacterial cell-wall biosynthesis. After complete formation of cell wall, immature bacteria are converted to mature or virulent bacteria which are harmful to us during bacterial infections. Use of antibiotics as drug inhibits the bacterial cell wall formation. After application of antibiotics within body, the released bacterial enzyme binds with antibiotic molecule instead of its functional site during the cell wall synthesis in a competitive inhibition approach. As a consequence, the bacterial cell-wall formation as well as maturation process of pathogenic bacteria is halted and the disease is cured with lysis of bacterial cells. With this idea, a mathematical model has been developed in the present research investigation to review the inhibition of biosynthesis of bacterial cell wall by the application of antibiotics as drug in the light of enzyme kinetics. This approach helps to estimate the expected time to extinction of the pathogenic bacteria. Our mathematical approach based on the enzyme kinetic model for finding out expected time to extinction contributes favorable results for understanding of disease dynamics. Analytical and numerical results based on simulated findings validate our mathematical model.

BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool

ERIC Educational Resources Information Center

Chen, T. Y.; Grant, D. D.; Lau, M. F.; Ng, S. P.; Vasa, V. R.

2006-01-01

BEAT is a Web-based system that generates fault-based test cases from Boolean expressions. It is based on the integration of our several fault-based test case selection strategies. The generated test cases are considered to be fault-based, because they are aiming at the detection of particular faults. For example, when the Boolean expression is in…

Test Platforms for Model-Based Flight Research

NASA Astrophysics Data System (ADS)

Dorobantu, Andrei

Demonstrating the reliability of flight control algorithms is critical to integrating unmanned aircraft systems into the civilian airspace. For many potential applications, design and certification of these algorithms will rely heavily on mathematical models of the aircraft dynamics. Therefore, the aerospace community must develop flight test platforms to support the advancement of model-based techniques. The University of Minnesota has developed a test platform dedicated to model-based flight research for unmanned aircraft systems. This thesis provides an overview of the test platform and its research activities in the areas of system identification, model validation, and closed-loop control for small unmanned aircraft.

Synthesis and Antimicrobial Evaluation of Amixicile-Based Inhibitors of the Pyruvate-Ferredoxin Oxidoreductases of Anaerobic Bacteria and Epsilonproteobacteria

PubMed Central

Kennedy, Andrew J.; Bruce, Alexandra M.; Gineste, Catherine; Ballard, T. Eric; Olekhnovich, Igor N.; Macdonald, Timothy L.

2016-01-01

Amixicile is a promising derivative of nitazoxanide (an antiparasitic therapeutic) developed to treat systemic infections caused by anaerobic bacteria, anaerobic parasites, and members of the Epsilonproteobacteria (Campylobacter and Helicobacter). Amixicile selectively inhibits pyruvate-ferredoxin oxidoreductase (PFOR) and related enzymes by inhibiting the function of the vitamin B1 cofactor (thiamine pyrophosphate) by a novel mechanism. Here, we interrogate the amixicile scaffold, guided by docking simulations, direct PFOR inhibition assays, and MIC tests against Clostridium difficile, Campylobacter jejuni, and Helicobacter pylori. Docking simulations revealed that the nitro group present in nitazoxanide interacts with the protonated N4′-aminopyrimidine of thiamine pyrophosphate (TPP). The ortho-propylamine on the benzene ring formed an electrostatic interaction with an aspartic acid moiety (B456) of PFOR that correlated with improved PFOR-inhibitory activity and potency by MIC tests. Aryl substitution with electron-withdrawing groups and substitutions of the propylamine with other alkyl amines or nitrogen-containing heterocycles both improved PFOR inhibition and, in many cases, biological activity against C. difficile. Docking simulation results correlate well with mechanistic enzymology and nuclear magnetic resonance (NMR) studies that show members of this class of antimicrobials to be specific inhibitors of vitamin B1 function by proton abstraction, which is both novel and likely to limit mutation-based drug resistance. PMID:27090174

Design and realization of the compound text-based test questions library management system

NASA Astrophysics Data System (ADS)

Shi, Lei; Feng, Lin; Zhao, Xin

2011-12-01

The test questions library management system is the essential part of the on-line examination system. The basic demand for which is to deal with compound text including information like images, formulae and create the corresponding Word documents. Having compared with the two current solutions of creating documents, this paper presents a design proposal of Word Automation mechanism based on OLE/COM technology, and discusses the way of Word Automation application in detail and at last provides the operating results of the system which have high reference value in improving the generated efficiency of project documents and report forms.

Exploration of indigenous bacteria in an intensive aquaculture system of African catfish (Clarias sp.) in Banyuwangi, Indonesia

NASA Astrophysics Data System (ADS)

Prayogo; Rahardja, B. S.; Asshanti, A. N.; Dewi, N. N.; Santanumurti, M. B.

2018-04-01

Intensive African catfish culture in tarpaulin pond was popular in Banyuwangi, Indonesia since the government supported the fisheries sector. Unfortunately, the failure of African catfish culture still occurred since the waste from fish metabolite process and feed residue decreased the water quality. Bacteria in the water could be the solution to increase the success rate of aquaculture by improving the water quality. This study purpose was to obtained indigenous bacteria in intensive aquaculture system of African catfish to improve water quality. This study successfully isolated bacteria contained with amylase, protease and lipase characteristic. Isolated bacteria in this study were identified as Pseudomonas pseudomallei (97.81%), Bacillus subtilis (95.81%) and Pseudomonas stutzeri (61.21%).

High-Value, Cost-Conscious Care: Iterative Systems-Based Interventions to Reduce Unnecessary Laboratory Testing.

PubMed

Sadowski, Brett W; Lane, Alison B; Wood, Shannon M; Robinson, Sara L; Kim, Chin Hee

2017-09-01

Inappropriate testing contributes to soaring healthcare costs within the United States, and teaching hospitals are vulnerable to providing care largely for academic development. Via its "Choosing Wisely" campaign, the American Board of Internal Medicine recommends avoiding repetitive testing for stable inpatients. We designed systems-based interventions to reduce laboratory orders for patients admitted to the wards at an academic facility. We identified the computer-based order entry system as an appropriate target for sustainable intervention. The admission order set had allowed multiple routine tests to be ordered repetitively each day. Our iterative study included interventions on the automated order set and cost displays at order entry. The primary outcome was number of routine tests controlled for inpatient days compared with the preceding year. Secondary outcomes included cost savings, delays in care, and adverse events. Data were collected over a 2-month period following interventions in sequential years and compared with the year prior. The first intervention led to 0.97 fewer laboratory tests per inpatient day (19.4%). The second intervention led to sustained reduction, although by less of a margin than order set modifications alone (15.3%). When extrapolating the results utilizing fees from the Centers for Medicare and Medicaid Services, there was a cost savings of $290,000 over 2 years. Qualitative survey data did not suggest an increase in care delays or near-miss events. This series of interventions targeting unnecessary testing demonstrated a sustained reduction in the number of routine tests ordered, without adverse effects on clinical care. Published by Elsevier Inc.

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

PubMed Central

Li, Yiyan; Yang, Xing; Zhao, Weian

2018-01-01

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies. PMID:28850804

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing.

PubMed

Li, Yiyan; Yang, Xing; Zhao, Weian

2017-12-01

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

Demonstration & Testing of ClimaStat for Improved DX Air-Conditioning Efficiency

DTIC Science & Technology

2013-04-01

impaired productivity and increased transmission of viruses and bacteria. Allowing indoor RH to rise above an average of 60%rh or a peak of 70%rh can...testing of an engineering prototype culminated in issuance of US Patent 6,427,454 in 2002. Then, development, testing and refinement of a production ...field tests on four Trane (American Standard) systems at a university site were concluded in 2009. A production prototype was constructed based on

Space Launch System Base Heating Test: Tunable Diode Laser Absorption Spectroscopy

NASA Technical Reports Server (NTRS)

Parker, Ron; Carr, Zak; MacLean, Matthew; Dufrene, Aaron; Mehta, Manish

2016-01-01

This paper describes the Tunable Diode Laser Absorption Spectroscopy (TDLAS) measurement of several water transitions that were interrogated during a hot-fire testing of the Space Launch Systems (SLS) sub-scale vehicle installed in LENS II. The temperature of the recirculating gas flow over the base plate was found to increase with altitude and is consistent with CFD results. It was also observed that the gas above the base plate has significant velocity along the optical path of the sensor at the higher altitudes. The line-by-line analysis of the H2O absorption features must include the effects of the Doppler shift phenomena particularly at high altitude. The TDLAS experimental measurements and the analysis procedure which incorporates the velocity dependent flow will be described.

Combined physico-chemical treatments based on enterocin AS-48 for inactivation of Gram-negative bacteria in soybean sprouts.

PubMed

Cobo Molinos, Antonio; Abriouel, Hikmate; López, Rosario Lucas; Valdivia, Eva; Omar, Nabil Ben; Gálvez, Antonio

2008-08-01

Enterocin AS-48 was tested for decontamination of soybean sprouts against Gram-negative bacteria. Although treatment with bacteriocin alone had no effect on Salmonella enterica, a synergistic antimicrobial effect was detected at pH 9.0 and in combination with moderate heat treatment. Greatest inactivation was achieved for sprouts heated for 5 min at 65 degrees C in an alkaline (pH 9.0) enterocin AS-48 solution of 25 microg/ml. Bactericidal activity against S. enterica increased greatly when enterocin AS-48 was used in washing solutions in combination with several chemical compounds: EDTA, lactic acid, peracetic acid, polyphosphoric acid, sodium hypochlorite, hexadecylpyridinium chloride, propyl-p-hydroxybenzoate, and hydrocinnamic acid. The combined treatment of enterocin AS-48 and polyphosphoric acid was tested against several other Gram-negative bacteria inoculated on sprouts. The bacteria tested showed great differences in sensitivity to polyphosphoric acid, but synergism with enterocin AS-48 was confirmed in all cases. Combinations of enterocin AS-48 (25 microg/ml) and polyphosphoric acid in a concentration range of 0.1 to 2.0% significantly reduced or inhibited growth of the populations of S. enterica, Escherichia coli O157:H7, Shigella spp., Enterobacter aerogenes, Yersinia enterocolitica, Aeromonas hydrophila and Pseudomonas fluorescens in sprout samples stored at 6 degrees C and 15 degrees C. The combined treatment could therefore be applied to reduce the risks of Gram-negative pathogenic as well as spoilage bacteria on sprouts.

A High Frame Rate Test System for the HEPS-BPIX Based on NI-sbRIO Board

NASA Astrophysics Data System (ADS)

Gu, Jingzi; Zhang, Jie; Wei, Wei; Ning, Zhe; Li, Zhenjie; Jiang, Xiaoshan; Fan, Lei; Shen, Wei; Ren, Jiayi; Ji, Xiaolu; Lan, Allan K.; Lu, Yunpeng; Ouyang, Qun; Liu, Peng; Zhu, Kejun; Wang, Zheng

2017-06-01

HEPS-BPIX is a silicon pixel detector designed for the future large scientific facility, high-energy photon sources (HEPS) in Beijing, China. It is a high frame rate hybrid pixel detector which works in the single-photon-counting mode. High frame rate leads to much higher readout data bandwidth than former systems, which is also the difficulty of the design. Aiming to test and calibrate the pixel detector, a test system based on the National Instruments single-board RIO 9626 and LabVIEW program environment has been designed. A series of tests has been carried out with X-ray machine as well as on the Beijing Synchrotron Radiation Facility 1W2B beamline. The test results show that the threshold uniformity is better than 60 electrons and the equivalent noise charge is less than 120 electrons. Besides, the required highest frame rate of 1.2 kHz has been realized. This paper will elaborate the test system design and present the latest testing results of the HEPS-BPIX system.

Preliminary evaluation of a micro-based repeated measures testing system

NASA Technical Reports Server (NTRS)

Kennedy, Robert S.; Wilkes, Robert L.; Lane, Norman E.

1985-01-01

A need exists for an automated performance test system to study the effects of various treatments which are of interest to the aerospace medical community, i.e., the effects of drugs and environmental stress. The ethics and pragmatics of such assessment demand that repeated measures in small groups of subjects be the customary research paradigm. Test stability, reliability-efficiency and factor structure take on extreme significance; in a program of study by the U.S. Navy, 80 percent of 150 tests failed to meet minimum metric requirements. The best is being programmed on a portable microprocessor and administered along with tests in their original formats in order to examine their metric properties in the computerized mode. Twenty subjects have been tested over four replications on a 6.0 minute computerized battery (six tests) and which compared with five paper and pencil marker tests. All tests achieved stability within the four test sessions, reliability-efficiencies were high (r greater than .707 for three minutes testing), and the computerized tests were largely comparable to the paper and pencil version from which they were derived. This computerized performance test system is portable, inexpensive and rugged.

Working with bacteria and putting bacteria to work: The biopolitics of synthetic biology for energy in the United Kingdom.

PubMed

McLeod, Carmen; Nerlich, Brigitte; Mohr, Alison

2017-08-01

The UK government has made significant investment into so called 'fourth-generation' biofuel technologies. These biofuels are based on engineering the metabolic pathways of bacteria in order to create products compatible with existing infrastructure. Bacteria play an important role in what is promoted as a potentially new biological industrial revolution, which could address some of the negative environmental legacies of the last. This article presents results from ethnographic research with synthetic biologists who are challenged with balancing the curiosity-driven and intrinsically fulfilling scientific task of working with bacteria, alongside the policy-driven task of putting bacteria to work for extrinsic economic gains. In addition, the scientists also have to balance these demands with a new research governance framework, Responsible Research and Innovation, which envisions technoscientific innovation will be responsive to societal concerns and work in collaboration with stakeholders and members of the public. Major themes emerging from the ethnographic research revolve around stewardship, care, responsibility and agency. An overall conflict surfaces between individual agents assuming responsibility for 'stewarding' bacteria, against funding systems and structures imposing responsibility for economic growth. We discuss these findings against the theoretical backdrop of a new concept of 'energopolitics' and an anthropology of ethics and responsibility.

Managing the potential risks of using bacteria-laden water in mineral processing to protect freshwater.

PubMed

Liu, Wenying; Moran, Chris J; Vink, Sue

2013-06-18

The minerals industry is being driven to access multiple water sources and increase water reuse to minimize freshwater withdrawal. Bacteria-laden water, such as treated effluent, has been increasingly used as an alternative to freshwater for mineral processing, in particular flotation, where conditions are favorable for bacterial growth. However, the risk posed by bacteria to flotation efficiency is poorly understood. This could be a barrier to the ongoing use of this water source. This study tested the potential of a previously published risk-based approach as a management tool to both assist mine sites in quantifying the risk from bacteria, and finding system-wide cost-effective solutions for risk mitigation. The result shows that the solution of adjusting the flotation chemical regime could only partly control the risk. The second solution of using tailings as an absorbent was shown to be effective in the laboratory in reducing bacterial concentration and thus removing the threat to flotation recovery. The best solution is likely to combine internal and external approaches, that is, inside and outside processing plants. Findings in this study contribute possible methods applicable to managing the risk from water-borne bacteria to plant operations that choose to use bacteria-containing water, when attempting to minimize freshwater use, and avoiding the undesirable consequences of increasing its use.

Verification of an Automated, Digital Dispensing Platform for At-Will Broth Microdilution-Based Antimicrobial Susceptibility Testing.

PubMed

Smith, Kenneth P; Kirby, James E

2016-09-01

With rapid emergence of multidrug-resistant bacteria, there is often a need to perform susceptibility testing for less commonly used or newer antimicrobial agents. Such testing can often be performed only by using labor-intensive, manual dilution methods and lies outside the capacity of most clinical labs, necessitating reference laboratory testing and thereby delaying the availability of susceptibility data. To address the compelling clinical need for microbiology laboratories to perform such testing in-house, we explored a novel, automated, at-will broth microdilution-based susceptibility testing platform. Specifically, we used the modified inkjet printer technology in the HP D300 digital dispensing system to dispense, directly from stock solutions into a 384-well plate, the 2-fold serial dilution series required for broth microdilution testing. This technology was combined with automated absorbance readings and data analysis to determine MICs. Performance was verified by testing members of the Enterobacteriaceae for susceptibility to ampicillin, cefazolin, ciprofloxacin, colistin, gentamicin, meropenem, and tetracycline in comparison to the results obtained with a broth microdilution reference standard. In precision studies, essential and categorical agreement levels were 96.8% and 98.3%, respectively. Furthermore, significantly fewer D300-based measurements were outside ±1 dilution from the modal MIC, suggesting enhanced reproducibility. In accuracy studies performed using a panel of 80 curated clinical isolates, rates of essential and categorical agreement and very major, major, and minor errors were 94%, 96.6%, 0%, 0%, and 3.4%, respectively. Based on these promising initial results, it is anticipated that the D300-based methodology will enable hospital-based clinical microbiology laboratories to perform at-will broth microdilution testing of antimicrobials and to address a critical testing gap. Copyright © 2016, American Society for Microbiology. All

Evaluation of Polymerase Chain Reaction for Detecting Coliform Bacteria in Drinking Water Sources

PubMed Central

Isfahani, Bahram Nasr; Fazeli, Hossein; Babaie, Zeinab; Poursina, Farkhondeh; Moghim, Sharareh; Rouzbahani, Meisam

2017-01-01

Background: Coliform bacteria are used as indicator organisms for detecting fecal pollution in water. Traditional methods including microbial culture tests in lactose-containing media and enzyme-based tests for the detection of β-galactosidase; however, these methods are time-consuming and less specific. The aim of this study was to evaluate polymerase chain reaction (PCR) for detecting coliform. Materials and Methods: Totally, 100 of water samples from Isfahan drinking water source were collected. Coliform bacteria and Escherichia coli were detected in drinking water using LacZ and LamB genes in PCR method performed in comparison with biochemical tests for all samples. Results: Using phenotyping, 80 coliform isolates were found. The results of the biochemical tests illustrated 78.7% coliform bacteria and 21.2% E. coli. PCR results for LacZ and LamB genes were 67.5% and 17.5%, respectively. Conclusion: The PCR method was shown to be an effective, sensitive, and rapid method for detecting coliform and E. coli in drinking water from the Isfahan drinking water sources. PMID:29142893

Bacterial hybrid histidine kinases in plant-bacteria interactions.

PubMed

Borland, Stéphanie; Prigent-Combaret, Claire; Wisniewski-Dyé, Florence

2016-10-01

Two-component signal transduction systems are essential for many bacteria to maintain homeostasis and adapt to environmental changes. Two-component signal transduction systems typically involve a membrane-bound histidine kinase that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid histidine kinase (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra-fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere, where intricate plant-bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings on the mechanistic of their signalling properties. Recent insights into understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.

Knowledge Based Systems (KBS) Verification, Validation, Evaluation, and Testing (VVE&T) Bibliography: Topical Categorization

DTIC Science & Technology

2003-03-01

Different?," Jour. of Experimental & Theoretical Artificial Intelligence, Special Issue on Al for Systems Validation and Verification, 12(4), 2000, pp...Hamilton, D., " Experiences in Improving the State of Practice in Verification and Validation of Knowledge-Based Systems," Workshop Notes of the AAAI...Unsuspected Power of the Standard Turing Test," Jour. of Experimental & Theoretical Artificial Intelligence., 12, 2000, pp3 3 1-3 4 0 . [30] Gaschnig

Probing minority population of antibiotic-resistant bacteria.

PubMed

Huang, Tianxun; Zheng, Yan; Yan, Ya; Yang, Lingling; Yao, Yihui; Zheng, Jiaxin; Wu, Lina; Wang, Xu; Chen, Yuqing; Xing, Jinchun; Yan, Xiaomei

2016-06-15

The evolution and spread of antibiotic-resistant pathogens has become a major threat to public health. Advanced tools are urgently needed to quickly diagnose antibiotic-resistant infections to initiate appropriate treatment. Here we report the development of a highly sensitive flow cytometric method to probe minority population of antibiotic-resistant bacteria via single cell detection. Monoclonal antibody against TEM-1 β-lactamase and Alexa Fluor 488-conjugated secondary antibody were used to selectively label resistant bacteria green, and nucleic acid dye SYTO 62 was used to stain all the bacteria red. A laboratory-built high sensitivity flow cytometer (HSFCM) was applied to simultaneously detect the side scatter and dual-color fluorescence signals of single bacteria. By using E. coli JM109/pUC19 and E. coli JM109 as the model systems for antibiotic-resistant and antibiotic-susceptible bacteria, respectively, as low as 0.1% of antibiotic-resistant bacteria were accurately quantified. By monitoring the dynamic population change of a bacterial culture with the administration of antibiotics, we confirmed that under the antimicrobial pressure, the original low population of antibiotic-resistant bacteria outcompeted susceptible strains and became the dominant population after 5hours of growth. Detection of antibiotic-resistant infection in clinical urine samples was achieved without cultivation, and the bacterial load of susceptible and resistant strains can be faithfully quantified. Overall, the HSFCM-based quantitative method provides a powerful tool for the fundamental studies of antibiotic resistance and holds the potential to provide rapid and precise guidance in clinical therapies. Copyright © 2016 Elsevier B.V. All rights reserved.

Esculin hydrolysis by Gram positive bacteria. A rapid test and it's comparison with other methods.

PubMed

Qadri, S M; Smith, J C; Zubairi, S; DeSilva, M I

1981-01-01

A number of bacteria hydrolyze esculin enzymatically to esculetin. This characteristic is used by taxonomists and clinical microbiologists in the differentiation and identification of bacteria, especially to distinguish Lance-field group D streptococci from non-group D organisms and Listeria monocytogenes from morphologically similar Erysipelothrix rhusipoathiae and diphtheroids. Conventional methods used for esculin hydrolysis require 4--48 h for completion. We developed and evaluated a medium which gives positive results more rapidly. The 2,330 isolates used in this study consisted of 1,680 esculin positive and 650 esculin negative organisms. The sensitivity and specificity of this method were compared with the PathoTec esculin hydrolysis strip and the procedure of Vaughn and Levine (VL). Of the 1,680 esculin positive organisms, 97% gave positive reactions within 30 minutes with the rapid test whereas PathoTec required 3--4 h incubation for the same number of organisms to yield a positive reaction.

Energy Systems Test Area (ESTA). Power Systems Test Facilities

NASA Technical Reports Server (NTRS)

Situ, Cindy H.

2010-01-01

This viewgraph presentation provides a detailed description of the Johnson Space Center's Power Systems Facility located in the Energy Systems Test Area (ESTA). Facilities and the resources used to support power and battery systems testing are also shown. The contents include: 1) Power Testing; 2) Power Test Equipment Capabilities Summary; 3) Source/Load; 4) Battery Facilities; 5) Battery Test Equipment Capabilities Summary; 6) Battery Testing; 7) Performance Test Equipment; 8) Battery Test Environments; 9) Battery Abuse Chambers; 10) Battery Abuse Capabilities; and 11) Battery Test Area Resources.

Integrated vehicle-based safety systems (IVBSS) : light vehicle platform field operational test data analysis plan.

DOT National Transportation Integrated Search

2009-12-22

This document presents the University of Michigan Transportation Research Institutes plan to : perform analysis of data collected from the light vehicle platform field operational test of the : Integrated Vehicle-Based Safety Systems (IVBSS) progr...

Integrated vehicle-based safety systems (IVBSS) : heavy truck platform field operational test data analysis plan.

DOT National Transportation Integrated Search

2009-11-23

This document presents the University of Michigan Transportation Research Institutes plan to perform : analysis of data collected from the heavy truck platform field operational test of the Integrated Vehicle- : Based Safety Systems (IVBSS) progra...

Evaluation of Lighting Systems, Carbon Sources, and Bacteria Cultures on Photofermentative Hydrogen Production.

PubMed

Hu, Chengcheng; Choy, Sing-Ying; Giannis, Apostolos

2018-05-01

Fluorescent and incandescent lighting systems were applied for batch photofermentative hydrogen production by four purple non-sulfur photosynthetic bacteria (PNSB). The hydrogen production efficiency of Rhodopseudomonas palustris, Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodospirillum rubrum was evaluated using different carbon sources (acetate, butyrate, lactate, and malate). Incandescent light was found to be more effective for bacteria cell growth and hydrogen production. It was observed that PNSB followed substrate selection criteria for hydrogen production. Only R. palustris was able to produce hydrogen using most carbon sources. Cell density was almost constant, but cell growth rate and hydrogen production were significantly varied under the different lighting systems. The kinetics study suggested that initial substrate concentration had a positive correlation with lag phase duration. Among the PNSB, R. palustris grew faster and had higher hydrogen yields of 1.58, 4.92, and 2.57 mol H 2 /mol using acetate, butyrate, and lactate, respectively. In the integrative approach with dark fermentation effluents rich in organic acids, R. palustris should be enriched in the phototrophic microbial consortium of the continuous hydrogen production system.