NEXAFS Study of the Annealing Effect on the Local Structure of FIB-CVD DLC

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

Saikubo, Akihiko; Kato, Yuri; Igaki, Jun-ya

2007-01-19

Annealing effect on the local structure of diamond like carbon (DLC) formed by focused ion beam-chemical vapor deposition (FIB-CVD) was investigated by the measurement of near edge x-ray absorption fine structure (NEXAFS) and energy dispersive x-ray (EDX) spectra. Carbon K edge absorption NEXAFS spectrum of FIB-CVD DLC was measured in the energy range of 275-320 eV. In order to obtain the information on the location of the gallium in the depth direction, incidence angle dependence of NEXAFS spectrum was measured in the incident angle range from 0 deg. to 60 deg. . The peak intensity corresponding to the resonance transitionmore » of 1s{yields}{sigma}* originating from carbon-gallium increased from the FIB-CVD DLC annealed at 200 deg. C to the FIB-CVD DLC annealed at 400 deg. C and decreased from that at 400 deg. C to that at 600 deg. C. Especially, the intensity of this peak remarkably enhanced in the NEXAFS spectrum of the FIB-CVD DLC annealed at 400 deg. C at the incident angle of 60 deg. . On the contrary, the peak intensity corresponding to the resonance transition of 1s{yields}{pi}* originating from carbon double bonding of emission spectrum decreased from the FIB-CVD DLC annealed at 200 deg. C to that at 400 deg. C and increased from that at 400 deg. C to that at 600 deg. C. Gallium concentration in the FIB-CVD DLC decreased from {approx_equal}2.2% of the as-deposited FIB-CVD DLC to {approx_equal}1.5% of the FIB-CVD DLC annealed at 600 deg. C from the elementary analysis using EDX. Both experimental results indicated that gallium atom departed from FIB-CVD DLC by annealing at the temperature of 600 deg. C.« less

Seasonal variation of fecal indicator bacteria in storm events within the US stormwater database.

PubMed

Pan, Xubin; Jones, Kim D

2012-01-01

Bacteria are one of the major causes of surface water impairments in the USA. Over the past several years, best management practices, including detention basins, manufactured devices, grass swales, filters and bioretention cells have been used to remove bacteria and other pollutants from stormwater runoff. However, there are data gaps in the comprehensive studies of bacteria concentrations in stormwater runoff. In this paper, the event mean concentration (EMC) of fecal indicator bacteria (Enterococcus, Escherichia coli, fecal Streptococcus group bacteria, and fecal coliform) across the USA was retrieved from the international stormwater best management practices database to analyze the seasonal variations of inflow and outflow event mean concentrations and removal efficiencies. The Kruskal-Wallis test was employed to determine the seasonal variations of bacteria indicator concentrations and removals, and the two-sample Kolmogorov-Smirnov test was used for comparing different seasonal outcomes. The results indicate that all the inflow EMC of FIB in stormwater runoff is above the water quality criteria. The seasonal differences of fecal Streptococcus group bacteria and fecal coliform are significant. Summer has the potential to increase the bacteria EMC and illustrate the seasonal differences.

Seeing a Mycobacterium-Infected Cell in Nanoscale 3D: Correlative Imaging by Light Microscopy and FIB/SEM Tomography

PubMed Central

Beckwith, Marianne Sandvold; Beckwith, Kai Sandvold; Sikorski, Pawel; Skogaker, Nan Tostrup

2015-01-01

Mycobacteria pose a threat to the world health today, with pathogenic and opportunistic bacteria causing tuberculosis and non-tuberculous disease in large parts of the population. Much is still unknown about the interplay between bacteria and host during infection and disease, and more research is needed to meet the challenge of drug resistance and inefficient vaccines. This work establishes a reliable and reproducible method for performing correlative imaging of human macrophages infected with mycobacteria at an ultra-high resolution and in 3D. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) tomography is applied, together with confocal fluorescence microscopy for localization of appropriately infected cells. The method is based on an Aclar poly(chloro-tri-fluoro)ethylene substrate, micropatterned into an advantageous geometry by a simple thermomoulding process. The platform increases the throughput and quality of FIB/SEM tomography analyses, and was successfully applied to detail the intracellular environment of a whole mycobacterium-infected macrophage in 3D. PMID:26406896

Agrochemicals indirectly increase survival of E. coli O157:H7 and indicator bacteria by reducing ecosystem services.

PubMed

Staley, Zachery R; Rohr, Jason R; Senkbeil, Jacob K; Harwood, Valerie J

Storm water and agricultural runoff frequently contain agrochemicals, fecal indicator bacteria (FIB), and zoonotic pathogens. Entry of such contaminants into aquatic ecosystems may affect ecology and human health. This study tested the hypothesis that the herbicide atrazine and the fungicide chlorothalonil indirectly affect the survival of FIB (Escherichia coli and Enterococcus faecalis) and a pathogen (E. coli O157:H7) by altering densities of protozoan predators or by altering competition from autochthonous bacteria. Streptomycin-resistant E. coli, En. faecalis, and E. coli O157:H7 were added to microcosms composed of Florida river water containing natural protozoan and bacterial populations. FIB, pathogen, and protozoan densities were monitored over six days. Known metabolic inhibitors, cycloheximide and streptomycin, were used to inhibit autochthonous protozoa or bacteria, respectively. The inhibitors made it possible to isolate the effects of predation or competition on survival of allochthonous bacteria, and each treatment increased the survival of FIB and pathogens. Chlorothalonil's effect was similar to that of cycloheximide, significantly reducing protozoan densities and elevating densities of FIB and pathogens relative to the control. Atrazine treatment did not affect protozoan densities, but, through an effect on competition, resulted in significantly greater densities of En. faecalis and E. coli O157:H7. Hence, by reducing predaceous protozoa and bacterial competitors that facilitate purifying water bodies of FIBs and human pathogens, chlorothalonil and atrazine indirectly diminished an ecosystem service of fresh water.

Loading of fecal indicator bacteria in North Carolina tidal creek headwaters: hydrographic patterns and terrestrial runoff relationships.

PubMed

Stumpf, Curtis H; Piehler, Michael F; Thompson, Suzanne; Noble, Rachel T

2010-09-01

In the New River Estuary (NRE) in eastern North Carolina (NC), fecal indicator bacteria (FIB) levels exceed water quality standards, leading to closure of estuarine waters for shellfishing and classification of parts of the estuary as "impaired" per the Clean Water Act section 303(d) list. As a means to investigate fecal contamination and loading of FIB to the NRE, a continuous automated sampler (ISCO) outfitted with flow modules and water quality probes was placed in four first-order tidal creek headwaters. Total storm discharge and bacterial load for Escherichia coli (EC) and Enterococcus spp. (ENT) were calculated using graphical volumetric flow calculations and interpolation of FIB measurements over each storm's duration for 10 storms. Mean total load of 10(9)-10(12) EC and ENT cells (MPN) occurred over the course of each storm. Total storm loading, averaged across all storms, was as much as 30 and 37 times greater than equivalent duration of baseflow loading for EC and ENT, respectively. Within the first 30% of creek storm volume for all storms and all creeks combined, a mean cumulative load of only 37% and 44% of the total EC and ENT cells, respectively, was discharged, indicating these creeks are not demonstrating a 'first flush' scenario for FIB. The median storm Event Mean Concentrations (EMCs) were 6.37 × 10(2) and 2.03 × 10(2) MPN/100 mL, for EC and ENT, respectively, compared with median baseflow concentrations of 1.48 × 10(2) and 4.84 × 10(1) for EC and ENT, respectively, and were significantly different between base and storm flow events. FIB was correlated with TSS (weak), flow rate (strong), and different stages (base, rising, peak, and falling) of the hydrograph (strong). Pollutographs indicate large intra-storm variability of FIB, and the need for more intensive sampling throughout a storm in order to attain accurate FIB contaminant estimates. Instream sediment concentrations ranged from 5 to 478 (MPN/g) and 13 to 776 (MPN/g) for EC and ENT

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

EPA Science Inventory

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial ...

COMPARATIVE STUDY OF FIB-4 INDEX AND TRANSIENT ELASTOGRAPHY AMONG PATIENTS WITH CHRONIC HEPATITIS C VIRUS INFECTION IN GEORGIA.

PubMed

Dolmazashvili, E; Karchava, M; Abutidze, A; Sharvadze, L; Tsertsvadze, T

2017-03-01

Liver biopsy remains the reference standard for fibrosis staging. However, it has several limitations, which have led to the development of non-invasive methods. We evaluated liver fibrosis severity among HCV infected patients by comparing transient elastography (TE) and FIB-4 index. Retrospective study was conducted. Clinical data for 750 patients were obtained. The mean age of the study population was 51 years; 595 (79.3%) were male and 155 (20.7%) were female. TE and tests on biological samples were performed within one-week timeframe. Additional analyses of prothrombin index, albumin concentration, splenomegaly on abdominal ultrasound and esophageal varices on upper gastrointestinal endoscopy were performed among selected patients. Comparable results were observed among 534 patients (71.2%). FIB-4<1.45 had a negative predictive value of 89% to exclude significant fibrosis and FIB-4>3.25 had a positive predictive value of 100 % to confirm the existence of significant fibrosis. Inconclusive FIB-4 score was obtained in 170 (22.7%) patients. Of them 127 (74.7%) had significant fibrosis (F3-F4) by TE. Discordant results (FIB-4 <1.45 and Liver Stiffness Measurement (LSM) >9.5 kpa) were observed in 46 (6.1%) of patients. Low prothrombin index, low albumin concentration, splenomegaly and esophageal varices were significantly (p<0.001) correlated with TE results. Discrepancy showing high FIB-4 score and low LSM was not observed in our cohort. There was a good correlation between TE and FIB-4 score. FIB-4 could rapidly replace expensive methods to assess liver fibrosis severity in some scenarios. However, our study demonstrated superiority of TE. LSM correlated better with indirect markers of significant fibrosis.

The compartment bag test (CBT) for enumerating fecal indicator bacteria: Basis for design and interpretation of results.

PubMed

Gronewold, Andrew D; Sobsey, Mark D; McMahan, Lanakila

2017-06-01

For the past several years, the compartment bag test (CBT) has been employed in water quality monitoring and public health protection around the world. To date, however, the statistical basis for the design and recommended procedures for enumerating fecal indicator bacteria (FIB) concentrations from CBT results have not been formally documented. Here, we provide that documentation following protocols for communicating the evolution of similar water quality testing procedures. We begin with an overview of the statistical theory behind the CBT, followed by a description of how that theory was applied to determine an optimal CBT design. We then provide recommendations for interpreting CBT results, including procedures for estimating quantiles of the FIB concentration probability distribution, and the confidence of compliance with recognized water quality guidelines. We synthesize these values in custom user-oriented 'look-up' tables similar to those developed for other FIB water quality testing methods. Modified versions of our tables are currently distributed commercially as part of the CBT testing kit. Published by Elsevier B.V.

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

PubMed

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of new FIB technology for EUVL mask repair

NASA Astrophysics Data System (ADS)

Aramaki, Fumio; Ogawa, Takashi; Matsuda, Osamu; Kozakai, Tomokazu; Sugiyama, Yasuhiko; Oba, Hiroshi; Yasaka, Anto; Amano, Tsuyoshi; Shigemura, Hiroyuki; Suga, Osamu

2011-04-01

The next generation EUVL masks beyond hp15nm are difficult to repair for the current repair technologies including focused ion beam (FIB) and electron beam (EB) in view of the minimum repairable size. We developed a new FIB technology to repair EUVL masks. Conventional FIB use gallium ions (Ga+) generated by a liquid metal ion source (LMIS), but the new FIB uses hydrogen ions (H2+) generated by a gas field ion source (GFIS). The minimum reaction area of H2+ FIB is theoretically much smaller than that of EB. We investigated the repair performance of H2+ FIB. In the concrete, we evaluated image resolution, scan damage, etching rate, material selectivity of etching and actinic image of repaired area. The most important result is that there was no difference between the repaired area and the non-repaired one on actinic images. That result suggests that the H2+ GFIS technology is a promising candidate for the solution to repair the next generation EUVL masks beyond hp15nm.

Focused Ion Beam (FIB) combined with SEM (FIB/SEM) and TEM: Advanced tools for nano-analysis in Geosciences

NASA Astrophysics Data System (ADS)

Wirth, R.; Morales, L. G.

2011-12-01

Focused ion beam (FIB) techniques have been successfully applied to the preparation of site-specific electron transparent membranes for transmission electron microscopy (TEM) investigations in Geosciences since several years. For example, systematic TEM studies of nano-inclusions in diamond foils prepared with FIB have improved our knowledge on diamond formation. However, FIB is not exclusively used for sample preparation for TEM application because it has been proved that one and the same TEM foil can also be used for Synchrotron IR, Synchrotron X-Ray fluorescence (XRF), scanning transmission X-Ray microscopy (STXM) and NanoSIMS analysis. In addition, FIB milling turned out to be very useful for sample preparation of Brillouin scattering experiments and has a strong potential for preparation of highly-polished, micrometer-scale samples. However, a real break through in FIB application was achieved combining a Ga-ion source of the FIB with an electron source of a scanning electron microscope (SEM) in one single instrument. The combination of FIB/SEM renders access to the third dimension of the sample possible. A cavity normal to the sample surface is sputtered with Ga-ions and this newly created inner surface is imaged with the electron beam. Alternating slicing and viewing along these cavities allow the acquisition of a sequence of images that allows the observation in 3 dimensions. Recently, this technique has been successfully applied to image the structure of grain or phase boundaries in metamorphic rocks as well as micro- and nanoporosity in shales, but its applicability goes far beyond these few examples. Combining slicing and viewing with X-Ray and electron backscatter diffraction (EBSD) analysis can provide 3D elemental mapping and 3D crystallographic orientation mapping of crystalline materials. Combined FIB/SEM devices also facilitate the preparation of substantially thinner and cleaner TEM foils (approximately 30 nm) because electron beam imaging

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

USDA-ARS?s Scientific Manuscript database

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. These contaminants can be mobilized into the water column due to resuspension events, thus affecting overall water quality. Along with the contaminants, other markers such as microbia...

Improving yield and reliability of FIB modifications using electrical testing

NASA Astrophysics Data System (ADS)

Desplats, Romain; Benbrik, Jamel; Benteo, Bruno; Perdu, Philippe

1998-08-01

Focused Ion Beam technology has two main areas of application for ICs: modification and preparation for technological analysis. The most solicited area is modification. This involves physically modifying a circuit by cutting lines and creating new ones in order to change the electrical function of the circuit. IC planar technologies have an increasing number of metal interconnections making FIB modifications more complex and decreasing their changes of success. The yield of FIB operations on ICs reflects a downward trend that imposes a greater number of circuits to be modified in order to successfully correct a small number of them. This requires extended duration, which is not compatible with production line turn around times. To respond to this problem, two solutions can be defined: either, reducing the duration of each FIB operation or increasing the success rate of FIB modifications. Since reducing the time depends mainly on FIB operator experience, insuring a higher success rate represents a more crucial aspect as both experienced and novice operators could benefit from this improvement. In order to insure successful modifications, it is necessary to control each step of a FIB operation. To do this, we have developed a new method using in situ electrical testing which has a direct impact on the yield of FIB modifications. We will present this innovative development through a real case study of a CMOS ASIC for high-speed communications. Monitoring the electrical behavior at each step in a FIB operation makes it possible to reduce the number of circuits to be modified and consequently reduces system costs thanks to better yield control. Knowing the internal electrical behavior also gives us indications about the impact on reliability of FIB modified circuits. Finally, this approach can be applied to failure analysis and FIB operations on flip chip circuits.

Lack of direct effects of agrochemicals on zoonotic pathogens and fecal indicator bacteria.

PubMed

Staley, Zachery R; Senkbeil, Jacob K; Rohr, Jason R; Harwood, Valerie J

2012-11-01

Agrochemicals, fecal indicator bacteria (FIB), and pathogens frequently contaminate water simultaneously. No significant direct effects of fertilizer, atrazine, malathion, and chlorothalonil on the survival of Escherichia coli, Enterococcus faecalis, Salmonella enterica, human polyomaviruses, and adenovirus were detected, supporting the assertion that previously observed effects of agrochemicals on FIB were indirect.

Association of Fecal Indicator Bacteria with Human Viruses and Microbial Source Tracking Markers at Coastal Beaches Impacted by Nonpoint Source Pollution

PubMed Central

McQuaig, Shannon; Griffith, John

2012-01-01

Water quality was assessed at two marine beaches in California by measuring the concentrations of culturable fecal indicator bacteria (FIB) and by library-independent microbial source tracking (MST) methods targeting markers of human-associated microbes (human polyomavirus [HPyV] PCR and quantitative PCR, Methanobrevibacter smithii PCR, and Bacteroides sp. strain HF183 PCR) and a human pathogen (adenovirus by nested PCR). FIB levels periodically exceeded regulatory thresholds at Doheny and Avalon Beaches for enterococci (28.5% and 31.7% of samples, respectively) and fecal coliforms (20% and 5.8%, respectively). Adenoviruses were detected at four of five sites at Doheny Beach and were correlated with detection of HPyVs and human Bacteroides HF183; however, adenoviruses were not detected at Avalon Beach. The most frequently detected human source marker at both beaches was Bacteroides HF183, which was detected in 27% of samples. Correlations between FIBs and human markers were much more frequent at Doheny Beach than at Avalon Beach; e.g., adenovirus was correlated with HPyVs and HF183. Human sewage markers and adenoviruses were routinely detected in samples meeting FIB regulatory standards. The toolbox approach of FIB measurement coupled with analysis of several MST markers targeting human pathogens used here demonstrated that human sewage is at least partly responsible for the degradation of water quality, particularly at Doheny Beach, and resulted in a more definitive assessment of recreational water quality and human health risk than reliance on FIB concentrations alone could have provided. PMID:22773625

Lack of Direct Effects of Agrochemicals on Zoonotic Pathogens and Fecal Indicator Bacteria

PubMed Central

Staley, Zachery R.; Senkbeil, Jacob K.; Rohr, Jason R.

2012-01-01

Agrochemicals, fecal indicator bacteria (FIB), and pathogens frequently contaminate water simultaneously. No significant direct effects of fertilizer, atrazine, malathion, and chlorothalonil on the survival of Escherichia coli, Enterococcus faecalis, Salmonella enterica, human polyomaviruses, and adenovirus were detected, supporting the assertion that previously observed effects of agrochemicals on FIB were indirect. PMID:22961900

A simple bedside blood test (Fibrofast; FIB-5) is superior to FIB-4 index for the differentiation between non-significant and significant fibrosis in patients with chronic hepatitis C.

PubMed

Shiha, G; Seif, S; Eldesoky, A; Elbasiony, M; Soliman, R; Metwally, A; Zalata, K; Mikhail, N

2017-05-01

A simple non-invasive score (Fibrofast, FIB-5) was developed using five routine laboratory tests (ALT, AST, alkaline phosphatase, albumin and platelets count) for the detection of significant hepatic fibrosis in patients with chronic hepatitis C. The FIB-4 index is a non-invasive test for the assessment of liver fibrosis, and a score of ≤1.45 enables the correct identification of patients who have non-significant (F0-1) from significant fibrosis (F2-4), and could avoid liver biopsy. The aim of this study was to compare the performance characteristics of FIB-5 and FIB-4 to differentiate between non-significant and significant fibrosis. A cross-sectional study included 604 chronic HCV patients. All liver biopsies were scored using the METAVIR system. Both FIB-5 and FIB-4 scores were measured and the performance characteristics were calculated using the ROC curve. The performance characteristics of FIB-5 at ≥7.5 and FIB-4 at ≤1.45 for the differentiation between non-significant fibrosis and significant fibrosis were: specificity 94.4%, PPV 85.7%, and specificity 54.9%, PPV 55.7% respectively. FIB-5 score at the new cutoff is superior to FIB-4 index for the differentiation between non-significant and significant fibrosis.

Sources of fecal indicator bacteria to groundwater, Malibu Lagoon and the near-shore ocean, Malibu, California, USA

USGS Publications Warehouse

Izbicki, John A.; Swarzenski, Peter W.; Burton, Carmen A.; Van De Werfhorst, Laurie; Holden, Patricia A.; Dubinsky, Eric A.

2012-01-01

Onsite wastewater treatment systems (OWTS) used to treat residential and commercial sewage near Malibu, California have been implicated as a possible source of fecal indicator bacteria (FIB) to Malibu Lagoon and the near-shore ocean. For this to occur, treated wastewater must first move through groundwater before discharging to the Lagoon or ocean. In July 2009 and April 2010, δ18O and δD data showed that some samples from water-table wells contained as much as 70% wastewater; at that time FIB concentrations in those samples were generally less than the detection limit of 1 Most Probable Number (MPN) per 100 milliliters (mL). In contrast, Malibu Lagoon had total coliform, Escherichia coli, and enterococci concentrations as high as 650,000, 130,000, and 5,500 MPN per 100 mL, respectively, and as many as 12% of samples from nearby ocean beaches exceeded the U.S. Environmental Protection Agency single sample enterococci standard for marine recreational water of 104 MPN per 100 mL. Human-associated Bacteroidales, an indicator of human-fecal contamination, were not detected in water from wells, Malibu Lagoon, or the near-shore ocean. Similarly, microarray (PhyloChip) data show Bacteroidales and Fimicutes Operational Taxanomic Units (OTUs) present in OWTS were largely absent in groundwater; in contrast, 50% of Bacteroidales and Fimicutes OTUs present in the near-shore ocean were also present in gull feces. Terminal-Restriction Length Fragment Polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) data showed that microbial communities in groundwater were different and less abundant than communities in OWTS, Malibu Lagoon, or the near-shore ocean. However, organic compounds indicative of wastewater (such as fecal sterols, bisphenol-A and cosmetics) were present in groundwater having a high percentage of wastewater and were present in groundwater discharging to the ocean. FIB in the near-shore ocean varied with tides, ocean swells, and waves. Movement of water from

Focused ion beam (FIB)/scanning electron microscopy (SEM) in tissue structural research.

PubMed

Leser, Vladka; Milani, Marziale; Tatti, Francesco; Tkalec, Ziva Pipan; Strus, Jasna; Drobne, Damjana

2010-10-01

The focused ion beam (FIB) and scanning electron microscope (SEM) are commonly used in material sciences for imaging and analysis of materials. Over the last decade, the combined FIB/SEM system has proven to be also applicable in the life sciences. We have examined the potential of the focused ion beam/scanning electron microscope system for the investigation of biological tissues of the model organism Porcellio scaber (Crustacea: Isopoda). Tissue from digestive glands was prepared as for conventional SEM or as for transmission electron microscopy (TEM). The samples were transferred into FIB/SEM for FIB milling and an imaging operation. FIB-milled regions were secondary electron imaged, back-scattered electron imaged, or energy dispersive X-ray (EDX) analyzed. Our results demonstrated that FIB/SEM enables simultaneous investigation of sample gross morphology, cell surface characteristics, and subsurface structures. The same FIB-exposed regions were analyzed by EDX to provide basic compositional data. When samples were prepared as for TEM, the information obtained with FIB/SEM is comparable, though at limited magnification, to that obtained from TEM. A combination of imaging, micro-manipulation, and compositional analysis appears of particular interest in the investigation of epithelial tissues, which are subjected to various endogenous and exogenous conditions affecting their structure and function. The FIB/SEM is a promising tool for an overall examination of epithelial tissue under normal, stressed, or pathological conditions.

FIB-4 and imaging for measuring fibrosis in hepatitis C virus.

PubMed

Turner, Barbara J; Liang, Yuanyuan; Singal, Amit G

2017-02-01

Noninvasive measures are widely used to assess fibrosis and may be used to prioritize hepatitis C virus (HCV) treatment. We examined risks for likely fibrosis in patients with chronic HCV infection using fibrosis-4 (FIB-4) and imaging. A HCV screening program diagnosed chronic HCV in patients born from 1945 to 1965 admitted in a safety net hospital. Likely fibrosis was based on FIB-4 (≥1.45) alone or combined with imaging interpreted as fibrosis or cirrhosis. Logistic regression was used to calculate adjusted odds ratios (AORs) for demographic, clinical, and insurance factors associated with each outcome. Using multiple linear regression among patients with likely fibrosis, we examined associations with higher Model for End-Stage Liver Disease (MELD) scores. Using FIB-4 alone, 57% (83/146) of patients had likely fibrosis versus 43% (63/148) using FIB-4 plus imaging. Obesity/overweight and Hispanic ethnicity had over three-fold to four-fold higher AORs for fibrosis, respectively, based on FIB-4 plus imaging, but both AORs were only two-fold greater with FIB-4 alone. Being uninsured was significantly associated with fibrosis based on FIB-4 alone [AOR=2.40 (95% confidence interval 1.01-5.70)] but not with imaging. Heavy alcohol use and older age were associated with higher AORs of fibrosis with both measures (all P<0.004). MELD scores were ∼3 points higher for uninsured patients, regardless of measure (both P<0.05). Using FIB-4 plus imaging to identify fibrosis in chronic HCV, higher risks are seen for Hispanics and overweight/obese individuals than using FIB-4 alone. Higher MELD scores at diagnosis for the uninsured indicate delayed access to care.

FIB-SEM tomography in biology.

PubMed

Kizilyaprak, Caroline; Bittermann, Anne Greet; Daraspe, Jean; Humbel, Bruno M

2014-01-01

Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

An assessment of fecal indicator and other bacteria from an urbanized coastal lagoon in the City of Los Angeles, California, USA.

PubMed

Dorsey, John H; Carmona-Galindo, Víctor D; Leary, Christopher; Huh, Julie; Valdez, Jennifer

2013-03-01

A study was performed in Del Rey Lagoon, City of Los Angeles, to determine if the lagoon was as a source or sink for fecal indicator bacteria (FIB: total coliforms, Escherichia coli, enterococci) and to screen for the presence of other potentially pathogenic bacteria. The lagoon receives tidal flows from the adjacent Ballona Estuary whose water usually is contaminated with FIB originating from the highly urbanized Ballona Creek Watershed. During 16 sampling events from February 2008 through March 2009, replicate water samples (n = 3) were collected 1 h prior to the high tide and 1 h prior to the following low tide. FIB concentrations were measured by the defined substrate method (IDEXX, Westbrook, Me) followed by culturing of bacterial isolates sampled from positive IDEXX Quanti-Tray wells and were identified using the Vitek 2 Compact (bioMérieux, Durham, NC). Mean concentrations of FIB often differed by an order of magnitude from flood to ebb flow conditions. The lagoon tended to act as a sink for total coliforms based on the ratio of mean flood to ebb densities (R (F/E)) >1.0 during 56 % of the sampling events and during ebb flows, as a source for E. coli and enterococci (R (F/E) <1.69 % of events). Approximately 54 species were identified from 277 isolates cultured from the IDEXX Quanti-Trays. Of these, 54 % were species known to include pathogenic strains that can be naturally occurring, introduced in runoff, or originated from other sources. Diversity and cluster analyses indicated a dynamic assemblage that changes in species composition with day-to-day fluctuations as well as tidal action. The concept of monitoring the lagoon and estuary as a sentinel habitat for pathogenic assemblages is discussed.

The monomeric, tetrameric, and fibrillar organization of Fib: the dynamic building block of the bacterial linear motor of Spiroplasma melliferum BC3.

PubMed

Cohen-Krausz, Sara; Cabahug, Pamela C; Trachtenberg, Shlomo

2011-07-08

Spiroplasmas belong to the class Mollicutes, representing the minimal, free-living, and self-replicating forms of life. Spiroplasmas are helical wall-less bacteria and the only ones known to swim by means of a linear motor (rather than the near-universal rotary bacterial motor). The linear motor follows the shortest path along the cell's helical membranal tube. The motor is composed of a flat monolayered ribbon of seven parallel fibrils and is believed to function in controlling cell helicity and motility through dynamic, coordinated, differential length changes in the fibrils. The latter cause local perturbations of helical symmetry, which are essential for net directional displacement in environments with a low Reynolds number. The underlying fibrils' core building block is a circular tetramer of the 59-kDa protein Fib. The fibrils' differential length changes are believed to be driven by molecular switching of Fib, leading consequently to axial ratio and length changes in tetrameric rings. Using cryo electron microscopy, diffractometry, single-particle analysis of isolated ribbons, and sequence analyses of Fib, we determined the overall molecular organization of the Fib monomer, tetramer, fibril, and linear motor of Spiroplasma melliferum BC3 that underlies cell geometry and motility. Fib appears to be a bidomained molecule, of which the N-terminal half is apparently a globular phosphorylase. By a combination of reversible rotation and diagonal shift of Fib monomers, the tetramer adopts either a cross-like nonhanded conformation or a ring-like handed conformation. The sense of Fib rotation may determine the handedness of the linear motor and, eventually, of the cell. A further change in the axial ratio of the ring-like tetramers controls fibril lengths and the consequent helical geometry. Analysis of tetramer quadrants from adjacent fibrils clearly demonstrates local differential fibril lengths. Copyright © 2011 Elsevier Ltd. All rights reserved.

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

Dopant mapping in thin FIB prepared silicon samples by Off-Axis Electron Holography.

PubMed

Pantzer, Adi; Vakahy, Atsmon; Eliyahou, Zohar; Levi, George; Horvitz, Dror; Kohn, Amit

2014-03-01

Modern semiconductor devices function due to accurate dopant distribution. Off-Axis Electron Holography (OAEH) in the transmission electron microscope (TEM) can map quantitatively the electrostatic potential in semiconductors with high spatial resolution. For the microelectronics industry, ongoing reduction of device dimensions, 3D device geometry, and failure analysis of specific devices require preparation of thin TEM samples, under 70 nm thick, by focused ion beam (FIB). Such thicknesses, which are considerably thinner than the values reported to date in the literature, are challenging due to FIB induced damage and surface depletion effects. Here, we report on preparation of TEM samples of silicon PN junctions in the FIB completed by low-energy (5 keV) ion milling, which reduced amorphization of the silicon to 10nm thick. Additional perpendicular FIB sectioning enabled a direct measurement of the TEM sample thickness in order to determine accurately the crystalline thickness of the sample. Consequently, we find that the low-energy milling also resulted in a negligible thickness of electrically inactive regions, approximately 4nm thick. The influence of TEM sample thickness, FIB induced damage and doping concentrations on the accuracy of the OAEH measurements were examined by comparison to secondary ion mass spectrometry measurements as well as to 1D and 3D simulations of the electrostatic potentials. We conclude that for TEM samples down to 100 nm thick, OAEH measurements of Si-based PN junctions, for the doping levels examined here, resulted in quantitative mapping of potential variations, within ~0.1 V. For thinner TEM samples, down to 20 nm thick, mapping of potential variations is qualitative, due to a reduced accuracy of ~0.3 V. This article is dedicated to the memory of Zohar Eliyahou. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection of Helicobacter pylori and fecal indicator bacteria in five North American rivers.

USGS Publications Warehouse

Voytek, M.A.; Ashen, J.B.; Fogarty, L.R.; Kirshtein, J.D.; Landa, E.R.

2005-01-01

This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H. pylori from five North American rivers of different size and with different land use characteristics. Primers designed to amplify genes specific to Helicobacter spp. and H. pylori were evaluated for their efficacy in detection and quantification in environmental samples. Helicobacter spp. were detected in 18/33 (55%) of river samples. H. pylori was detected in 11/33 (33%) of river samples. FIB were found in 32/33 (96%) of river samples. When FIB abundance exceeded USEPA water quality standards for single samples, Helicobacter or H. pylori were detected in 7/15 (47%) cases. No numerical correlation was found between the presence of FIB and either Helicobacter spp. or H. pylori. This suggests that the presence of FIB will be of limited use for detection of Helicobacter spp. or H. pylori by public health agencies.

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water (ASM 2017 Presentation)

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

FIB-4 index is associated with hepatocellular carcinoma risk in HIV-infected patients.

PubMed

Park, Lesley S; Tate, Janet P; Justice, Amy C; Lo Re, Vincent; Lim, Joseph K; Bräu, Norbert; Brown, Sheldon T; Butt, Adeel A; Gibert, Cynthia; Goetz, Matthew Bidwell; Rimland, David; Rodriguez-Barradas, Maria C; Dubrow, Robert

2011-12-01

Chronic inflammation caused by hepatitis B virus infection, hepatitis C virus infection, and/or heavy alcohol use can lead to fibrosis, cirrhosis, and eventually hepatocellular carcinoma (HCC). FIB-4 is an index score calculated from platelet count, alanine transaminase, aspartate transaminase, and age that predicts fibrosis and cirrhosis. We hypothesized that high FIB-4 would be associated with development of HCC in HIV-infected persons, who are at high risk due to high prevalence of viral hepatitis and alcohol consumption, and possibly due to HIV infection itself. Using proportional hazards models, we tested this hypothesis among 22,980 HIV-infected men from the Veterans Aging Cohort Study. We identified incident HCC cases from the Veterans Affairs Central Cancer Registry. During follow-up, there were 112 incident HCC diagnoses. The age- and race/ethnic group-adjusted HR was 4.2 [95% confidence interval (CI), 2.4-7.4] for intermediate FIB-4 and 13.0 (95% CI, 7.2-23.4) for high FIB-4, compared with low FIB-4. After further adjustment for enrollment year, CD4 count, HIV-1 RNA level, antiretroviral therapy use, hepatitis B and C virus infection, alcohol abuse/dependency, and diabetes, FIB-4 remained a strong, significant, independent risk factor for HCC. The multivariate-adjusted HR was 3.6 (95% CI, 2.1-6.4) for intermediate FIB-4 and 9.6 (95% CI, 5.2-17.4) for high FIB-4. Calculated from routine, noninvasive laboratory tests, FIB-4 is a strong, independent HCC risk factor in HIV-infected patients. FIB-4 might prove valuable as an easily measured index to identify those at highest risk for HCC, even prior to development of clinical cirrhosis.

Simulation of FIB-SEM images for analysis of porous microstructures.

PubMed

Prill, Torben; Schladitz, Katja

2013-01-01

Focused ion beam nanotomography-scanning electron microscopy tomography yields high-quality three-dimensional images of materials microstructures at the nanometer scale combining serial sectioning using a focused ion beam with SEM. However, FIB-SEM tomography of highly porous media leads to shine-through artifacts preventing automatic segmentation of the solid component. We simulate the SEM process in order to generate synthetic FIB-SEM image data for developing and validating segmentation methods. Monte-Carlo techniques yield accurate results, but are too slow for the simulation of FIB-SEM tomography requiring hundreds of SEM images for one dataset alone. Nevertheless, a quasi-analytic description of the specimen and various acceleration techniques, including a track compression algorithm and an acceleration for the simulation of secondary electrons, cut down the computing time by orders of magnitude, allowing for the first time to simulate FIB-SEM tomography. © Wiley Periodicals, Inc.

Detection of multiple potentially pathogenic bacteria in Matang mangrove estuaries, Malaysia.

PubMed

Ghaderpour, Aziz; Mohd Nasori, Khairul Nazrin; Chew, Li Lee; Chong, Ving Ching; Thong, Kwai Lin; Chai, Lay Ching

2014-06-15

The deltaic estuarine system of the Matang Mangrove Forest Reserve of Malaysia is a site where several human settlements and brackish water aquaculture have been established. Here, we evaluated the level of fecal indicator bacteria (FIB) and the presence of potentially pathogenic bacteria in the surface water and sediments. Higher levels of FIB were detected at downstream sampling sites from the fishing village, indicating it as a possible source of anthropogenic pollution to the estuary. Enterococci levels in the estuarine sediments were higher than in the surface water, while total coliforms and E. coli in the estuarine sediments were not detected in all samples. Also, various types of potentially pathogenic bacteria, including Klebsiella pneumoniae, Serratia marcescens and Enterobacter cloacae were isolated. The results indicate that the Matang estuarine system is contaminated with various types of potential human bacterial pathogens which might pose a health risk to the public. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Improving microstructural quantification in FIB/SEM nanotomography.

PubMed

Taillon, Joshua A; Pellegrinelli, Christopher; Huang, Yi-Lin; Wachsman, Eric D; Salamanca-Riba, Lourdes G

2018-01-01

FIB/SEM nanotomography (FIB-nt) is a powerful technique for the determination and quantification of the three-dimensional microstructure in subsurface features. Often times, the microstructure of a sample is the ultimate determiner of the overall performance of a system, and a detailed understanding of its properties is crucial in advancing the materials engineering of a resulting device. While the FIB-nt technique has developed significantly in the 15 years since its introduction, advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain "advanced" microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of material systems. Finally, results from an analyzed sample are presented as a practical example of how these techniques can be implemented. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-scale characterization by FIB-SEM/TEM/3DAP.

PubMed

Ohkubo, T; Sepehri-Amin, H; Sasaki, T T; Hono, K

2014-11-01

ultra-fine grain Nd-Fe-B permanent magnet will be shown [1]. In order to improve the magnetic properties, especially to increase the coercivity (resistance against magnetization reversal) of the magnet, decreasing the grain size and isolating each grain by non-ferromagnetic grain boundary phase are quite important since the nucleation of magnetic reversal from grain boundary phase can be suppressed and pinning force of magnetic domain wall at the grain boundary phase can be strengthened. Therefore, micro and nano structure and chemistry analysis can shed a light do grain boundary engineering.Figure 1(a,b) shows SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet and the reconstructed 3D tomography of Nd-rich phases obtained by FIB/SEM serial sectioning. This data can provide us information about the distribution of Nd-rich phase and its volume fraction. Moreover, the HRTEM image from the grain boundary phase, the 3DAP maps and the concentration depth profiles are shown in Fig. 1(c,d,e). This magnet shows high coercivity (1517kA/m), and by comparing these results with the microstructures of low coercivity specimen, importance of grain boundary formation was confirmed and it gives us hint to improve the coercivity further. We will show the detail and results from other materials.jmicro;63/suppl_1/i6/DFU046F1F1DFU046F1Fig. 1.(a) SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet. (b) 3D FIB/SEM tomography of Nd-rich phases. (c) HRTEM image from the grain boundary phase. (d) 3DAP maps of Nd, Cu and Al. (e) Concentration depth profiles for Fe, Nd+Pr, B, Co, Cu and Al, determined from the selected box in (d)[1]. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Recent improvement of a FIB-SEM serial-sectioning method for precise 3D image reconstruction - application of the orthogonally-arranged FIB-SEM.

PubMed

Hara, Toru

2014-11-01

IntroductionWe installed the first "orthogonally-arranged" FIB-SEM in 2011. The most characteristic point of this instrument is that the FIB and SEM columns are perpendicularly mounted; this is specially designed to obtain a serial-sectioning dataset more accurately and precisely with higher contrast and higher spatial resolution compare to other current FIB-SEMs [1]. Since the installation in 2011, we have developed the hardware and methodology of the serial-sectioning based on this orthogonal FIB-SEM. In order to develop this technique, we have widely opened this instrument to every researcher of all fields. In the presentation, I would like to introduce some of application results that are obtained by users of this instrument. The characteristic points of the orthogonal systemFigure 1 shows a difference between the standard and the orthogonal FIB-SEM systems: In the standard system, shown in Fig.1(a), optical axes of a FIB and a SEM crosses around 60deg., while in the orthogonal system (Fig.1(b)), they are perpendicular to each other. The standard arrangement (a) is certainly suitable for TEM lamellae preparation etc. because the FIB and the SEM can see the same position simultaneously. However, for a serial-sectioning, it is not to say the best arrangement. One of the reasons is that the sliced plane by the FIB is not perpendicular to the electron beam so that the background contrast is not uniform and observed plane is distorted. On the other hand, in case of the orthogonally-arranged system,(b), these problems are resolved. In addition, spatial resolution can keep high enough even in a low accelerating voltage (e.g. 500V) because a working distance is set very small, 2mm. From these special design, we can obtain the serial-sectioning dataset from rather wide area (∼100um) with high spatial resolution (Max. 2×2×2nm). As this system has many kinds of detectors: SE, ET, Backscatter Electron(Energy-selective), EDS, EBSD, STEM(BF&ADF), with Ar+ ion-gun and a

Human cardiac telocytes: 3D imaging by FIB-SEM tomography

PubMed Central

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-01-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs’ three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. PMID:25327290

Dynamics of fecal indicator bacteria, bacterial pathogen genes, and organic wastewater contaminants in the Little Calumet River: Portage Burns Waterway, Indiana

USGS Publications Warehouse

Haack, Sheridan K.; Duris, Joseph W.

2013-01-01

Little information exists on the co-occurrence of fecal indicator bacteria (FIB), bacterial pathogens, and organic wastewater-associated chemicals (OWCs) within Great Lakes tributaries. Fifteen watershed sites and one beach site adjacent to the Little Calumet River–Portage Burns Waterway (LCRPBW) on Lake Michigan were tested on four dates for pH, dissolved oxygen, specific conductance, chloride, color, ammonia- and nitrate-nitrogen, soluble phosphorus, sulfate, turbidity, and atrazine; for concentrations of FIB; and for genes indicating the presence of human-pathogenic enterococci (ENT) and of Shiga-toxin producing Escherichia coli (EC) from various animal sources. Nineteen samples were also tested for 60 OWCs. Half of the watershed samples met EC recreational water quality standards; none met ENT standards. Human-wastewater-associated OWC detections were correlated with human-influence indicators such as population/km2, chloride concentrations, and the presence of WWTP effluents, but EC and ENT concentrations were not. Bacterial pathogen genes indicated rural human and several potential animal sources. OWCs of human or ecosystem health concern (musk fragrances AHTN and HHCB, alkylphenols, carbamazepine) and 3 bacterial pathogen genes were detected at the mouth of the LCRPBW, but no such OWCs and only 1 pathogen gene were detected at the beach. The LCRPBW has significant potential to deliver FIB, potential bacterial pathogens, and OWCs of human or ecosystem health concern to the nearshore of Lake Michigan, under conditions enhancing nearshore transport of the river plume. Nearshore mixing of lake and river water, and the lack of relationship between OWCs and FIB or pathogen genes, pose numerous challenges for watershed and nearshore assessment and remediation.

Human cardiac telocytes: 3D imaging by FIB-SEM tomography.

PubMed

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-11-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs' three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. © 2014 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Associations between fecal indicator bacteria prevalence and demographic data in private water supplies in Virginia.

PubMed

Smith, Tamara; Krometis, Leigh-Anne H; Hagedorn, Charles; Lawrence, Annie H; Benham, Brian; Ling, Erin; Ziegler, Peter; Marmagas, Susan West

2014-12-01

Over 1.7 million Virginians rely on private water sources to provide household water. The heaviest reliance on these systems occurs in rural areas, which are often underserved with respect to available financial resources and access to environmental health education. This study aimed to identify potential associations between concentrations of fecal indicator bacteria (FIB) (coliforms, Escherichia coli) in over 800 samples collected at the point-of-use from homes with private water supply systems and homeowner-provided demographic data (household income and education). Of the 828 samples tested, 349 (42%) of samples tested positive for total coliform and 55 (6.6%) tested positive for E. coli. Source tracking efforts targeting optical brightener concentrations via fluorometry and the presence of a human-specific Bacteroides marker via quantitative real-time polymerase chain reaction (qPCR) suggest possible contamination from human septage in over 20 samples. Statistical methods implied that household income has an association with the proportion of samples positive for total coliform, though the relationship between education level and FIB is less clear. Further exploration of links between demographic data and private water quality will be helpful in building effective strategies to improve rural drinking water quality.

Two novel approaches to study arthropod anatomy by using dualbeam FIB/SEM.

PubMed

Di Giulio, Andrea; Muzzi, Maurizio

2018-03-01

Transmission Electron Microscopy (TEM) has always been the conventional method to study arthropod ultrastructure, while the use of Scanning Electron Microscopy (SEM) was mainly devoted to the examination of the external cuticular structures by secondary electrons. The new generation field emission SEMs are capable to generate images at sub-cellular level, comparable to TEM images employing backscattered electrons. The potential of this kind of acquisition becomes very powerful in the dual beam FIB/SEM where the SEM column is combined with a Focused Ion Beam (FIB) column. FIB uses ions as a nano-scalpel to slice samples fixed and embedded in resin, replacing traditional ultramicrotomy. We here present two novel methods, which optimize the use of FIB/SEM for studying arthropod anatomy. Copyright © 2017 Elsevier Ltd. All rights reserved.

An improved cryo-FIB method for fabrication of frozen hydrated lamella.

PubMed

Zhang, Jianguo; Ji, Gang; Huang, Xiaojun; Xu, Wei; Sun, Fei

2016-05-01

Cryo-electron tomography (cryo-ET) provides great insights into the ultrastructure of cells and tissues in their native state and provides a promising way to study the in situ 3D structures of macromolecular complexes. However, this technique has been limited on the very thin specimen, which is not applicable for most cells and tissues. Besides cryo-sectioning approach, cryo focused ion beam (cryo-FIB) appeared recently to achieve 'artifact-free' thin frozen hydrated lamella via fabrication. Considering that the current cryo-FIB methods need modified holders or cartridges, here, with a "D-shaped" molybdenum grid and a specific shutter system, we developed a simple cryo-FIB approach for thin frozen hydrated lamella fabrication, which fits both standard transmission cryo-electron microscopes with side-entry cryo-holders and state-of-the-art ones with AutoGrids. Our approach will expand the usage of cryo-FIB approach in many labs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A Molecular MST Approach to Investigate Fecal Indicator Bacteria in Bioaerosols, Bathing Water, Seaweed Wrack, and Sand at Recreational Beaches

NASA Astrophysics Data System (ADS)

Thoren, K. M.; Sinigalliano, C. D.

2016-02-01

Despite numerous cases of beach bacteria affecting millions of people worldwide, the persistence of the bacteria populations in coastal areas is still not well understood. The purpose of this study was to test the levels of persistence of Fecal Indicating Bacteria (FIB) of enterococci, Escherichia coli, and Human-source Bacteroidales, within the intertidal "swash zone" and the deeper waist zone in which people commonly bathe and play. In addition, the study sought to determine if these bacterial contaminants may also be found in aerosols at the beach. Measuring solar insolation in relation to bacterial persistence in seaweed wrack was used to determine if sunlight plays a role in modifying concentrations of FIB at the beach. Light intensity measured by a solar photometer and air quality measured by aerosol plate counts and qPCR Microbial Source Tracking (MST) was compared to varying locations where the beach samples were collected. Results from water samples demonstrate that bacteria measured using plate counts and qPCR were indeed higher within the swash zone than in the waist zone. This is in contrast with the way that the EPA currently measures and determines the public safety of beach waters. They commonly measure the waist zone, but disregard the swash zone. Results from beach bio-aerosol samples showed a wide variety of fungi and bacteria in the beach air, and qPCR MST analysis of these bio-aerosols showed the presence of FIBs such as enterococci on several of the aerosol collection plates. This emphasizes the need to collect samples from the entire beach instead of just measuring at an isolated area, and that exposure to microbial contaminants may include bathing water, beach sand, seaweed wrack, and bio-aerosols. Thus, the data reveals a potential way to identify harmful levels of bacteria and dangerous levels of poor air quality at recreational beaches. These results expound the need for broader assessment of potential beach contamination, not only the

Three dimensional rock microstructures: insights from FIB-SEM tomography

NASA Astrophysics Data System (ADS)

Drury, Martyn; Pennock, Gill; de Winter, Matthijs

2016-04-01

Most studies of rock microstructures investigate two-dimensional sections or thin slices of three dimensional grain structures. With advances of X-ray and electron tomography methods the 3-D microstructure can be(relatively) routinely investigated on scales from a few microns to cm. 3D studies are needed to investigate the connectivity of microstructures and to test the assumptions we use to calculate 3D properties from 2D sections. We have used FIB-SEM tomography to study the topology of melts in synthetic olivine rocks, 3D crystal growth microstructures, pore networks and subgrain structures. The technique uses a focused ion beam to make serial sections with a spacing of tens to hundreds of nanometers. Each section is then imaged or mapped using the electron beam. The 3D geometry of grains and subgrains can be investigated using orientation contrast or EBSD mapping. FIB-SEM tomography of rocks and minerals can be limited by charging of the uncoated surfaces exposed by the ion beam. The newest generation of FIB-SEMs have much improved low voltage imaging capability allowing high resolution charge free imaging. Low kV FIB-SEM tomography is now widely used to study the connectivity of pore networks. In-situ fluids can also be studied using cryo-FIB-SEM on frozen samples, although special freezing techniques are needed to avoid artifacts produced by ice crystallization. FIB-SEM tomography is complementary, in terms of spatial resolution and sampled volume, to TEM tomography and X-ray tomography, and the combination of these methods can cover a wide range of scales. Our studies on melt topology in synthetic olivine rocks with a high melt content show that many grain boundaries are wetted by nanometre scale melt layers that are too thin to resolve by X-ray tomography. A variety of melt layer geometries occur consistent with several mechanisms of melt layer formation. The nature of melt geometries along triple line junctions and quadruple points can be resolved

Analysis of FIB-induced damage by electron channelling contrast imaging in the SEM.

PubMed

Gutierrez-Urrutia, Ivan

2017-01-01

We have investigated the Ga + ion-damage effect induced by focused ion beam (FIB) milling in a [001] single crystal of a 316 L stainless steel by the electron channelling contrast imaging (ECCI) technique. The influence of FIB milling on the characteristic electron channelling contrast of surface dislocations was analysed. The ECCI approach provides sound estimation of the damage depth produced by FIB milling. For comparison purposes, we have also studied the same milled surface by a conventional electron backscatter diffraction (EBSD) approach. We observe that the ECCI approach provides further insight into the Ga + ion-damage phenomenon than the EBSD technique by direct imaging of FIB artefacts in the scanning electron microscope. We envisage that the ECCI technique may be a convenient tool to optimize the FIB milling settings in applications where the surface crystal defect content is relevant. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Background of the FIB-4 index in Japanese non-alcoholic fatty liver disease.

PubMed

Wada, Takashi; Zeniya, Mikio

2015-01-01

We investigated the distribution and characteristics of the FIB-4 index of liver fibrosis in 1,441 Japanese men (age 50.7±10.2 years) and 304 women (age 53.9±10.3 years) who underwent comprehensive general health checkups and were identified as having non-alcoholic fatty liver disease. With respect to the FIB-4 index, differences according to sex, metabolic indices, and ultrasonic findings were investigated. Among 9,255 individuals who underwent comprehensive general health checkups, 2,750 (29.8%) were found to have mild fatty liver or fatty liver based on ultrasound findings. After excluding patients who consumed ≥150 g alcohol/week (818 individuals), those testing positive for hepatitis B surface antigens or hepatitis C virus antibody (184 individuals), and those for whom data were insufficient (three individuals), we investigated the FIB-4 indices in the remaining 1,745 subjects. There were no sex differences in the FIB-4 index. A total of 1,370 patients (78.5%) exhibited a low cut-off index (COI) (<1.30), 357 (20.5%), exhibited an indeterminate COI (1.30-2.67), and 18 (1.0%) exhibited a high COI (>2.67). There were no associations between the FIB-4 index and the constituent factors of metabolic syndrome. In contrast, there was a significant difference in the ln FIB-4 index between the patients with and without mild fatty liver or fatty liver on ultrasound among men (0.006±0.43 and -0.092±0.39, p<0.001), but not women. The FIB-4 index was is significantly lower in men, but not women, with fatty liver. The FIB-4 index must be calculated separately during medical checkups and evaluated in conjunction with ultrasound findings.

Bacteriophages as indicators of faecal pollution and enteric ...

EPA Pesticide Factsheets

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize concentrations of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in human waste, non-human waste, fresh and marine waters as well as removal through wastewater treatment processes. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the environment and provide an overview of the methods available for detection and enumeration of bacteriophages. In summary, concentrations of FIB bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Our investigation supports use of bacteriophages as viral surrogates especially for wastewater treatment processes, while additional research is needed to clarify their utility as indicators of viral fate and transport in the ambient water. Describes concentrations and removal through environmental and engineered systems of bacteriophages, fecal indicator bacteria and viral pathogens.

Temporal and spatial patterns for surf zone bacteria before and after disinfection of the orange county sanitation district effluent

USGS Publications Warehouse

Robertson, G.L.; Noble, M.A.; Xu, J. P.; Rosenfeld, L.K.; McGee, C.D.

2005-01-01

Data from pre- and post-disinfection fecal indicator bacteria (FIB) samples from final effluent, an offshore ocean outfall, and surf zone stations off Huntington Beach, CA were compared. Analysis of the results from these data sets confirmed that the ocean outfall was not the FIB source responsible for the postings and closures of local beaches that have occurred each summer since 1999. While FIB counts in the final effluent and offshore showed several order of magnitude reductions after disinfection, there were no significant reductions at the nearby surf zone stations. Additionally, the FIB spectral patterns suggest different sources. The dominant fortnightly cycle suggested that the source was related to the wetting and draining of the land from large spring tide tidal excursions.

Assessing the utility of FIB-SEM images for shale digital rock physics

NASA Astrophysics Data System (ADS)

Kelly, Shaina; El-Sobky, Hesham; Torres-Verdín, Carlos; Balhoff, Matthew T.

2016-09-01

Shales and other unconventional or low permeability (tight) reservoirs house vast quantities of hydrocarbons, often demonstrate considerable water uptake, and are potential repositories for fluid sequestration. The pore-scale topology and fluid transport mechanisms within these nanoporous sedimentary rocks remain to be fully understood. Image-informed pore-scale models are useful tools for studying porous media: a debated question in shale pore-scale petrophysics is whether there is a representative elementary volume (REV) for shale models? Furthermore, if an REV exists, how does it differ among petrophysical properties? We obtain three dimensional (3D) models of the topology of microscale shale volumes from image analysis of focused ion beam-scanning electron microscope (FIB-SEM) image stacks and investigate the utility of these models as a potential REV for shale. The scope of data used in this work includes multiple local groups of neighboring FIB-SEM images of different microscale sizes, corresponding core-scale (milli- and centimeters) laboratory data, and, for comparison, series of two-dimensional (2D) cross sections from broad ion beam SEM images (BIB-SEM), which capture a larger microscale field of view than the FIB-SEM images; this array of data is larger than the majority of investigations with FIB-SEM-derived microscale models of shale. Properties such as porosity, organic matter content, and pore connectivity are extracted from each model. Assessments of permeability with single phase, pressure-driven flow simulations are performed in the connected pore space of the models using the lattice-Boltzmann method. Calculated petrophysical properties are compared to those of neighboring FIB-SEM images and to core-scale measurements of the sample associated with the FIB-SEM sites. Results indicate that FIB-SEM images below ∼5000 μm3 volume (the largest volume analyzed) are not a suitable REV for shale permeability and pore-scale networks; i.e. field of view

Quantification of silver nanoparticle uptake and distribution within individual human macrophages by FIB/SEM slice and view.

PubMed

Guehrs, Erik; Schneider, Michael; Günther, Christian M; Hessing, Piet; Heitz, Karen; Wittke, Doreen; López-Serrano Oliver, Ana; Jakubowski, Norbert; Plendl, Johanna; Eisebitt, Stefan; Haase, Andrea

2017-03-21

Quantification of nanoparticle (NP) uptake in cells or tissues is very important for safety assessment. Often, electron microscopy based approaches are used for this purpose, which allow imaging at very high resolution. However, precise quantification of NP numbers in cells and tissues remains challenging. The aim of this study was to present a novel approach, that combines precise quantification of NPs in individual cells together with high resolution imaging of their intracellular distribution based on focused ion beam/ scanning electron microscopy (FIB/SEM) slice and view approaches. We quantified cellular uptake of 75 nm diameter citrate stabilized silver NPs (Ag 75 Cit) into an individual human macrophage derived from monocytic THP-1 cells using a FIB/SEM slice and view approach. Cells were treated with 10 μg/ml for 24 h. We investigated a single cell and found in total 3138 ± 722 silver NPs inside this cell. Most of the silver NPs were located in large agglomerates, only a few were found in clusters of fewer than five NPs. Furthermore, we cross-checked our results by using inductively coupled plasma mass spectrometry and could confirm the FIB/SEM results. Our approach based on FIB/SEM slice and view is currently the only one that allows the quantification of the absolute dose of silver NPs in individual cells and at the same time to assess their intracellular distribution at high resolution. We therefore propose to use FIB/SEM slice and view to systematically analyse the cellular uptake of various NPs as a function of size, concentration and incubation time.

FIB-SEM imaging of carbon nanotubes in mouse lung tissue.

PubMed

Købler, Carsten; Saber, Anne Thoustrup; Jacobsen, Nicklas Raun; Wallin, Håkan; Vogel, Ulla; Qvortrup, Klaus; Mølhave, Kristian

2014-06-01

Ultrastructural characterisation is important for understanding carbon nanotube (CNT) toxicity and how the CNTs interact with cells and tissues. The standard method for this involves using transmission electron microscopy (TEM). However, in particular, the sample preparation, using a microtome to cut thin sample sections for TEM, can be challenging for investigation of regions with agglomerations of large and stiff CNTs because the CNTs cut with difficulty. As a consequence, the sectioning diamond knife may be damaged and the uncut CNTs are left protruding from the embedded block surface excluding them from TEM analysis. To provide an alternative to ultramicrotomy and subsequent TEM imaging, we studied focused ion beam scanning electron microscopy (FIB-SEM) of CNTs in the lungs of mice, and we evaluated the applicability of the method compared to TEM. FIB-SEM can provide serial section volume imaging not easily obtained with TEM, but it is time-consuming to locate CNTs in the tissue. We demonstrate that protruding CNTs after ultramicrotomy can be used to locate the region of interest, and we present FIB-SEM images of CNTs in lung tissue. FIB-SEM imaging was applied to lung tissue from mice which had been intratracheally instilled with two different multiwalled CNTs; one being short and thin, and the other longer and thicker. FIB-SEM was found to be most suitable for detection of the large CNTs (Ø ca. 70 nm), and to be well suited for studying CNT agglomerates in biological samples which is challenging using standard TEM techniques.

3D-profile measurement of advanced semiconductor features by using FIB as reference metrology

NASA Astrophysics Data System (ADS)

Takamasu, Kiyoshi; Iwaki, Yuuki; Takahashi, Satoru; Kawada, Hiroki; Ikota, Masami

2017-03-01

A novel method of sub-nanometer uncertainty for the 3D-profile measurement and LWR (Line Width Roughness) measurement by using FIB (Focused Ion Beam) processing, and TEM (Transmission Electron Microscope) and CD-SEM (Critical Dimension Scanning Electron Microscope) images measurement is proposed to standardize 3D-profile measurement through reference metrology. In this article, we apply the methodology to line profile measurements and roughness measurement of advanced FinFET (Fin-shaped Field-Effect Transistor) features. The FinFET features are horizontally sliced as a thin specimen by FIB micro sampling system. Horizontally images of the specimens are obtained then by a planar TEM. LWR is calculated from the edges positions on TEM images. Moreover, we already have demonstrated the novel on-wafer 3D-profile metrology as "FIB-to-CDSEM method" with FIB slope cut and CD-SEM measuring. Using the method, a few micrometers wide on a wafer is coated and cut by 45-degree slope using FIB tool. Then, the wafer is transferred to CD-SEM to measure the cross section image by top down CD-SEM measurement. We applied FIB-to-CDSEM method to a CMOS image sensor feature. The 45-degree slope cut surface is observed using AFM. The surface profile of slope cut surface and line profiles are analyzed for improving the accuracy of FIB-to-CDSEM method.

Evaluation of methods to sample fecal indicator bacteria in foreshore sand and pore water at freshwater beaches.

PubMed

Vogel, Laura J; Edge, Thomas A; O'Carroll, Denis M; Solo-Gabriele, Helena M; Kushnir, Caitlin S E; Robinson, Clare E

2017-09-15

Fecal indicator bacteria (FIB) are known to accumulate in foreshore beach sand and pore water (referred to as foreshore reservoir) where they act as a non-point source for contaminating adjacent surface waters. While guidelines exist for sampling surface waters at recreational beaches, there is no widely-accepted method to collect sand/sediment or pore water samples for FIB enumeration. The effect of different sampling strategies in quantifying the abundance of FIB in the foreshore reservoir is unclear. Sampling was conducted at six freshwater beaches with different sand types to evaluate sampling methods for characterizing the abundance of E. coli in the foreshore reservoir as well as the partitioning of E. coli between different components in the foreshore reservoir (pore water, saturated sand, unsaturated sand). Methods were evaluated for collection of pore water (drive point, shovel, and careful excavation), unsaturated sand (top 1 cm, top 5 cm), and saturated sand (sediment core, shovel, and careful excavation). Ankle-depth surface water samples were also collected for comparison. Pore water sampled with a shovel resulted in the highest observed E. coli concentrations (only statistically significant at fine sand beaches) and lowest variability compared to other sampling methods. Collection of the top 1 cm of unsaturated sand resulted in higher and more variable concentrations than the top 5 cm of sand. There were no statistical differences in E. coli concentrations when using different methods to sample the saturated sand. Overall, the unsaturated sand had the highest amount of E. coli when compared to saturated sand and pore water (considered on a bulk volumetric basis). The findings presented will help determine the appropriate sampling strategy for characterizing FIB abundance in the foreshore reservoir as a means of predicting its potential impact on nearshore surface water quality and public health risk. Copyright © 2017 Elsevier Ltd. All rights

Temporal Synchronization Analysis for Improving Regression Modeling of Fecal Indicator Bacteria Levels

EPA Science Inventory

Multiple linear regression models are often used to predict levels of fecal indicator bacteria (FIB) in recreational swimming waters based on independent variables (IVs) such as meteorologic, hydrodynamic, and water-quality measures. The IVs used for these analyses are traditiona...

Real-time observation of FIB-created dots and ripples on GaAs

NASA Astrophysics Data System (ADS)

Rose, F.; Fujita, H.; Kawakatsu, H.

2008-01-01

We report a phenomenological study of Ga dots and ripples created by a focused ion beam (FIB) on the GaAs(001) surface. Real-time observation of dot diffusion and ripple formation was made possible by recording FIB movies. In the case of FIB irradiation with a 40 nA current of Ga+ ions accelerated under 40 kV with an incidence angle of θ = 30°, increasing ion dose gives rise to three different regimes. In Regime 1, dots with lateral sizes in the range 50-460 nm are formed. Dots diffuse under continuous sputtering. In Regime 2, dots self-assemble into Bradley and Harper (BH) type ripples with a pseudo-period of λ = 1150 ± 25 nm. In Regime 3, ripples are eroded and the surface topology evolves into microplanes. In the case of normal incidence, FIB sputtering leads only to the formation of dots, without surface rippling.

Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM.

PubMed

He, Jie; Hsieh, Chyongere; Wu, Yongping; Schmelzer, Thomas; Wang, Pan; Lin, Ying; Marko, Michael; Sui, Haixin

2017-08-01

Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET. Commercial cryosystems are available for cryo-FIB specimen preparation, however re-engineering and additional fixtures are often essential for reliable results with a particular cryo-FIB and cryo-transmission electron microscope (cryo-TEM). Here, we describe our optimized protocol and modified instrumentation for cryo-FIB milling to produce thin lamellae and subsequent damage-free cryotransfer of the lamellae into our cartridge-type cryo-TEM. Published by Elsevier Inc.

FIB Secondary Etching Method for Fabrication of Fine CNT Forest Metamaterials

NASA Astrophysics Data System (ADS)

Pander, Adam; Hatta, Akimitsu; Furuta, Hiroshi

2017-10-01

Anisotropic materials, like carbon nanotubes (CNTs), are the perfect substitutes to overcome the limitations of conventional metamaterials; however, the successful fabrication of CNT forest metamaterial structures is still very challenging. In this study, a new method utilizing a focused ion beam (FIB) with additional secondary etching is presented, which can obtain uniform and fine patterning of CNT forest nanostructures for metamaterials and ranging in sizes from hundreds of nanometers to several micrometers. The influence of the FIB processing parameters on the morphology of the catalyst surface and the growth of the CNT forest was investigated, including the removal of redeposited material, decreasing the average surface roughness (from 0.45 to 0.15 nm), and a decrease in the thickness of the Fe catalyst. The results showed that the combination of FIB patterning and secondary etching enabled the growth of highly aligned, high-density CNT forest metamaterials. The improvement in the quality of single-walled CNTs (SWNTs), defined by the very high G/D peak ratio intensity of 10.47, demonstrated successful fine patterning of CNT forest for the first time. With a FIB patterning depth of 10 nm and a secondary etching of 0.5 nm, a minimum size of 150 nm of CNT forest metamaterials was achieved. The development of the FIB secondary etching method enabled for the first time, the fabrication of SWNT forest metamaterials for the optical and infrared regime, for future applications, e.g., in superlenses, antennas, or thermal metamaterials.

3D imaging of cells and tissues by focused ion beam/scanning electron microscopy (FIB/SEM).

PubMed

Drobne, Damjana

2013-01-01

Integration of a scanning electron microscope (SEM) and focused ion beam (FIB) technology into a single FIB/SEM system permits use of the FIB as a nano-scalpel to reveal site-specific subsurface microstructures which can be examined in great detail by SEM. The FIB/SEM technology is widely used in the semiconductor industry and material sciences, and recently its use in the life sciences has been initiated. Samples for FIB/SEM investigation can be either embedded in a plastic matrix, the traditional means of preparation of transmission electron microscopy (TEM) specimens, or simply dried as in samples prepared for SEM imaging. Currently, FIB/SEM is used in the life sciences for (a) preparation by the lift-out technique of lamella for TEM analysis, (b) tomography of samples embedded in a matrix, and (c) in situ site-specific FIB milling and SEM imaging using a wide range of magnifications. Site-specific milling and imaging has attracted wide interest as a technique in structural research of single eukaryotic and prokaryotic cells, small animals, and different animal tissue, but it still remains to be explored more thoroughly. In the past, preparation of samples for site-specific milling and imaging by FIB/SEM has typically adopted the embedding techniques used for TEM samples, and which have been very well described in the literature. Sample preparation protocols for the use of dried samples in FIB/SEM have been less well investigated. The aim of this chapter is to encourage application of FIB/SEM on dried biological samples. A detailed description of conventional dried sample preparation and FIB/SEM investigation of dried biological samples is presented. The important steps are described and illustrated, and direct comparison between embedded and dried samples of same tissues is provided. The ability to discover links between gross morphology of the tissue or organ, surface characteristics of any selected region, and intracellular structural details on the nanometer

HIV mono-infection is associated with FIB-4 - A noninvasive index of liver fibrosis - in women.

PubMed

Blackard, Jason T; Welge, Jeffrey A; Taylor, Lynn E; Mayer, Kenneth H; Klein, Robert S; Celentano, David D; Jamieson, Denise J; Gardner, Lytt; Sherman, Kenneth E

2011-03-01

FIB-4 represents a noninvasive, composite index that is a validated measure of hepatic fibrosis, which is an important indicator of liver disease. To date, there are limited data regarding hepatic fibrosis in women. FIB-4 was evaluated in a cohort of 1227 women, and associations were evaluated in univariate and multivariate regression models among 4 groups of subjects classified by their human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection status. The median FIB-4 scores were 0.60 in HIV-/HCV- women, 0.83 in HIV-/HCV+ women, 0.86 in HIV+/HCV- women, and 1.30 in HIV+/HCV+ women. In the HIV/HCV co-infected group, multivariate analysis showed that CD4(+) cell count and albumin level were negatively associated with FIB-4 (P <.0001), whereas antiretroviral therapy (ART) was positively associated with FIB-4 score (P =.0008). For the HIV mono-infected group, multivariate analysis showed that CD4(+) cell count (P <.0001) and albumin level (P =.0019) were negatively correlated with FIB-4 score, ART was positively associated with FIB-4 score (P =.0008), and plasma HIV RNA level was marginally associated with FIB-4 score (P =.080). In 72 HIV mono-infected women who were also hepatitis B surface antigen negative, ART naive, and reported no recent alcohol intake, plasma HIV RNA level was associated with increased FIB-4 score (P =.030). HIV RNA level was associated with increased FIB-4 score in the absence of hepatitis B, hepatitis C, ART, or alcohol use, suggesting a potential relationship between HIV infection and hepatic fibrosis in vivo. A better understanding of the various demographic and virologic variables that contribute to hepatic fibrosis may lead to more effective treatment of HIV infection and its co-morbid conditions.

Mineralized iron oxidizing bacteria from hydrothermal vents: targeting biosignatures on Mars

NASA Astrophysics Data System (ADS)

Leveille, R. J.

2010-12-01

Putative hydrothermal systems have been identified on Mars based on orbital imagery and rover-based analyses. Based on Earth analogs, hydrothermal systems on Mars would be highly attractive for their potential for preserving organic and inorganic biosignatures. For example, iron oxidizing bacteria are ubiquitous in marine and terrestrial hydrothermal systems, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Microfossils of iron oxidizing bacteria have been found in ancient Si-Fe deposits and iron oxidation may be an ancient and widespread metabolic pathway. In order to investigate mineralized iron oxidizing bacteria as a biosignature, we have examined samples collected from extinct hydrothermal vents along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic iron oxidizing bacteria, isolated from active Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and O2 concentration (5%) in a controlled bioreactor system. Samples and experimental products were examined with a combination of variable-pressure and field-emission scanning electron microscopy (SEM), in some cases by preparing samples with a focused ion beam (FIB) milling system. Light-toned seafloor samples display abundant filamentous forms resembling, in both size and shape (1-5 microns in diameter and up to several microns in length), the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Some samples consist entirely of low-density masses of silica (>90% Si) encrusted filamentous forms. The presence of unmineralized filamentous matter rich in C and Fe suggests that these are the remains of iron oxidizing bacteria. Mineralized filaments sectioned by FIB show variable internal material within semi-hollow, tubular-like features. Silica encrustations also show pseudo-concentric growth bands. In the bioreactor runs, abundant microbial growth and

Predictive Power of Clean Bed Filtration Theory for Fecal Indicator Bacteria Removal in Stormwater Biofilters

NASA Astrophysics Data System (ADS)

Parker, E.; Rippy, M.; Mehring, A.; Winfrey, B.; Ambrose, R. F.; Levin, L. A.; Grant, S. B.

2017-12-01

Green infrastructure (also referred to as low impact development, or LID) has the potential to transform urban stormwater runoff from an environmental threat to a valuable water resource. Here we focus on the removal of fecal indicator bacteria (FIB, a pollutant responsible for runoff associated inland and coastal beach closures) in stormwater biofilters (a common type of green infrastructure). Drawing on a combination of previously published and new laboratory studies of FIB removal in biofilters, we find that 66% of the variance in FIB removal rates can be explained by clean bed filtration theory (CBFT, 31%), antecedent dry period (14%), study effect (8%), biofilter age (7%), and the presence or absence of shrubs (6%). Our analysis suggests that, with the exception of shrubs, plants affect FIB removal indirectly by changing the infiltration rate, not directly by changing the FIB removal mechanisms or altering filtration rates in ways not already accounted for by CBFT. The analysis presented here represents a significant step forward in our understanding of how physicochemical theories (such as CBFT) can be melded with hydrology, engineering design, and ecology to improve the water quality benefits of green infrastructure.

Rapid separation of very low concentrations of bacteria from blood.

PubMed

Buchanan, Clara M; Wood, Ryan L; Hoj, Taalin R; Alizadeh, Mahsa; Bledsoe, Colin G; Wood, Madison E; McClellan, Daniel S; Blanco, Rae; Hickey, Caroline L; Ravsten, Tanner V; Husseini, Ghaleb A; Robison, Richard A; Pitt, William G

2017-08-01

A rapid and accurate diagnosis of the species and antibiotic resistance of bacteria in septic blood is vital to increase survival rates of patients with bloodstream infections, particularly those with carbapenem-resistant enterobacteriaceae (CRE) infections. The extremely low levels in blood (1 to 100CFU/ml) make rapid diagnosis difficult. In this study, very low concentrations of bacteria (6 to 200CFU/ml) were separated from 7ml of whole blood using rapid sedimentation in a spinning hollow disk that separated plasma from red and white cells, leaving most of the bacteria suspended in the plasma. Following less than a minute of spinning, the disk was slowed, the plasma was recovered, and the bacteria were isolated by vacuum filtration. The filters were grown on nutrient plates to determine the number of bacteria recovered from the blood. Experiments were done without red blood cell (RBC) lysis and with RBC lysis in the recovered plasma. While there was scatter in the data from blood with low bacterial concentrations, the mean average recovery was 69%. The gender of the blood donor made no statistical difference in bacterial recovery. These results show that this rapid technique recovers a significant amount of bacteria from blood containing clinically relevant low levels of bacteria, producing the bacteria in minutes. These bacteria could subsequently be identified by molecular techniques to quickly identify the infectious organism and its resistance profile, thus greatly reducing the time needed to correctly diagnose and treat a blood infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Salmonella and fecal indicator bacteria survival in soils amended with poultry manure

USDA-ARS?s Scientific Manuscript database

Minimizing the risks associated with manure-borne pathogenic microorganisms requires an understanding of microbial survival under realistic field conditions. The objective of this 3-year study was to assess the fate of Salmonella (SALM) and fecal indicator bacteria (FIB), E. coli (EC) and enterococc...

Improving Recreational Water Quality Assessments Through Novel Approaches to Quantifying Measurement Uncertainty

EPA Science Inventory

Bacteriological water quality in the Great Lakes is typically measured by the concentration of fecal indicator bacteria (FIB), and is reported via most probable number (MPN) or colony forming unit (CFU) values derived from algorithms relating \\raw data" in a FIB analysis procedu...

The FIB-4 score predicts postoperative short-term outcomes of hepatocellular carcinoma fulfilling the milan criteria.

PubMed

Dong, J; Xu, X-h; Ke, M-y; Xiang, J-x; Liu, W-y; Liu, X-m; Wang, B; Zhang, X-f; Lv, Y

2016-05-01

The fibrosis score 4 (FIB-4) score is a useful tool to determine the degree of hepatic fibrosis. Liver fibrosis and cirrhosis are well-known predictors of postoperative complications after hepatectomy. This study examined the impact of FIB-4 on postoperative short-term outcomes of patients with hepatocellular carcinoma (HCC). Three hundred and fifty patients undergoing hepatectomy for HCC between 2008 and 2013 were enrolled. The receiver operating characteristic (ROC) curve analysis was performed to determine the cutoff value of the FIB-4. Univariate and multivariate analysis was performed to identify the risk factors. The correlation of the preoperative FIB-4 value with clinicopathological parameters was examined. Postoperative complications were observed in 202 (57.7%) patients. The optimal cutoff value of the FIB-4 was set at 2.88 and 3.85 for postoperative complications and intraoperative blood loss respectively. It was also an independent prognostic factor for postoperative complications (hazard ratio [HR], 1.202; 95% CI, 1.076-1.344; P = 0.001) and intraoperative blood loss (HR, 1.196; 95% CI, 1.091-1.343; P < 0.001) by multivariate analysis. The FIB-4 was significantly correlated with age, liver function, coagulation function, blood loss, intraoperative blood transfusion (all P < 0.05). Preoperative FIB-4 is a useful index to predict postoperative outcomes in patients with HCC. The FIB-4 should be assessed routinely for hepatocellular carcinoma patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enhanced FIB-SEM systems for large-volume 3D imaging

DOE PAGES

Xu, C. Shan; Hayworth, Kenneth J.; Lu, Zhiyuan; ...

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processesmore » and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.« less

Enhanced FIB-SEM systems for large-volume 3D imaging.

PubMed

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 µm 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

Microfluidic concentration of bacteria by on-chip electrophoresis

PubMed Central

Puchberger-Enengl, Dietmar; Podszun, Susann; Heinz, Helene; Hermann, Carsten; Vulto, Paul; Urban, Gerald A.

2011-01-01

In this contribution, we present a system for efficient preconcentration of pathogens without affecting their viability. Development of miniaturized molecular diagnostic kits requires concentration of the sample, molecule extraction, amplification, and detection. In consequence of low analyte concentrations in real-world samples, preconcentration is a critical step within this workflow. Bacteria and viruses exhibit a negative surface charge and thus can be electrophoretically captured from a continuous flow. The concept of phaseguides was applied to define gel membranes, which enable effective and reversible collection of the target species. E. coli of the strains XL1-blue and K12 were used to evaluate the performance of the device. By suppression of the electroosmotic flow both strains were captured with efficiencies of up to 99%. At a continuous flow of 15 μl/min concentration factors of 50.17 ± 2.23 and 47.36 ± 1.72 were achieved in less than 27 min for XL1-blue and K12, respectively. These results indicate that free flow electrophoresis enables efficient concentration of bacteria and the presented device can contribute to rapid analyses of swab-derived samples. PMID:22207893

Decay of Fecal Indicator Bacteria and Microbial Source Tracking Markers in Cattle Feces

EPA Science Inventory

The survival of fecal indicator bacteria (FIB) and microbial source tracking (MST) markers in water microcosms and manure amended soils has been well documented; however, little is known about the survival of MST markers in bovine feces deposited on pastures. We conducted a study...

Concentrations of fecal coliform bacteria in creeks, Anchorage, Alaska, August and September 1998

USGS Publications Warehouse

Dorava, Joseph M.; Love, Andra

1999-01-01

Water samples were collected from five creeks in undeveloped, semi-developed, and developed areas of Anchorage, Alaska, during August and September 1998 to determine concentrations of fecal coliform bacteria. In undeveloped areas of Ship, Chester, and Campbell Creeks, and the semi-developed area of Rabbit Creek, concentrations of fecal coliform bacteria ranged from less than 1 to 16 colonies per 100 milliliters of water. In the semi-developed area of Little Rabbit Creek, concentrations ranged from 30 to 860 colonies per 100 milliliters of water. In developed areas of the creeks, concentrations of fecal coliform bacteria ranged from 6 to 80 colonies per 100 milliliters of water.

E. coli release from streambed to water column during base flow periods: a modeling study

USDA-ARS?s Scientific Manuscript database

Microbial quality of stream water is important for recreation, irrigation, and other uses. It is usually evaluated by concentrations of fecal indicator bacteria (FIB) such as E. coli. Streambed sediments have been shown to harbor large FIB populations that could be released into the water column dur...

The role of singlet oxygen and oxygen concentration in photodynamic inactivation of bacteria

PubMed Central

Maisch, Tim; Baier, Jürgen; Franz, Barbara; Maier, Max; Landthaler, Michael; Szeimies, Rolf-Markus; Bäumler, Wolfgang

2007-01-01

New antibacterial strategies are required in view of the increasing resistance of bacteria to antibiotics. One promising technique involves the photodynamic inactivation of bacteria. Upon exposure to light, a photosensitizer in bacteria can generate singlet oxygen, which oxidizes proteins or lipids, leading to bacteria death. To elucidate the oxidative processes that occur during killing of bacteria, Staphylococcus aureus was incubated with a standard photosensitizer, and the generation and decay of singlet oxygen was detected directly by its luminescence at 1,270 nm. At low bacterial concentrations, the time-resolved luminescence of singlet oxygen showed a decay time of 6 ± 2 μs, which is an intermediate time for singlet oxygen decay in phospholipids of membranes (14 ± 2 μs) and in the surrounding water (3.5 ± 0.5 μs). Obviously, at low bacterial concentrations, singlet oxygen had sufficient access to water outside of S. aureus by diffusion. Thus, singlet oxygen seems to be generated in the outer cell wall areas or in adjacent cytoplasmic membranes of S. aureus. In addition, the detection of singlet oxygen luminescence can be used as a sensor of intracellular oxygen concentration. When singlet oxygen luminescence was measured at higher bacterial concentrations, the decay time increased significantly, up to ≈40 μs, because of oxygen depletion at these concentrations. This observation is an important indicator that oxygen supply is a crucial factor in the efficacy of photodynamic inactivation of bacteria, and will be of particular significance should this approach be used against multiresistant bacteria. PMID:17431036

Enhanced FIB-SEM systems for large-volume 3D imaging

PubMed Central

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-01-01

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 106 µm3. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology. DOI: http://dx.doi.org/10.7554/eLife.25916.001 PMID:28500755

Environmental assessment of three egg production systems - Part III: Airborne bacteria concentrations and emissions.

PubMed

Zhao, Y; Zhao, D; Ma, H; Liu, K; Atilgan, A; Xin, H

2016-07-01

Airborne microorganism level is an important indoor air quality indicator, yet it has not been well documented for laying-hen houses in the United States. As a part of the Coalition for Sustainable Egg Supply (CSES) environmental monitoring project, this study comparatively monitored the concentrations and emissions of airborne total and Gram-negative (Gram(-)) bacteria in three types of commercial laying-hen houses, i.e., conventional cage (CC), aviary (AV), and enriched colony (EC) houses, over a period of eight months covering the mid and late stages of the flock cycle. It also delineated the relationship between airborne total bacteria and particulate matter smaller than 10 μm in aerodynamic diameter (PM10). The results showed airborne total bacteria concentrations (log CFU/m(3)) of 4.7 ± 0.3 in CC, 6.0 ± 0.8 in AV, and 4.8 ± 0.3 in EC, all being higher than the level recommended for human environment (3.0 log CFU/m(3)). The much higher concentrations in AV arose from the presence of floor litter and hen activities on it, as evidenced by the higher concentrations in the afternoon (with litter access) than in the morning (without litter access). The overall means and standard deviation of airborne total bacteria emission rates, in log CFU/[h-hen] (or log CFU/[h-AU], AU = animal unit or 500 kg live weight) were 4.8 ± 0.4 (or 7.3 ± 0.4) for CC, 6.1 ± 0.7 (or 8.6 ± 0.7) for AV, and 4.8 ± 0.5 (or 7.3 ± 0.5) for EC. Both concentration and emission rate of airborne total bacteria were positively related to PM10 Gram(-) bacteria were present at low concentrations in all houses; and only 2 samples (6%) in CC, 7 (22%) samples in AV, and 2 (6%) samples in EC out of 32 air samples collected in each house were found positive with Gram(-) bacteria. The concentration of airborne Gram(-) bacteria was estimated to be <2% of the total bacteria. Total bacteria counts in manure on belt (in all houses) and floor litter (only in AV) were similar; however, the manure had

HIV Mono-infection Is Associated With FIB-4 – A Noninvasive Index of Liver Fibrosis – in Women

PubMed Central

Welge, Jeffrey A.; Taylor, Lynn E.; Mayer, Kenneth H.; Klein, Robert S.; Celentano, David D.; Jamieson, Denise J.; Gardner, Lytt; Sherman, Kenneth E.

2011-01-01

Background. FIB-4 represents a noninvasive, composite index that is a validated measure of hepatic fibrosis, which is an important indicator of liver disease. To date, there are limited data regarding hepatic fibrosis in women. Methods. FIB-4 was evaluated in a cohort of 1227 women, and associations were evaluated in univariate and multivariate regression models among 4 groups of subjects classified by their human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection status. Results. The median FIB-4 scores were 0.60 in HIV-/HCV- women, 0.83 in HIV-/HCV+ women, 0.86 in HIV+/HCV- women, and 1.30 in HIV+/HCV+ women. In the HIV/HCV co-infected group, multivariate analysis showed that CD4+ cell count and albumin level were negatively associated with FIB-4 (P <.0001), whereas antiretroviral therapy (ART) was positively associated with FIB-4 score (P =.0008). For the HIV mono-infected group, multivariate analysis showed that CD4+ cell count (P <.0001) and albumin level (P =.0019) were negatively correlated with FIB-4 score, ART was positively associated with FIB-4 score (P =.0008), and plasma HIV RNA level was marginally associated with FIB-4 score (P =.080). In 72 HIV mono-infected women who were also hepatitis B surface antigen negative, ART naive, and reported no recent alcohol intake, plasma HIV RNA level was associated with increased FIB-4 score (P =.030). Conclusions. HIV RNA level was associated with increased FIB-4 score in the absence of hepatitis B, hepatitis C, ART, or alcohol use, suggesting a potential relationship between HIV infection and hepatic fibrosis in vivo. A better understanding of the various demographic and virologic variables that contribute to hepatic fibrosis may lead to more effective treatment of HIV infection and its co-morbid conditions. PMID:21248367

FIB and MIP: understanding nanoscale porosity in molecularly imprinted polymers via 3D FIB/SEM tomography.

PubMed

Neusser, G; Eppler, S; Bowen, J; Allender, C J; Walther, P; Mizaikoff, B; Kranz, C

2017-10-05

We present combined focused ion beam/scanning electron beam (FIB/SEM) tomography as innovative method for differentiating and visualizing the distribution and connectivity of pores within molecularly imprinted polymers (MIPs) and non-imprinted control polymers (NIPs). FIB/SEM tomography is used in cell biology for elucidating three-dimensional structures such as organelles, but has not yet been extensively applied for visualizing the heterogeneity of nanoscopic pore networks, interconnectivity, and tortuosity in polymers. To our best knowledge, the present study is the first application of this strategy for analyzing the nanoscale porosity of MIPs. MIPs imprinted for propranolol - and the corresponding NIPs - were investigated establishing FIB/SEM tomography as a viable future strategy complementing conventional isotherm studies. For visualizing and understanding the properties of pore networks in detail, polymer particles were stained with osmium tetroxide (OsO 4 ) vapor, and embedded in epoxy resin. Staining with OsO 4 provides excellent contrast during high-resolution SEM imaging. After optimizing the threshold to discriminate between the stained polymer matrix, and pores filled with epoxy resin, a 3D model of the sampled volume may be established for deriving not only the pore volume and pore surface area, but also to visualize the interconnectivity and tortuosity of the pores within the sampled polymer volume. Detailed studies using different types of cross-linkers and the effect of hydrolysis on the resulting polymer properties have been investigated. In comparison of MIP and NIP, it could be unambiguously shown that the interconnectivity of the visualized pores in MIPs is significantly higher vs. the non-imprinted polymer, and that the pore volume and pore area is 34% and approx. 35% higher within the MIP matrix. This confirms that the templating process not only induces selective binding sites, but indeed also affects the physical properties of such

Seasonal variability of faecal indicator bacteria numbers and die-off rates in the Red River basin, North Viet Nam

NASA Astrophysics Data System (ADS)

Nguyen, Huong Thi Mai; Le, Quynh Thi Phuong; Garnier, J.; Janeau, J.-L.; Rochelle-Newall, E.

2016-02-01

The Red River is the second largest river in Viet Nam and constitutes the main water source for a large percentage of the population of North Viet Nam. Here we present the results of an annual survey of Escherichia coli (EC) and Total Coliforms (TC) in the Red River basin, North Viet Nam. The objective of this work was to obtain information on faecal indicator bacteria (FIB) numbers over an annual cycle and, secondly, to determine the die-off rates of these bacterial indicators. Monthly observations at 10 stations from July 2013-June 2014 showed that TC and EC reached as high as 39100 cfu (colony forming units) 100 ml-1 and 15300 colonies 100 ml-1, respectively. We observed a significant seasonal difference for TC (p < 0.05) with numbers being higher during the wet season. In contrast, no significant seasonal difference was found for EC. The FIB die-off rates ranged from 0.01 d-1 to a maximum of 1.13 d-1 for EC and from 0.17 d-1 to 1.33 d-1 for TC. Die-off rates were significantly higher for free bacteria than for total (free + particle attached) bacteria, suggesting that particle attachment provided a certain level of protection to FIB in this system.

Seasonal variability of faecal indicator bacteria numbers and die-off rates in the Red River basin, North Viet Nam.

PubMed

Nguyen, Huong Thi Mai; Le, Quynh Thi Phuong; Garnier, J; Janeau, J-L; Rochelle-Newall, E

2016-02-12

The Red River is the second largest river in Viet Nam and constitutes the main water source for a large percentage of the population of North Viet Nam. Here we present the results of an annual survey of Escherichia coli (EC) and Total Coliforms (TC) in the Red River basin, North Viet Nam. The objective of this work was to obtain information on faecal indicator bacteria (FIB) numbers over an annual cycle and, secondly, to determine the die-off rates of these bacterial indicators. Monthly observations at 10 stations from July 2013-June 2014 showed that TC and EC reached as high as 39100 cfu (colony forming units) 100 ml(-1) and 15300 colonies 100 ml(-1), respectively. We observed a significant seasonal difference for TC (p < 0.05) with numbers being higher during the wet season. In contrast, no significant seasonal difference was found for EC. The FIB die-off rates ranged from 0.01 d(-1) to a maximum of 1.13 d(-1) for EC and from 0.17 d(-1) to 1.33 d(-1) for TC. Die-off rates were significantly higher for free bacteria than for total (free + particle attached) bacteria, suggesting that particle attachment provided a certain level of protection to FIB in this system.

Evaluation of 111In-labeled EPep and FibPep as tracers for fibrin SPECT imaging.

PubMed

Starmans, Lucas W E; van Duijnhoven, Sander M J; Rossin, Raffaella; Berben, Monique; Aime, Silvio; Daemen, Mat J A P; Nicolay, Klaas; Grüll, Holger

2013-11-04

Fibrin targeting is an attractive strategy for nuclear imaging of thrombosis, atherosclerosis and cancer. Recently, FibPep, an (111)In-labeled fibrin-binding peptide, was established as a tracer for fibrin SPECT imaging and was reported to allow sensitive detection of minute thrombi in mice using SPECT. In this study, we developed EPep, a novel (111)In-labeled fibrin-binding peptide containing the fibrin-binding domain of the clinically verified EP-2104R peptide, and sought to compare the potential of EPep and FibPep as tracers for fibrin SPECT imaging. In vitro, both EPep and FibPep showed high stability in serum, but were less stable in liver and kidney homogenate assays. Both peptide probes displayed comparable affinities toward human and mouse derived fibrin (Kd ≈ 1 μM), and similarly to FibPep, EPep showed fast blood clearance, low nontarget uptake and high thrombus uptake (6.8 ± 1.2% ID g(-1)) in a mouse carotid artery thrombosis model. Furthermore, EPep showed a similar affinity toward rat derived fibrin (Kd ≈ 1 μM), displayed high thrombus uptake in a rat carotid artery thrombosis model (0.74 ± 0.39% ID g(-1)), and allowed sensitive detection of thrombosis in rats using SPECT. In contrast, FibPep displayed a significantly lower affinity toward rat derived fibrin (Kd ≈ 14 μM) and low uptake in rat thrombi (0.06 ± 0.02% ID g(-1)) and did not allow clear visualization of carotid artery thrombosis in rats using SPECT. These results were confirmed ex vivo by autoradiography, which showed a 7-fold higher ratio of activity in the thrombus over the contralateral carotid artery for EPep in comparison to FibPep. These findings suggest that the FibPep binding fibrin epitope is not fully homologous between humans and rats, and that preclinical rat models of disease should not be employed to gauge the clinical potential of FibPep. In conclusion, both peptides showed approximately similar metabolic stability and affinity toward human and mouse derived fibrin

Validation of APRI and FIB-4 score in an Antwerp cohort of chronic hepatitis C patients.

PubMed

Verlinden, Wim; Bourgeois, Stefan; De Maeyer, Marc; Vonghia, Luisa; Vanwolleghem, Thomas; Michielsen, Peter; Francque, Sven

2015-12-01

Evaluation of liver fibrosis in chronic hepatitis C patients guides clinical decision-making. The aim of this study is to validate APRI and FIB-4, two easily calculated noninvasive tests to predict fibrosis, in chronic HCV patients using biopsy as a gold standard and to compare accuracy between HCV monoinfected and HIV/HCV coinfected patients. We retrospectively studied HCV patients of two centres who underwent liver biopsy. Liver fibrosis was staged according to METAVIR. 136 patients were included. The AUROC of FIB-4 (0.896) to discriminate F0-F2 vs. F3-F4 was significantly higher (p=0.0186) than the AUROC of APRI (0.842). The difference in AUROC between HIV-negative and positive patients was not significant for APRI (p=0.471), nor for FIB-4 (p=0.495). Performance status was lower in HIV-positive patients with 46.7% and 69.0% of patients correctly classified using APRI and FIB-4, compared to 56.6% and 73.6% in HIV-negative patients, respectively. Conversion of transaminase values from one hospital to the other did not significantly change the AUROC of FIB-4 (p=0.928). APRI and FIB-4 have a better performance status in HCV monoinfected patients compared to HIV/HCV coinfected patients. FIB-4 has a better AUROC compared to APRI and is the preferred noninvasive fibrosis score to discriminate between F0-F2 and F3-F4. Different hospitals should use their local absolute serum transaminase values without conversion. © Acta Gastro-Enterologica Belgica.

Transient Elastography is Superior to FIB-4 in Assessing the Risk of Hepatocellular Carcinoma in Patients With Chronic Hepatitis B.

PubMed

Kim, Seung Up; Kim, Beom Kyung; Park, Jun Yong; Kim, Do Young; Ahn, Sang Hoon; Song, Kijun; Han, Kwang-Hyub

2016-05-01

Liver stiffness (LS), assessed using transient elastography (TE), and (FIB-4) can both estimate the risk of developing hepatocellular carcinoma (HCC). We compared prognostic performances of LS and FIB-4 to predict HCC development in patients with chronic hepatitis B (CHB).Data from 1308 patients with CHB, who underwent TE, were retrospectively analyzed. FIB-4 was calculated for all patients. The cumulative rate of HCC development was assessed using Kaplan-Meier curves. The predictive performances of LS and FIB-4 were evaluated using time-dependent receiver-operating characteristic (ROC) curves.The mean age (883 men) was 50 years. During follow-up (median 6.1 years), 119 patients developed HCC. The areas under the ROC curves (AUROCs) predicting HCC risk at 3, 5, and 7 years were consistently greater for LS than for FIB-4 (0.791-0.807 vs 0.691-0.725; all P < 0.05). Similarly, when the respective AUROCs for LS and FIB-4 at every time point during the 7-year follow-up were plotted, LS also showed consistently better performance than FIB-4 after 1 year of enrollment. The combined use of LS and FIB-4 significantly enhanced the prognostic performance compared with the use of FIB-4 alone (P < 0.05), but the performance of the combined scores was statistically similar to that of LS alone (P > 0.05).LS showed significantly better performance than FIB-4 in assessing the risk of HCC development, and the combined use of LS and FIB-4 did not provide additional benefit compared with the use of LS alone. Hence, LS assessed using TE might be helpful for optimizing HCC surveillance strategies.

Electrical characterization of FIB processed metal layers for reliable conductive-AFM on ZnO microstructures

NASA Astrophysics Data System (ADS)

Pea, M.; Maiolo, L.; Giovine, E.; Rinaldi, A.; Araneo, R.; Notargiacomo, A.

2016-05-01

We report on the conductive-atomic force microscopy (C-AFM) study of metallic layers in order to find the most suitable configuration for electrical characterization of individual ZnO micro-pillars fabricated by focused ion beam (FIB). The electrical resistance between the probe tip and both as deposited and FIB processed metal layers (namely, Cr, Ti, Au and Al) has been investigated. Both chromium and titanium evidenced a non homogenous and non ohmic behaviour, non negligible scanning probe induced anodic oxidation associated to electrical measurements, and after FIB milling they exhibited significantly higher tip-sample resistance. Aluminium had generally a more apparent non conductive behaviour. Conversely, gold films showed very good tip-sample conduction properties being less sensitive to FIB processing than the other investigated metals. We found that a reliable C-AFM electrical characterization of ZnO microstructures obtained by FIB machining is feasible by using a combination of metal films as top contact layer. An Au/Ti bilayer on top of ZnO was capable to sustain the FIB fabrication process and to form a suitable ohmic contact to the semiconductor, allowing for reliable C-AFM measurement. To validate the consistency of this approach, we measured the resistance of ZnO micropillars finding a linear dependence on the pillar height, as expected for an ohmic conductor, and evaluated the resistivity of the material. This procedure has the potential to be downscaled to nanometer size structures by a proper choice of metal films type and thickness.

Influence of seasonal and inter-annual hydro-meteorological variability on surface water fecal coliform concentration under varying land-use composition.

PubMed

St Laurent, Jacques; Mazumder, Asit

2014-01-01

Quantifying the influence of hydro-meteorological variability on surface source water fecal contamination is critical to the maintenance of safe drinking water. Historically, this has not been possible due to the scarcity of data on fecal indicator bacteria (FIB). We examined the relationship between hydro-meteorological variability and the most commonly measured FIB, fecal coliform (FC), concentration for 43 surface water sites within the hydro-climatologically complex region of British Columbia. The strength of relationship was highly variable among sites, but tended to be stronger in catchments with nival (snowmelt-dominated) hydro-meteorological regimes and greater land-use impacts. We observed positive relationships between inter-annual FC concentration and hydro-meteorological variability for around 50% of the 19 sites examined. These sites are likely to experience increased fecal contamination due to the projected intensification of the hydrological cycle. Seasonal FC concentration variability appeared to be driven by snowmelt and rainfall-induced runoff for around 30% of the 43 sites examined. Earlier snowmelt in nival catchments may advance the timing of peak contamination, and the projected decrease in annual snow-to-precipitation ratio is likely to increase fecal contamination levels during summer, fall, and winter among these sites. Safeguarding drinking water quality in the face of such impacts will require increased monitoring of FIB and waterborne pathogens, especially during periods of high hydro-meteorological variability. This data can then be used to develop predictive models, inform source water protection measures, and improve drinking water treatment. Copyright © 2013 Elsevier Ltd. All rights reserved.

High liver fibrosis index FIB-4 is highly predictive of hepatocellular carcinoma in chronic hepatitis B carriers.

PubMed

Suh, Beomseok; Park, Sehhoon; Shin, Dong Wook; Yun, Jae Moon; Yang, Hyung-Kook; Yu, Su Jong; Shin, Cheong-Il; Kim, Jin-Soo; Ahn, Eunmi; Lee, Hyejin; Park, Jin Ho; Cho, BeLong

2015-04-01

Screening for hepatocellular carcinoma (HCC) is clinically important given that its early detection has remarkable survival benefits. We investigated the possible role of FIB-4, a recently developed noninvasive marker for liver fibrosis based on routine laboratory tests, as a clinical indicator for predicting future HCC among hepatitis B surface antigen (HBsAg) carriers. Our retrospective cohort study involved 986 Korean HBsAg carriers 40 years of age or older who visited Seoul National University Hospital for a health checkup. National medical service claims data were used to determine HCC incidence. Median follow-up time was 5.4 years (interquartile range: 4.4 years). Adjusted for age, sex, body mass index, smoking, alcohol, and antiviral medication for hepatitis B, compared to subjects with FIB-4 <1.25, subjects with 1.7≤ FIB-4 <2.4 showed an adjusted hazard ratio (aHR) of 4.57 (95% confidence interval [CI]: 1.50-13.92) and subjects with FIB-4 ≥2.4 showed an aHR of 21.34 (95% CI: 7.73-58.92) for HCC incidence. FIB-4 was shown to have incremental predictive value to ultrasonographic liver cirrhosis for HCC incidence (C-index: 0.701 vs. 0.831; P = 0.001). FIB-4 was also better predictive of HCC incidence, compared to that of ultrasonographic liver cirrhosis (C-index: 0.775 vs. 0.701; P = 0.040). High FIB-4 is a highly predictive risk factor for HCC incidence among Korean HBsAg carriers. FIB-4 is a promising, easily applicable, and cost-effective clinical tool in identifying a subpopulation of HBsAg carriers who are at heightened risk. Our study needs to be replicated in larger future studies on various ethnic groups; nonetheless, our study suggests that FIB-4 may play a valuable role in HCC screening among HBsAg carriers. © 2014 by the American Association for the Study of Liver Diseases.

Matrices pattern using FIB; 'Out-of-the-box' way of thinking.

PubMed

Fleger, Y; Gotlib-Vainshtein, K; Talyosef, Y

2017-03-01

Focused ion beam (FIB) is an extremely valuable tool in nanopatterning and nanofabrication for potentially high-resolution patterning, especially when refers to He ion beam microscopy. The work presented here demonstrates an 'out-of-the-box' method of writing using FIB, which enables creating very large matrices, up to the beam-shift limitation, in short times and with high accuracy unachievable by any other writing technique. The new method allows combining different shapes in nanometric dimensions and high resolutions for wide ranges. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Transient Elastography is Superior to FIB-4 in Assessing the Risk of Hepatocellular Carcinoma in Patients With Chronic Hepatitis B

PubMed Central

Kim, Seung Up; Kim, Beom Kyung; Park, Jun Yong; Kim, Do Young; Ahn, Sang Hoon; Song, Kijun; Han, Kwang-Hyub

2016-01-01

Abstract Liver stiffness (LS), assessed using transient elastography (TE), and (FIB-4) can both estimate the risk of developing hepatocellular carcinoma (HCC). We compared prognostic performances of LS and FIB-4 to predict HCC development in patients with chronic hepatitis B (CHB). Data from 1308 patients with CHB, who underwent TE, were retrospectively analyzed. FIB-4 was calculated for all patients. The cumulative rate of HCC development was assessed using Kaplan–Meier curves. The predictive performances of LS and FIB-4 were evaluated using time-dependent receiver-operating characteristic (ROC) curves. The mean age (883 men) was 50 years. During follow-up (median 6.1 years), 119 patients developed HCC. The areas under the ROC curves (AUROCs) predicting HCC risk at 3, 5, and 7 years were consistently greater for LS than for FIB-4 (0.791–0.807 vs 0.691–0.725; all P < 0.05). Similarly, when the respective AUROCs for LS and FIB-4 at every time point during the 7-year follow-up were plotted, LS also showed consistently better performance than FIB-4 after 1 year of enrollment. The combined use of LS and FIB-4 significantly enhanced the prognostic performance compared with the use of FIB-4 alone (P < 0.05), but the performance of the combined scores was statistically similar to that of LS alone (P > 0.05). LS showed significantly better performance than FIB-4 in assessing the risk of HCC development, and the combined use of LS and FIB-4 did not provide additional benefit compared with the use of LS alone. Hence, LS assessed using TE might be helpful for optimizing HCC surveillance strategies. PMID:27196449

Counting Synapses Using FIB/SEM Microscopy: A True Revolution for Ultrastructural Volume Reconstruction.

PubMed

Merchán-Pérez, Angel; Rodriguez, José-Rodrigo; Alonso-Nanclares, Lidia; Schertel, Andreas; Defelipe, Javier

2009-01-01

The advent of transmission electron microscopy (TEM) in the 1950s represented a fundamental step in the study of neuronal circuits. The application of this technique soon led to the realization that the number of synapses changes during the course of normal life, as well as under certain pathological or experimental circumstances. Since then, one of the main goals in neurosciences has been to define simple and accurate methods to estimate the magnitude of these changes. Contrary to analysing single sections, TEM reconstructions are extremely time-consuming and difficult. Therefore, most quantitative studies use stereological methods to define the three-dimensional characteristics of synaptic junctions that are studied in two dimensions. Here, to count the exact number of synapses per unit of volume we have applied a new three-dimensional reconstruction method that involves the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM). We show that the images obtained with FIB/SEM are similar to those obtained with TEM, but with the advantage that FIB/SEM permits serial reconstructions of large volumes of tissue to be generated rapidly and automatically. Furthermore, we compared the estimates of the number of synapses obtained with stereological methods with the values obtained by FIB/SEM reconstructions. We concluded that FIB/SEM not only provides the actual number of synapses per volume but it is also much easier and faster to use than other currently available TEM methods. More importantly, it also avoids most of the errors introduced by stereological methods and overcomes the difficulties associated with these techniques.

Association of plasma 25-hydroxyvitamin d concentrations and pathogenic oral bacteria in postmenopausal females.

PubMed

Sahli, Michelle W; Wactawski-Wende, Jean; Ram, Pavani K; LaMonte, Michael J; Hovey, Kathleen M; Genco, Robert J; Andrews, Christopher A; Millen, Amy E

2014-07-01

Previous findings of an association between 25-hydroxyvitamin D [25(OH)D] concentrations and periodontal disease may be partially explained by the antimicrobial properties of vitamin D. To the best of the authors' knowledge, no study has investigated the association between 25(OH)D and pathogenic oral bacteria, a putative cause of periodontal disease. The association between plasma 25(OH)D concentrations and pathogenic oral bacteria was examined among postmenopausal females in the Buffalo Osteoporosis and Periodontal Disease Study (1997 to 2000), an ancillary study of the Women's Health Initiative Observational Study. Subgingival plaque samples were assessed using immunofluorescence for the presence of Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, Prevotella intermedia, and Campylobacter rectus. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for prevalent bacteria by quintile (Q) of 25(OH)D concentrations, adjusting for age and body mass index. Of the 855 participants, 288 (34%) had deficient/inadequate (<50 nmol/L) 25(OH)D concentrations, and 496 (58%) had at least one species of pathogenic bacteria. No significant association was found between 25(OH)D and presence of any of these bacteria (adjusted OR for high [Q5] compared to low [Q1] 25(OH)D = 0.96; 95% CI: 0.61 to 1.50; P for trend = 0.50). Inverse, although not statistically significant, associations were found between 25(OH)D and more than one species of pathogenic bacteria (adjusted OR for adequate compared to deficient/inadequate 25(OH)D = 0.85; 95% CI: 0.60 to 1.19). No association was observed between pathogenic oral bacteria and 25(OH)D concentrations in postmenopausal females. This may be attributable to the species of bacteria assessed, small effect size, or a true absence of an association.

Epitaxial graphene growth on FIB patterned 3C-SiC nanostructures on Si (111): reducing milling damage.

PubMed

Amjadipour, Mojtaba; MacLeod, Jennifer; Lipton-Duffin, Josh; Iacopi, Francesca; Motta, Nunzio

2017-08-25

Epitaxial growth of graphene on SiC is a scalable procedure that does not require any further transfer step, making this an ideal platform for graphene nanostructure fabrication. Focused ion beam (FIB) is a very promising tool for exploring the reduction of the lateral dimension of graphene on SiC to the nanometre scale. However, exposure of graphene to the Ga + beam causes significant surface damage through amorphisation and contamination, preventing epitaxial graphene growth. In this paper we demonstrate that combining a protective silicon layer with FIB patterning implemented prior to graphene growth can significantly reduce the damage associated with FIB milling. Using this approach, we successfully achieved graphene growth over 3C-SiC/Si FIB patterned nanostructures.

FIB-4 Index is a Predictor of Background Liver Fibrosis and Long-Term Outcomes After Curative Resection of Hepatocellular Carcinoma.

PubMed

Okamura, Yukiyasu; Ashida, Ryo; Yamamoto, Yusuke; Ito, Takaaki; Sugiura, Teiichi; Uesaka, Katsuhiko

2016-08-01

The FIB-4 index is a simple formula for predicting the degree of liver fibrosis. This study aimed to examine the relationship between the preoperative FIB-4 index and liver fibrosis in non-tumor regions of surgical specimens and to investigate whether the FIB-4 index is a useful predictor for long-term outcomes experienced by hepatocellular carcinoma (HCC) patients after curative resection. This study retrospectively analyzed 493 HCC patients treated with curative resection. The utility of the FIB-4 index as a predictor of advanced liver fibrosis (F3 or F4) was assessed. The cutoff value for the FIB-4 index was determined using a receiver operating characteristic curve analysis, and the impact of the FIB-4 index on overall and recurrence-free survival after surgery was evaluated. Advanced liver fibrosis was found in 236 patients (47.9 %). The FIB-4 index was significantly higher for the patients with advanced liver fibrosis than for those without this condition (P < 0.001). An FIB-4 index of 2.87 was the optimal cutoff point for predicting advanced liver fibrosis. The multivariate analysis showed the FIB-4 index to be an independent prognostic factor for recurrence-free and overall survival after curative resection only for patients who underwent hepatectomy as initial treatment (hazard ratio, 1.47 and 1.59; 95 % confidence interval, 1.12-1.93 and 1.09-2.32; P = 0.006 and 0.016, respectively). The study showed the FIB4-index to be a predictor of background liver fibrosis and long-term outcomes for HCC patients who underwent hepatectomy as their initial treatment.

Biotic Interactions and Sunlight Affect Persistence of Fecal Indicator Bacteria and Microbial Source Tracking Genetic Markers in the Upper Mississippi River

PubMed Central

McMinn, Brian R.; Shanks, Orin C.; Sivaganesan, Mano; Fout, G. Shay; Ashbolt, Nicholas J.

2014-01-01

The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of human-associated genetic markers (r2, 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence. PMID:24747902

Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds.

PubMed

Sercu, Bram; Van De Werfhorst, Laurie C; Murray, Jill; Holden, Patricia A

2009-01-15

Coastal urbanized areas in Southern California experience frequent beach water quality warnings in summer due to high concentrations of fecal indicator bacteria (FIB). Remediation can be difficult, as sources are often unknown. During two summers, we sampled three urbanized watersheds in Santa Barbara, CA at sites with historically high FIB concentrations to determine if human fecal matter was influencing water quality. By quantification of a human-specific Bacteroides marker (HBM), human waste was evidenced throughout both transects, and concentrations were highest in the discharges of several flowing storm drains. The HBM concentrations in storm drain discharges varied by up to 5 orders of magnitude on the same day. While the exact points of entry into the storm drain systems were not definitively determined, further inspection of the drain infrastructure suggested exfiltrating sanitary sewers as possible sources. The HBM and FIB concentrations were not consistently correlated, although the exclusive occurrence of high HBM concentrations with high FIB concentrations warrants the use of FIB analyses for a first tier of sampling. The association of human fecal pollution with dry weather drainage could be a window into a larger problem for other urbanized coastal areas with Mediterranean-type climates.

Utility of the FIB-4 Index for hepatocarcinogenesis in hepatitis C virus carriers with normal alanine aminotransferase levels.

PubMed

Ito, T; Kumada, T; Toyoda, H; Tada, T; Kiriyama, S; Tanikawa, M; Hisanaga, Y; Kanamori, A; Kitabatake, S

2015-10-01

The FIB-4 index is a simple formula using age, aspartate aminotransferase, alanine aminotransferase (ALT) and platelet count to evaluate liver fibrosis. We investigated the ability of the FIB-4 index for hepatocarcinogenesis in hepatitis C virus (HCV) carriers with normal ALT levels. A total of 516 patients with ALT levels persistently at or below 40 IU/L during an observation period of over 3 years were included. Factors associated with the development of HCC were determined. Hepatocellular carcinoma (HCC) developed in 60 of 516 patients (11.6%). The incidence rate of HCC at 5 and 10 years was 2.6% and 17.6%, respectively. When patients were categorized according to the FIB-4 index as ≤ 2.0 (n = 226), >2.0 and ≤ 4.0 (n = 169), and > 4.0 (n = 121), the cumulative incidence of HCC at 5 years was 0.5%, 1.3% and 8.0%, respectively, and 2.8%, 25.6% and 37.1% at 10 years, respectively. Patients with FIB-4 index >4.0 were at the highest risk (P < 0.001). Factors that were significantly associated with HCC in the multivariate analysis were FIB-4 index >2.0 (hazard ratio (HR), 7.690), FIB-4 index >4.0 (HR, 8.991), α-fetoprotein (AFP) >5 ng/mL (HR, 2.742), AFP >10 ng/mL (HR, 4.915) and total bilirubin >1.2 mg/dL (HR, 2.142). A scoring system for hepatocarcinogenesis that combines the FIB-4 index and AFP predicted patient outcomes with excellent discriminative ability. The FIB-4 index is strongly associated with the risk of HCC in HCV carriers with normal ALT levels. © 2015 John Wiley & Sons Ltd.

A laboratory marker, FIB-4 index, as a predictor for long-term outcomes of hepatocellular carcinoma patients after curative hepatic resection.

PubMed

Toyoda, Hidenori; Kumada, Takashi; Tada, Toshifumi; Kaneoka, Yuji; Maeda, Atsuyuki

2015-04-01

Liver fibrosis is associated with the prognosis of patients with hepatocellular carcinoma (HCC) after treatment. The laboratory marker for liver fibrosis, the FIB-4 index, is reportedly correlated with the degree of liver fibrosis. We evaluated the predictive value of FIB-4 index on the recurrence and survival of HCC patients who underwent curative hepatectomy. A total of 431 consecutive patients who underwent hepatectomy for primary, nonrecurrent HCC were analyzed. The FIB-4 index was calculated from the patient's age, serum alanine aminotransferase and aspartate aminotransferase levels, and platelet count at the time of HCC diagnosis. Postoperative recurrence and survival rates were compared according to tumor characteristics, tumor markers, Child-Pugh class, and the FIB-4 index. The pretreatment FIB-4 index was associated with recurrence and survival rates, independent of HCC progression or tumor marker levels in a multivariate analysis. Recurrence rates after hepatectomy were higher in patients with a FIB-4 index >3.25 versus ≤3.25 (5-year recurrence rates 69.6% vs 54.8%; P = .0049). Survival was also worse in patients with a FIB-4 index >3.25 than those with a FIB-4 index ≤3.25 (5-year survival rates 67.1% vs 72.2%; P = .0030). The FIB-4 index is a predictive marker for long-term outcomes in patients with HCC treated with curative hepatic resection. Copyright © 2015 Elsevier Inc. All rights reserved.

The use of minimum selectable concentrations (MSCs) for determining the selection of antimicrobial resistant bacteria.

PubMed

Khan, Sadia; Beattie, Tara K; Knapp, Charles W

2017-03-01

The use of antimicrobial compounds is indispensable in many industries, especially drinking water production, to eradicate microorganisms. However, bacterial growth is not unusual in the presence of disinfectant concentrations that would be typically lethal, as bacterial populations can develop resistance. The common metric of population resistance has been based on the Minimum Inhibitory Concentration (MIC), which is based on bacteria lethality. However, sub-lethal concentrations may also select for resistant bacteria due to the differences in bacterial growth rates. This study determined the Minimal Selective Concentrations (MSCs) of bacterial populations exposed to free chlorine and monochloramine, representing a metric that possibly better reflects the selective pressures occurring at lower disinfectant levels than MIC. Pairs of phylogenetically similar bacteria were challenged to a range of concentrations of disinfectants. The MSCs of free chlorine and monochloramine were found to range between 0.021 and 0.39 mg L -1 , which were concentrations 1/250 to 1/5 than the MICs of susceptible bacteria (MIC susc ). This study indicates that sub-lethal concentrations of disinfectants could result in the selection of resistant bacterial populations, and MSCs would be a more sensitive indicator of selective pressure, especially in environmental systems.

Fossilization of Iron-Oxidizing Bacteria at Hydrothermal Vents: a Useful Biosignature on Mars?

NASA Astrophysics Data System (ADS)

Leveille, R. J.; Lui, S.

2009-05-01

Iron oxidizing bacteria are ubiquitous in marine and terrestrial environments on Earth, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Putative microfossils of iron oxidizing bacteria have been found in jaspers as old as 490Ma and microbial iron oxidation may be an ancient metabolic pathway. In order to investigate the usefulness of mineralized iron oxidizing bacteria as a biosignature, we have examined mineral samples collected from relict hydrothermal systems along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic, neutrophilic iron oxidizing bacteria, isolated from Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and oxygen concentration (5 percent) in a controlled bioreactor system. Both natural samples and experimental products were examined with a combination of variable pressure scanning electron microscopy (SEM), field emission gun SEM, and in some cases by preparing samples with a focused ion beam (FIB) milling system. Natural seafloor samples display abundant filamentous forms often resembling, in both size and shape, the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Generally, these filamentous features are 1-5 microns in diameter and up to several microns in length. Some samples consist entirely of low- density, porous masses of silica encrusted filamentous forms. Presumably, these masses were formed by a rapid precipitation by the influx of silica-rich fluids into a microbial mat dominated by bacteria with filamentous morphologies. The presence of rare, amorphous (unmineralized) filamentous matter rich in C and Fe suggests that these bacteria were iron oxidizers. There is no evidence that sulfur oxidizers were present. Filamentous features sectioned by FIB milling show internal material within semi-hollow tubular-like features. Silica encrustations also show pseudo-concentric

Weather and environmental factors associated with F+ coliphages and fecal indicator bacteria in beach sand at two recreational marine beaches

EPA Science Inventory

Studies have demonstrated that fecal indicator bacteria (FIB) and pathogens may be present in beach sand and suggest an increased risk of enteric illness among beachgoers contacting sand. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR...

Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the Upper Mississippi River

EPA Science Inventory

Sanitary quality of recreational waters is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); organisms present in the gastrointestinal tract of humans and many other animals, hence providing no information about the pollution source. Micro...

Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources.

PubMed

Khajanchi, Bijay K; Hasan, Nur A; Choi, Seon Young; Han, Jing; Zhao, Shaohua; Colwell, Rita R; Cerniglia, Carl E; Foley, Steven L

2017-08-02

The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid. In this study, we examined sequence diversity and the contribution of factors encoded on the IncFIB plasmid to the virulence of S. enterica. Whole genome sequences of seven S. enterica isolates were compared to genomes of serovars of S. enterica isolated from food, animal, and human sources. SeqSero analysis predicted that six strains were serovar Typhimurium and one was Heidelberg. Among the S. Typhimurium strains, single nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that five of the isolates clustered as a single monophyletic S. Typhimurium subclade, while one of the other strains branched with S. Typhimurium from a bovine source. DNA sequence based phylogenetic diversity analyses showed that the IncFIB plasmid-encoded Sit and aerobactin iron acquisition systems are conserved among bacterial species including S. enterica. The IncFIB plasmid was transferred to an IncFIB plasmid deficient strain of S. enterica by conjugation. The transconjugant SE819::IncFIB persisted in human intestinal epithelial (Caco-2) cells at a higher rate than the recipient SE819. Genes of the Sit and aerobactin operons in the IncFIB plasmid were differentially expressed in iron-rich and iron-depleted growth media. Minimal sequence diversity was detected in the Sit and aerobactin operons in the IncFIB plasmids present among different bacterial species, including foodborne Salmonella strains. IncFIB plasmid encoded factors play a role during infection under low-iron conditions in host cells.

Significance of beach geomorphology on fecal indicator bacteria levels.

PubMed

Donahue, Allison; Feng, Zhixuan; Kelly, Elizabeth; Reniers, Ad; Solo-Gabriele, Helena M

2017-08-15

Large databases of fecal indicator bacteria (FIB) measurements are available for coastal waters. With the assistance of satellite imagery, we illustrated the power of assessing data for many sites by evaluating beach features such as geomorphology, distance from rivers and canals, presence of piers and causeways, and degree of urbanization coupled with the enterococci FIB database for the state of Florida. We found that beach geomorphology was the primary characteristic associated with enterococci levels that exceeded regulatory guidelines. Beaches in close proximity to marshes or within bays had higher enterococci exceedances in comparison to open coast beaches. For open coast beaches, greater enterococci exceedances were associated with nearby rivers and higher levels of urbanization. Piers and causeways had a minimal contribution, as their effect was often overwhelmed by beach geomorphology. Results can be used to understand the potential causes of elevated enterococci levels and to promote public health. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of poultry decontaminants concentration on growth kinetics for pathogenic and spoilage bacteria.

PubMed

del Río, Elena; González de Caso, Beatriz; Prieto, Miguel; Alonso-Calleja, Carlos; Capita, Rosa

2008-10-01

Various chemical compounds are currently under review for final approval as poultry decontaminants in the European Union (EU). Concentration is among the factors considered by the EU authorities in the evaluation of these treatments. The aim of this research was to compare the growth parameters for pathogenic and spoilage bacteria in presence of high and low concentrations of poultry decontaminants to assess whether such treatments could involve a potential sanitary risk for consumers. Growth curves for Salmonella enterica serotype Enteritidis, Listeria monocytogenes, Pseudomonas fluorescens and Brochothrix thermosphacta were obtained at different levels of trisodium phosphate (TSP; 1.74%; 0.58%), acidified sodium chlorite (ASC; 210 ppm; 70 ppm) and citric acid (CA; 0.27%; 0.09%). The modified Gompertz equation was used as primary model to fit observed data. ASC and TSP were the most effective compounds in increasing lag phase (L) and reducing maximum growth rate (mu) in Gram-negative bacteria. Gram-positive bacteria were more influenced by CA. At high TSP levels, mu for Salmonella decreased. Low TSP levels increased mu for Salmonella and Listeria relative to control samples. In presence of 0.27% CA, Brochothrix showed the highest L and the lowest mu among strains tested. These results suggest that low TSP and high CA concentrations could favour the outgrowth of pathogenic bacteria (e.g. Salmonella) relative to spoilage bacteria, rending these treatments potentially dangerous for consumers. The findings of this study may be useful to the EU authorities and meat processors in their efforts to select adequate treatments for control of bacteria on poultry.

Ordered arrays of Au catalysts by FIB assisted heterogeneous dewetting.

PubMed

Benkouider, A; Ronda, A; David, T; Favre, L; Abbarchi, M; Naffouti, M; Osmond, J; Delobbe, A; Sudraud, P; Berbezier, I

2015-12-18

Synthesizing Au0.8Si0.2 nanocatalysts that are homogeneous in size and have controlled position is becoming a challenging and crucial prequisite for the fabrication of ordered semiconductor nanowires. In this study, Au0.8Si0.2 nanocatalysts are synthesized via dewetting of Au layers on Si(111) during thermal annealing in an ultra-high vacuum. In the first part of the paper, the mechanism of homogeneous dewetting is analyzed as a function of the Au-deposited thickness (h Au). We distinguish three different dewetting regimes: (I) for a low thickness ([Formula: see text]), a submonolyer coverage of Au is stabilized and there is no dewetting. (II) For an intermediate thickness ([Formula: see text]), there is both dewetting and Au0.8Si0.2 phase formation. The size and density of the Au0.8Si0.2 clusters are directly related to h Au. When cooling down to room temperature, the clusters decompose and reject the Si at the Au/Si substrate interface. (III) For a large thickness ([Formula: see text]), only dewetting takes place, without forming AuSi clusters. In this regime, the dewetting is kinetically controlled by the self-diffusion of Au (activation energy ∼0.43 eV) without evidence of an Si-alloying effect. As a practical consequence, when relying solely on the homogeneous dewetting of Au/Si(111) to form the Au0.8Si0.2 catalysts (without a supply of Si atoms from vapor), regime II should be used to obtain good size and density control. In the second part of the paper, a process for ordering the catalysts using focused ion beam-(FIB) assisted dewetting (heterogeneous dewetting) is developed. We show that no matter what the FIB milling conditions and the Au nominal thickness are, dewetting is promoted by ion beam irradiation and is accompanied by the formation of Au0.8Si0.2 droplets. The droplets preferentially form on the patterned areas, while in similar annealing conditions, they do not form on the unpatterned areas. This behavior is attributed to the larger Au

Super-resolution for asymmetric resolution of FIB-SEM 3D imaging using AI with deep learning.

PubMed

Hagita, Katsumi; Higuchi, Takeshi; Jinnai, Hiroshi

2018-04-12

Scanning electron microscopy equipped with a focused ion beam (FIB-SEM) is a promising three-dimensional (3D) imaging technique for nano- and meso-scale morphologies. In FIB-SEM, the specimen surface is stripped by an ion beam and imaged by an SEM installed orthogonally to the FIB. The lateral resolution is governed by the SEM, while the depth resolution, i.e., the FIB milling direction, is determined by the thickness of the stripped thin layer. In most cases, the lateral resolution is superior to the depth resolution; hence, asymmetric resolution is generated in the 3D image. Here, we propose a new approach based on an image-processing or deep-learning-based method for super-resolution of 3D images with such asymmetric resolution, so as to restore the depth resolution to achieve symmetric resolution. The deep-learning-based method learns from high-resolution sub-images obtained via SEM and recovers low-resolution sub-images parallel to the FIB milling direction. The 3D morphologies of polymeric nano-composites are used as test images, which are subjected to the deep-learning-based method as well as conventional methods. We find that the former yields superior restoration, particularly as the asymmetric resolution is increased. Our super-resolution approach for images having asymmetric resolution enables observation time reduction.

Relationship between virological response and FIB-4 index in chronic hepatitis B patients with entecavir therapy

PubMed Central

Li, Ni; Xu, Jing-Hang; Yu, Min; Wang, Sa; Si, Chong-Wen; Yu, Yan-Yan

2015-01-01

AIM: To investigate whether long-term low-level hepatitis B virus (HBV) DNA influences dynamic changes of the FIB-4 index in chronic hepatitis B (CHB) patients receiving entecavir (ETV) therapy with partial virological responses. METHODS: We retrospectively analyzed 231 nucleos(t)ide (NA) naïve CHB patients from our previous study (NCT01926288) who received continuous ETV or ETV maleate therapy for three years. The patients were divided into partial virological response (PVR) and complete virological response (CVR) groups according to serum HBV DNA levels at week 48. Seventy-six patients underwent biopsies at baseline and at 48 wk. The performance of the FIB-4 index and area under the receiver operating characteristic (AUROC) curve for predicting fibrosis were determined for the patients undergoing biopsy. The primary objective of the study was to compare the cumulative probabilities of virological responses between the two groups during the treatment period. The secondary outcome was to observe dynamic changes of the FIB-4 index between CVR patients and PVR patients. RESULTS: For hepatitis B e antigen (HBeAg)-positive patients (n = 178), the cumulative probability of achieving undetectable levels at week 144 was 95% and 69% for CVR and PVR patients, respectively (P < 0.001). In the Cox proportional hazards model, a lower pretreatment serum HBV DNA level was an independent factor predicting maintained viral suppression. The cumulative probability of achieving undetectable levels of HBV DNA for HBeAg-negative patients (n = 53) did not differ between the two groups. The FIB-4 index efficiently identified fibrosis, with an AUROC of 0.80 (95%CI: 0.69-0.89). For HBeAg-positive patients, the FIB-4 index was higher in CVR patients than in PVR patients at baseline (1.89 ± 1.43 vs 1.18 ± 0.69, P < 0.001). There was no significant difference in the reduction of the FIB-4 index between the CVR and PVR groups from weeks 48 to 144 (-0.11 ± 0.47 vs -0.13 ± 0.49, P = 0

Relationship between virological response and FIB-4 index in chronic hepatitis B patients with entecavir therapy.

PubMed

Li, Ni; Xu, Jing-Hang; Yu, Min; Wang, Sa; Si, Chong-Wen; Yu, Yan-Yan

2015-11-21

To investigate whether long-term low-level hepatitis B virus (HBV) DNA influences dynamic changes of the FIB-4 index in chronic hepatitis B (CHB) patients receiving entecavir (ETV) therapy with partial virological responses. We retrospectively analyzed 231 nucleos(t)ide (NA) naïve CHB patients from our previous study (NCT01926288) who received continuous ETV or ETV maleate therapy for three years. The patients were divided into partial virological response (PVR) and complete virological response (CVR) groups according to serum HBV DNA levels at week 48. Seventy-six patients underwent biopsies at baseline and at 48 wk. The performance of the FIB-4 index and area under the receiver operating characteristic (AUROC) curve for predicting fibrosis were determined for the patients undergoing biopsy. The primary objective of the study was to compare the cumulative probabilities of virological responses between the two groups during the treatment period. The secondary outcome was to observe dynamic changes of the FIB-4 index between CVR patients and PVR patients. For hepatitis B e antigen (HBeAg)-positive patients (n = 178), the cumulative probability of achieving undetectable levels at week 144 was 95% and 69% for CVR and PVR patients, respectively (P < 0.001). In the Cox proportional hazards model, a lower pretreatment serum HBV DNA level was an independent factor predicting maintained viral suppression. The cumulative probability of achieving undetectable levels of HBV DNA for HBeAg-negative patients (n = 53) did not differ between the two groups. The FIB-4 index efficiently identified fibrosis, with an AUROC of 0.80 (95%CI: 0.69-0.89). For HBeAg-positive patients, the FIB-4 index was higher in CVR patients than in PVR patients at baseline (1.89 ± 1.43 vs 1.18 ± 0.69, P < 0.001). There was no significant difference in the reduction of the FIB-4 index between the CVR and PVR groups from weeks 48 to 144 (-0.11 ± 0.47 vs -0.13 ± 0.49, P = 0.71). At week 144, the FIB-4

FIB-SEM tomography of human skin telocytes and their extracellular vesicles

PubMed Central

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-01-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) – the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. PMID:25823591

Three-dimensional ultrastructure of osteocytes assessed by focused ion beam-scanning electron microscopy (FIB-SEM).

PubMed

Hasegawa, Tomoka; Yamamoto, Tomomaya; Hongo, Hiromi; Qiu, Zixuan; Abe, Miki; Kanesaki, Takuma; Tanaka, Kawori; Endo, Takashi; de Freitas, Paulo Henrique Luiz; Li, Minqi; Amizuka, Norio

2018-04-01

The aim of this study is to demonstrate the application of focused ion beam-scanning electron microscopy, FIB-SEM for revealing the three-dimensional features of osteocytic cytoplasmic processes in metaphyseal (immature) and diaphyseal (mature) trabeculae. Tibiae of eight-week-old male mice were fixed with aldehyde solution, and treated with block staining prior to FIB-SEM observation. While two-dimensional backscattered SEM images showed osteocytes' cytoplasmic processes in a fragmented fashion, three-dimensional reconstructions of FIB-SEM images demonstrated that osteocytes in primary metaphyseal trabeculae extended their cytoplasmic processes randomly, thus maintaining contact with neighboring osteocytes and osteoblasts. In contrast, diaphyseal osteocytes extended thin cytoplasmic processes from their cell bodies, which ran perpendicular to the bone surface. In addition, these osteocytes featured thick processes that branched into thinner, transverse cytoplasmic processes; at some point, however, these transverse processes bend at a right angle to run perpendicular to the bone surface. Osteoblasts also possessed thicker cytoplasmic processes that branched off as thinner processes, which then connected with cytoplasmic processes of neighboring osteocytes. Thus, FIB-SEM is a useful technology for visualizing the three-dimensional structures of osteocytes and their cytoplasmic processes.

USING HYDROGRAPHIC DATA AND THE EPA VIRTUAL BEACH MODEL TO TEST PREDICTIONS OF BEACH BACTERIA CONCENTRATIONS

EPA Science Inventory

A modeling study of 2006 Huntington Beach (Lake Erie) beach bacteria concentrations indicates multi-variable linear regression (MLR) can effectively estimate bacteria concentrations compared to the persistence model. Our use of the Virtual Beach (VB) model affirms that fact. VB i...

Correlation of two-photon in vivo imaging and FIB/SEM microscopy

PubMed Central

Blazquez-Llorca, L; Hummel, E; Zimmerman, H; Zou, C; Burgold, S; Rietdorf, J; Herms, J

2015-01-01

Advances in the understanding of brain functions are closely linked to the technical developments in microscopy. In this study, we describe a correlative microscopy technique that offers a possibility of combining two-photon in vivo imaging with focus ion beam/scanning electron microscope (FIB/SEM) techniques. Long-term two-photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool for studying the dynamics of neurodegenerative diseases, such as Alzheimer’s disease. However, light microscopy has important limitations in revealing alterations occurring at the synaptic level and when this is required, electron microscopy is mandatory. FIB/SEM microscopy is a novel tool for three-dimensional high-resolution reconstructions, since it acquires automated serial images at ultrastructural level. Using FIB/SEM imaging, we observed, at 10 nm isotropic resolution, the same dendrites that were imaged in vivo over 9 days. Thus, we analyzed their ultrastructure and monitored the dynamics of the neuropil around them. We found that stable spines (present during the 9 days of imaging) formed typical asymmetric contacts with axons, whereas transient spines (present only during one day of imaging) did not form a synaptic contact. Our data suggest that the morphological classification that was assigned to a dendritic spine according to the in vivo images did not fit with its ultrastructural morphology. The correlative technique described herein is likely to open opportunities for unravelling the earlier unrecognized complexity of the nervous system. Lay Description Neuroscience and the understanding of brain functions are closely linked to the technical advances in microscopy. In this study we performed a correlative microscopy technique that offers the possibility to combine 2 photon in vivo imaging and FIB/SEM microscopy. Long term 2 photon in vivo imaging allows the

Predicting E. Coli and Enterococci Concentrations in the South Fork Broad River Watershed Using Virtual Beach

EPA Science Inventory

Virtual Beach (VB) is a decision support tool that constructs site-specific statistical models to predict fecal indicator bacteria (FIB) at locations of exposure. Although primarily designed for making decisions regarding beach closures or issuance of swimming advisories based on...

Inactivation of faecal indicator bacteria in a roof-captured rainwater system under ambient meteorological conditions.

PubMed

Ahmed, W; Richardson, K; Sidhu, J P S; Jagals, P; Toze, S

2014-01-01

In this study, faecal indicator bacteria (FIB) namely Escherichia coli and Enterococcus spp. were seeded into slurries of possum faeces and placed on the roof and in the gutter of a roof-captured rainwater (RCR) system. The persistence of FIB in these circumstances was determined under ambient climatic conditions. FIB persistence was also determined under in situ conditions in tank water using diffusion chambers. The numbers of surviving FIB at different time intervals were enumerated using culture-based methods. Both FIB were rapidly inactivated on the roof under sunlight conditions (T(90) = 2 h) compared with shade conditions (T(90) = 9-53 h). Significant differences were observed between sunlight and shade conditions on the roof for both T90 values of E. coli (P < 0·001) and Enterococcus spp. (P < 0·001). E. coli showed biphasic inactivation patterns under both clean and unclean gutter conditions. Enterococcus spp., however, showed rapid inactivation (T(90) = 2 h for the clean gutter and T(90) = 6 h for the unclean gutter) compared with E. coli (T(90) = 22 h for the clean gutter and T(90) = 20 h for the unclean gutter). Significant differences were also observed between the T(90) values of E. coli and Enterococcus spp. for both clean (P < 0·001) and unclean (P < 0·001) gutters. Both E. coli and Enterococcus spp. showed nonlinear biphasic inactivation in tank water. Significant difference was observed between the T(90) value of E. coli inactivation compared with Enterococcus spp. (P < 0·001) in the tank water. In this study, FIB were observed to survive longer (T(90) = 9-53 h) on the roof under shade conditions compared with sunlight conditions (T(90) = 2 h). If there is a rainfall event within two to three days after the deposition of faecal maters on the roof, it is highly likely that FIB would be transported to the tank water. When introduced into the tank, a relatively slow inactivation process may take place (T(90) = 38-72 h). The presence of FIB in

Three-Dimensional FIB/EBSD Characterization of Irradiated HfAl3-Al Composite

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

Hua, Zilong; Guillen, Donna Post; Harris, William

2016-09-01

A thermal neutron absorbing material, comprised of 28.4 vol% HfAl3 in an Al matrix, was developed to serve as a conductively cooled thermal neutron filter to enable fast flux materials and fuels testing in a pressurized water reactor. In order to observe the microstructural change of the HfAl3-Al composite due to neutron irradiation, an EBSD-FIB characterization approach is developed and presented in this paper. Using the focused ion beam (FIB), the sample was fabricated to 25µm × 25µm × 20 µm and mounted on the grid. A series of operations were carried out repetitively on the sample top surface tomore » prepare it for scanning electron microscopy (SEM). First, a ~100-nm layer was removed by high voltage FIB milling. Then, several cleaning passes were performed on the newly exposed surface using low voltage FIB milling to improve the SEM image quality. Last, the surface was scanned by Electron Backscattering Diffraction (EBSD) to obtain the two-dimensional image. After 50 to 100 two-dimensional images were collected, the images were stacked to reconstruct a three-dimensional model using DREAM.3D software. Two such reconstructed three-dimensional models were obtained from samples of the original and post-irradiation HfAl3-Al composite respectively, from which the most significant microstructural change caused by neutron irradiation apparently is the size reduction of both HfAl3 and Al grains. The possible reason is the thermal expansion and related thermal strain from the thermal neutron absorption. This technique can be applied to three-dimensional microstructure characterization of irradiated materials.« less

An improved FIB sample preparation technique for site-specific plan-view specimens: A new cutting geometry.

PubMed

Li, Chen; Habler, Gerlinde; Baldwin, Lisa C; Abart, Rainer

2018-01-01

Focused ion beam (FIB) sample preparation technique in plan-view geometry allows direct correlations of the atomic structure study via transmission electron microscopy with micrometer-scale property measurements. However, one main technical difficulty is that a large amount of material must be removed underneath the specimen. Furthermore, directly monitoring the milling process is difficult unless very large material volumes surrounding the TEM specimen site are removed. In this paper, a new cutting geometry is introduced for FIB lift-out sample preparation with plan-view geometry. Firstly, an "isolated" cuboid shaped specimen is cut out, leaving a "bridge" connecting it with the bulk material. Subsequently the two long sides of the "isolated" cuboid are wedged, forming a triangular prism shape. A micromanipulator needle is used for in-situ transfer of the specimen to a FIB TEM grid, which has been mounted parallel with the specimen surface using a simple custom-made sample slit. Finally, the grid is transferred to the standard FIB grid holder for final thinning with standard procedures. This new cutting geometry provides clear viewing angles for monitoring the milling process, which solves the difficulty of judging whether the specimen has been entirely detached from the bulk material, with the least possible damage to the surrounding materials. With an improved success rate and efficiency, this plan-view FIB lift-out specimen preparation technique should have a wide application for material science. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Thinning of Large Biological Cells for Cryo-TEM Characterization by Cryo-FIB Milling

PubMed Central

Strunk, Korrinn M.; Ke, Danxia; Gray, Jennifer L.; Zhang, Peijun

2013-01-01

SUMMARY Focused ion beam milling at cryogenic temperatures (cryo-FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis in a cryo-transmission electron microscope (cryo-TEM) in their frozen-hydrated state. This technique offers the potential benefit of eliminating the mechanical artifacts that are typically found with cryo-ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. In order to address these problems, we have designed a new sample cryo-shuttle that specifically accepts Polara TEM cartridges directly in order to simplify the transfer process between the FIB and TEM. We used the quality of the ice in the sample as an indicator to test various parameters used the process, and demonstrated with successful milling of large mammalian cells. By comparing the results from larger HeLa cells to those from E. coli cells, we discuss some of the artifacts and challenges we have encountered using this technique. PMID:22906009

Prediction of future hepatocellular carcinoma incidence in moderate to heavy alcohol drinkers with the FIB-4 liver fibrosis index.

PubMed

Suh, Beomseok; Yun, Jae Moon; Park, Sehhoon; Shin, Dong Wook; Lee, Tae Hoon; Yang, Hyung-Kook; Ahn, Eunmi; Lee, Hyejin; Park, Jin Ho; Cho, BeLong

2015-11-01

Although heavy alcoholics are at heightened risk for hepatocellular carcinoma (HCC), there are no guidelines that recommend HCC screening for heavy alcoholics. This study investigated FIB-4, a noninvasive and easily applicable liver fibrosis index, as a risk factor for HCC incidence among alcohol drinkers without viral hepatitis. This retrospective cohort study included 6661 generally healthy adults who were 30 years old or older, did not have chronic viral hepatitis, and visited Seoul National University Hospital for a general, routine health evaluation. The future HCC incidence was determined from National Health Insurance medical service claims data (median follow-up, 6.2 years). With adjustments for age, sex, body mass index, smoking, and alcohol, compared with subjects with FIB-4 values less 1.00, subjects with FIB-4 values greater than or equal to 1.75 and less than 2.10 and subjects with FIB-4 values greater than or equal to 2.10 had adjusted hazard ratios (aHRs) of 5.18 (95% confidence interval [CI], 1.12-24.00) and 13.63 (95% CI, 3.77-49.33), respectively, for HCC incidence. This was heightened in subjects who drank more 30 g of alcohol per day: the aHRs were 8.39 (95% CI, 1.28-54.87) and 16.58 (95% CI, 3.87-71.04), respectively. FIB-4 was shown to have a higher predictive value for HCC incidence than ultrasonographically detected liver cirrhosis (C-index, 0.665 vs 0.527; P = .044). High FIB-4 is a risk factor with a high predictive value for HCC incidence, especially among moderate to heavy alcoholics (>30 g/d). FIB-4 is a readily available and probably cost-effective clinical tool with potential value for identifying subpopulations of alcoholics at particularly high risk who would benefit from regular HCC screening. Further investigations are warranted to validate our results; nonetheless, our study suggests that FIB-4 may be useful in HCC screening among alcoholics. © 2015 American Cancer Society.

Predicting recreational water quality advisories: A comparison of statistical methods

USGS Publications Warehouse

Brooks, Wesley R.; Corsi, Steven R.; Fienen, Michael N.; Carvin, Rebecca B.

2016-01-01

Epidemiological studies indicate that fecal indicator bacteria (FIB) in beach water are associated with illnesses among people having contact with the water. In order to mitigate public health impacts, many beaches are posted with an advisory when the concentration of FIB exceeds a beach action value. The most commonly used method of measuring FIB concentration takes 18–24 h before returning a result. In order to avoid the 24 h lag, it has become common to ”nowcast” the FIB concentration using statistical regressions on environmental surrogate variables. Most commonly, nowcast models are estimated using ordinary least squares regression, but other regression methods from the statistical and machine learning literature are sometimes used. This study compares 14 regression methods across 7 Wisconsin beaches to identify which consistently produces the most accurate predictions. A random forest model is identified as the most accurate, followed by multiple regression fit using the adaptive LASSO.

Quick Estimation Model for the Concentration of Indoor Airborne Culturable Bacteria: An Application of Machine Learning.

PubMed

Liu, Zhijian; Li, Hao; Cao, Guoqing

2017-07-30

Indoor airborne culturable bacteria are sometimes harmful to human health. Therefore, a quick estimation of their concentration is particularly necessary. However, measuring the indoor microorganism concentration (e.g., bacteria) usually requires a large amount of time, economic cost, and manpower. In this paper, we aim to provide a quick solution: using knowledge-based machine learning to provide quick estimation of the concentration of indoor airborne culturable bacteria only with the inputs of several measurable indoor environmental indicators, including: indoor particulate matter (PM 2.5 and PM 10 ), temperature, relative humidity, and CO₂ concentration. Our results show that a general regression neural network (GRNN) model can sufficiently provide a quick and decent estimation based on the model training and testing using an experimental database with 249 data groups.

FIB-SEM tomography of human skin telocytes and their extracellular vesicles.

PubMed

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-04-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) - the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

[Mutant prevention concentrations of antibacterial agents to ocular pathogenic bacteria].

PubMed

Liang, Qing-Feng; Wang, Zhi-Qun; Li, Ran; Luo, Shi-Yun; Deng, Shi-Jing; Sun, Xu-Guang

2009-01-01

To establish a method to measure mutant prevention concentration (MPC) in vitro, and to measure MPC of antibacterial agents for ocular bacteria caused keratitis. It was an experimental study. Forty strains of ocular bacteria were separated from cornea in Beijing Institute of Ophthalmology, which included 8 strains of Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Pseudomonas aeruginosa and Klebsiella pneumoniae respectively. The minimal inhibitory concentration (MIC) of the levofloxacin (LVF), ofloxacin (OFL), ciprofloxacin (CIP), norfloxacin (NFL), tobramycin (TOB) and chloromycetin (CHL) were determined by agar dilution method from National Committee of Clinical Laboratory Standard (NCCLS). The MPC were measured by accumulate-bacterial methods with bacterial population inoculated more than 1.2 x 10(10) colony forming units per milliliter with Mueller-Hinton broth and tryptic soy agar plate. With the software of SPSS 11.0, the datum such as the range of MIC, MPC, MIC90 and MPC90 were calculated, and the selection index (MPC90/ MI90) and mutant selection window (MSW) were obtained. The MI90 of LVF and TOB (4 mg/L) to Staphylococcus aureus strains were the lowest. CIP showed the lowest MIC90 (0.25 mg/L) to Pseudomonas aeruginosa among six kinds of antibacterial agents. The MIC90 of LVF to Staphylococcus epidermidis (256 mg/L), Streptococcus pneumoniae (1 mg/L) and Klebsiella pneumoniae (0.25 mg/L) were lower than other antibacterial agents. The MPC90, MSW and the MPC90/MIC90 of levofloxacin showed lower values compared with other antibacterial medicines. From all the datum, the MIC90 of CHL was the highest and the activity was the weakest. Although the activity of LVF was higher to every kind of bacteria, CIP had the highest activity antibacterial to Pseudomonas aeruginosa. The capacity of CHL and TOB was weaker than Quinolones for restricting resistant mutants on ocular bacteria. LVF had the strongest capacity for restricting resistant

Rapid detection of contaminant bacteria in platelet concentrate using differential impedance.

PubMed

Zhao, Z; Chalmers, A; Rieder, R

2014-08-01

Current FDA-approved culture-based methods for the bacterial testing of platelet concentrate (PC) can yield false-negative results attributed to Poisson-limited sampling errors incurred near the time of collection that result in undetectable bacterial concentrations. Testing PC at the point of issue (POI) extends the incubation period for any contaminant bacteria increasing the probability of detection. Data are presented from time-course experiments designed to simulate POI testing of bacterially contaminated PCs at different stages of growth using differential impedance sensing. Whole-blood-derived PCs were typically spiked with low numbers of bacteria (approximately 100 CFU/ml) and incubated under standard PC storage conditions. Each infected unit was evaluated every two hours over a 12-h period. All samples were treated with a chemical compound that induces stress in the bacterial cells only. The development of any bacterial stress was monitored by detecting changes in the dielectric properties of the PC using differential impedance. Differential impedance measurements and corresponding cell counts at the different time-points are presented for six organisms implicated in post-transfusion-septic reactions. All infected PCs were detected once contaminant bacteria reached concentrations ranging between 0·6 × 10(3) and 6 × 10(3)  CFU/ml irrespective of the phase of growth. Results were obtained within 30 min after the start of the assay and without the need for cell lysis or centrifugation. Differential impedance sensing can detect bacterial contamination in PC rapidly at concentrations below clinical thresholds known to cause adverse effects. © 2014 International Society of Blood Transfusion.

FIB-4 index for assessing the prognosis of hepatocellular carcinoma in patients with Child-Pugh class A liver function.

PubMed

Ito, Takanori; Kumada, Takashi; Toyoda, Hidenori; Tada, Toshifumi

2015-07-01

We evaluated the prognosis of hepatocellular carcinoma (HCC) patients with Child-Pugh (C-P) class A based on FIB-4 index, which is a liver fibrosis marker. A total of 915 HCC patients with C-P class A were investigated. We assessed the prognosis using FIB-4 index, and factors associated with survival rates were analyzed in these patients. When patients were categorized according to FIB-4 index as <2.0 (n = 93), ≥ 2.0 and <4.0 (n = 311), and ≥ 4.0 (n = 511), survival rates at 5 years were 70.5% [95% confidence interval (CI) 59.0-79.9], 56.4% (95% CI 50.1-62.5), and 47.1% (95% CI 42.2-52.1), respectively. Patients with FIB-4 index <2.0 had a higher survival rate than the other groups (≥ 4.0 vs ≥ 2.0 and <4.0, p = 0.010; ≥ 2.0 and <4.0 vs <2.0, p = 0.028). We were able to predict prognosis in patients with C-P score 5 by FIB-4 index, but survival rate did not significantly differ in patients with C-P score 6. Multivariate analysis identified C-P score, FIB-4 index [≥ 2.0 and <4.0; hazard ratios (HRs) 1.638 (95% CI 1.084-2.474); p = 0.019/≥ 4.0; HR 1.828 (95% CI 1.217-2.744); p = 0.004], Lens culinaris agglutinin-reactive α-fetoprotein, tumor size, number, vascular invasion, antiviral therapy, and hepatectomy as independent predictive factors for survival. The FIB-4 index is useful for assessing prognosis in HCC patients with C-P class A, especially those with C-P score 5.

Predictive value of FIB-4 and APRI versus METAVIR on sustained virologic response in genotype 1 hepatitis C patients.

PubMed

Ferenci, Peter; Aires, Rodrigo; Beavers, Kimberly L; Curescu, Manuela; Abrão Ferreira, Paulo R; Gschwantler, Michael; Ion, Stefan; Larrey, Dominique; Maticic, Mojca; Puoti, Massimo; Schuller, János; Tornai, Istvan; Tusnádi, Anna; Messinger, Diethelm; Tatsch, Fernando; Horban, Andrzej

2014-01-01

Advanced liver fibrosis is a negative predictor of virologic response in genotype 1 chronic hepatitis C (CHC) patients. Biopsy, however, is invasive, costly, and carries some risk of complications. Using data from the prospective, international cohort study PROPHESYS, we assessed two alternative noninvasive measures of fibrosis, the FIB-4 and AST-to-platelet ratio index (APRI), to predict virologic response in CHC patients. CHC genotype 1, monoinfected, treatment-naive patients prescribed peginterferon alfa-2a (40 KD)/ribavirin in accordance with country-specific legal and regulatory requirements and who had baseline METAVIR, FIB-4, and APRI scores (N = 1,592) were included in this analysis. Patients were stratified according to the baseline METAVIR, FIB-4, or APRI score to assess virologic response [hepatitis C virus (HCV) RNA <50 IU/mL] by week 4 of treatment (rapid virologic response) and 24 weeks after untreated follow-up ]sustained virologic response (SVR)]. Baseline predictors of SVR were explored by multiple logistic regression, and the strength of the association between each fibrosis measure and SVR was evaluated. Both FIB-4 and APRI scores increased with increasing levels of biopsy-assessed fibrosis. The association between FIB-4 and SVR (p < 0.1 × 10(-30)) was stronger than that between METAVIR (p = 3.86 × 10(-13)) or APRI (p = 5.48 × 10(-6)) and SVR. Baseline factors significantly associated with SVR included male gender, lower HCV RNA, lower FIB-4 score, no steatosis, and higher alanine aminotransferase ratio. The FIB-4 index provides a valuable, noninvasive measure of fibrosis and can be used to predict virologic response in patients treated with peginterferon alfa-2a (40  KD)/ribavirin.

Diagnostic accuracy of APRI and FIB-4 for predicting hepatitis B virus-related liver fibrosis accompanied with hepatocellular carcinoma.

PubMed

Xiao, Guangqin; Zhu, Feng; Wang, Min; Zhang, Hang; Ye, Dawei; Yang, Jiayin; Jiang, Li; Liu, Chang; Yan, Lunan; Qin, Renyi

2016-10-01

Aspartate aminotransferase to platelet ratio index (APRI) and the fibrosis index based on four factors (FIB-4) are the two most focused non-invasive models to assess liver fibrosis. We aimed to examine the validity of these two models for predicting hepatitis B virus (HBV)-related liver fibrosis accompanied with hepatocellular carcinoma (HCC). We enrolled HBV-infected patients with liver cancer who had received hepatectomy. The accuracy of APRI and FIB-4 for diagnosing liver fibrosis was assessed based on their sensitivity, specificity, diagnostic efficiency, positive predictive value (PPV), negative predictive value (NPV), kappa (κ) value and area under the receiver-operating characteristic curve (AUC). Finally 2176 patients were included, with 1682 retrospective subjects and 494 prospective subjects. APRI (rs=0.310) and FIB-4 (rs=0.278) were positively correlated with liver fibrosis. And χ(2) analysis demonstrated that APRI and FIB-4 values correlated with different levels of liver fibrosis with all P values less than 0.01. The AUC values for APRI and FIB-4 were 0.685 and 0.626 (P=0.73) for predicting significant fibrosis, 0.681 and 0.648 (P=0.81) for differentiation of advanced fibrosis and 0.676 and 0.652 (P=0.77) for diagnosing cirrhosis. APRI and FIB-4 correlate with liver fibrosis. However these two models have low accuracy for predicting HBV-related liver fibrosis in HCC patients. Copyright © 2016. Published by Elsevier Ltd.

Elevated liver fibrosis index FIB-4 is not reliable for HCC risk stratification in predominantly non-Asian CHB patients.

PubMed

Demir, Münevver; Grünewald, Friederike; Lang, Sonja; Schramm, Christoph; Bowe, Andrea; Mück, Vera; Kütting, Fabian; Goeser, Tobias; Steffen, Hans-Michael

2016-09-01

We aimed to validate the liver fibrosis index FIB-4 as a model for risk stratification of hepatocellular carcinoma development in predominantly non-Asian patients with chronic hepatitis B infection seen at a tertiary referral center in Germany.We retrospectively analyzed 373 adult patients with chronic hepatitis B infection. Patient demographics, hepatitis B markers, antiviral treatment, laboratory parameters, results from liver imaging and histology were recorded. Patients were divided into 2 groups according to their FIB-4 levels and their hazard ratios for developing hepatocellular carcinoma were analyzed adjusted for age, sex, body mass index, alcohol consumption, and antiviral medication.Median follow-up was 8.7 years (range 1-21.3 years), 93% of patients were of non-Asian origin, and 64% were male. Compared with patients with a low FIB-4 (<1.25) patients with FIB-4 ≥1.25 showed a hazard ratio for incidence of hepatocellular carcinoma of 3.03 (95% confidence interval (CI): 1.24-7.41) and an adjusted hazard ratio of 1.75 (95% CI: 0.64-4.74). Notably, 68% of patients with liver cirrhosis and 68% of those who developed HCC during observation had a low FIB-4 (<1.25).We could not confirm that a FIB-4 value ≥1.25 is a reliable clinical indicator for incidence of hepatocellular carcinoma in predominantly non-Asian patients with chronic hepatitis B. Further studies in geographically and ethnically diverse populations are needed to prove its utility as a predictive tool.

The FIB-4 index is a significant prognostic factor in patients with non-B non-C hepatocellular carcinoma after curative surgery.

PubMed

Okamura, Yukiyasu; Ashida, Ryo; Yamamoto, Yusuke; Ito, Takaaki; Sugiura, Teiichi; Bekku, Emima; Aramaki, Takeshi; Uesaka, Katsuhiko

2016-03-01

The aspartate aminotransferase to platelet ratio index (APRI) and fibrosis-4 (FIB-4) index were developed as a non-invasive parameter for predicting liver fibrosis. This study aimed to validate the APRI and FIB-4 indexes in patients treated with curative therapy for non-B non-C (NBNC) hepatocellular carcinoma (HCC). Accumulated database comprising 399 patients who underwent hepatectomy was reviewed retrospectively. Analyses were performed to evaluate whether the APRI and FIB-4 indexes are predictors of liver cirrhosis and/or the prognosis in patients with NBNC-HCC. Forty-seven patients with NBNC-HCC who underwent curative radiofrequency ablation therapy (RFA) in the same period were enrolled as the validation set. The APRI and FIB-4 indexes were significantly higher in the cirrhosis group than in the no-cirrhosis group (P = 0.001 and P < 0.001, respectively). A receiver operating characteristic curve analysis showed that the FIB-4 index was more accurate in predicting background liver cirrhosis than the APRI. According to a multivariate analysis, an FIB-4 index larger than 2.7 (hazard ratio 2.11 and 2.21, 95 % confidence interval 1.06-4.18 and 1.38-3.54, P = 0.033 and P = 0.001) remained significant independent predictors of overall and recurrence-free survival, respectively. The present findings showed that the FIB-4 index is a significant predictor of background liver cirrhosis and the prognosis after curative resection for NBNB-HCC.

Quick Estimation Model for the Concentration of Indoor Airborne Culturable Bacteria: An Application of Machine Learning

PubMed Central

Liu, Zhijian; Li, Hao; Cao, Guoqing

2017-01-01

Indoor airborne culturable bacteria are sometimes harmful to human health. Therefore, a quick estimation of their concentration is particularly necessary. However, measuring the indoor microorganism concentration (e.g., bacteria) usually requires a large amount of time, economic cost, and manpower. In this paper, we aim to provide a quick solution: using knowledge-based machine learning to provide quick estimation of the concentration of indoor airborne culturable bacteria only with the inputs of several measurable indoor environmental indicators, including: indoor particulate matter (PM2.5 and PM10), temperature, relative humidity, and CO2 concentration. Our results show that a general regression neural network (GRNN) model can sufficiently provide a quick and decent estimation based on the model training and testing using an experimental database with 249 data groups. PMID:28758941

Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns

PubMed Central

Spencer, J.; Schwarzacher, W.

2016-01-01

ABSTRACT In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli. Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. IMPORTANCE Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved

Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns.

PubMed

Correia Carreira, S; Spencer, J; Schwarzacher, W; Seddon, A M

2016-06-15

In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved within 15 min. This

Comparing the efficiency of Fib-4, Egy-score, APRI, and GUCI in liver fibrosis staging in Egyptians with chronic hepatitis C.

PubMed

Cordie, Ahmed; Salama, Ahmed; El-Sharkawy, Marwa; El-Nahaas, Saeed M; Khairy, Marwa; Elsharkawy, Aisha; Hassany, Mohamed; Esmat, Gamal

2018-06-01

Assessment of hepatic fibrosis in chronic hepatitis C virus patients by liver biopsy is not widely accepted despite its accuracy, being invasive, carrying complications, and adding cost. This paved the way to development and use of non-invasive markers of fibrosis in diagnosis of hepatic fibrosis. We aimed at evaluating the efficiency of Fib-4, Egy-score, Aspartate-to-platelet ratio index (APRI), and Göteborg University Cirrhosis Index (GUCI) in comparison to liver biopsy, in the assessment of hepatic fibrosis in chronic hepatitis C patients. This was a cross sectional study including 200 chronic HCV patients were divided into two groups according to stage of fibrosis (Metavir score) into non-significant fibrosis (Fib-4, Egyscore, APRI, and GUCI. Older age (P < 0.001) and higher BMI (P = 0.005) were significantly related to significant fibrosis and positively correlated with fibrosis progression (r = 0.361, P = 0.000, and r = 0.165, P = 0.019 respectively). Fib-4 >1.27, APRI >0.48, Egy-score >0.73, and GUCI >0.57 significantly predict significant fibrosis (P < 0.01). Fib-4 carries the best performance and significant reliability with AUROC 0.783, sensitivity 74%, specificity 69%, PPV 0.55, and NPV 0.86. The addition of BMI to Fib-4 improved the significant fibrosis AUROC curve performance but did not reach statistical significant improvement. We concluded that age and BMI are good predictors of hepatic fibrosis. Fib-4 (>1.27) is the best method of prediction of significant fibrosis compared to Egy-score, APRI, and GUCI. Addition of BMI to Fib-4 did not improve diagnostic value of Fib-4. © 2018 Wiley Periodicals, Inc.

Non-alcoholic fatty liver disease fibrosis score and FIB-4 scoring system could identify patients at risk of systemic complications.

PubMed

Takahashi, Yuka; Kurosaki, Masayuki; Tamaki, Nobuharu; Yasui, Yutaka; Hosokawa, Takanori; Tsuchiya, Kaoru; Nakanishi, Hiroyuki; Itakura, Jun; Izumi, Namiki

2015-06-01

To investigate the relation between systemic complications of non-alcoholic fatty liver disease (NAFLD) and non-invasive fibrosis scores. The NAFLD fibrosis score (NFS) and FIB-4 were measured in 1559 people who underwent a complete medical checkup at our hospital and were followed for more than 3 years. Correlation between these scores and prevalence and new incidence rates of diabetes or cerebral-cardiovascular diseases were analyzed. The 1559 cases were classified into two groups using the low cut-off values of NFS and FIB-4: group 1 (≥low cut-off score with fatty liver) and group 2 (the others). In group 1, the prevalence of diabetes and cerebral-cardiovascular diseases at baseline and additional incidences during the observation period was higher compared with group 2. Diabetes at baseline in group 1 versus group 2 were 31.5% versus 3.1% (NFS, P < 0.0001), 17.0% versus 4.7% (FIB-4, P < 0.0001), and cerebral-cardiovascular diseases at baseline were 7.7% versus 2.3% (NFS, P = 0.002) and 9.0% versus 2.3% (FIB-4, P = 0.0012). New incidences of diabetes were 4.5% versus 1.2% (NFS, P = 0.034) and 3.6% versus 1.2% (FIB-4, P = 0.11), and of cerebral-cardiovascular diseases were 5.0% versus 0.9% (NFS, P = 0.0019) and 5.4% versus 0.9% (FIB-4, P = 0.0034). NFS and FIB-4 are useful to extract cases with high risk of systemic complications of NAFLD in the public. © 2014 The Japan Society of Hepatology.

High pressure inertial focusing for separating and concentrating bacteria at high throughput

NASA Astrophysics Data System (ADS)

Cruz, J.; Hooshmand Zadeh, S.; Graells, T.; Andersson, M.; Malmström, J.; Wu, Z. G.; Hjort, K.

2017-08-01

Inertial focusing is a promising microfluidic technology for concentration and separation of particles by size. However, there is a strong correlation of increased pressure with decreased particle size. Theory and experimental results for larger particles were used to scale down the phenomenon and find the conditions that focus 1 µm particles. High pressure experiments in robust glass chips were used to demonstrate the alignment. We show how the technique works for 1 µm spherical polystyrene particles and for Escherichia coli, not being harmful for the bacteria at 50 µl min-1. The potential to focus bacteria, simplicity of use and high throughput make this technology interesting for healthcare applications, where concentration and purification of a sample may be required as an initial step.

Three-dimensional imaging of adherent cells using FIB/SEM and STEM.

PubMed

Villinger, Clarissa; Schauflinger, Martin; Gregorius, Heiko; Kranz, Christine; Höhn, Katharina; Nafeey, Soufi; Walther, Paul

2014-01-01

In this chapter we describe three different approaches for three-dimensional imaging of electron microscopic samples: serial sectioning transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM) tomography, and focused ion beam/scanning electron microscopy (FIB/SEM) tomography. With these methods, relatively large volumes of resin-embedded biological structures can be analyzed at resolutions of a few nm within a reasonable expenditure of time. The traditional method is serial sectioning and imaging the same area in all sections. Another method is TEM tomography that involves tilting a section in the electron beam and then reconstruction of the volume by back projection of the images. When the scanning transmission (STEM) mode is used, thicker sections (up to 1 μm) can be analyzed. The third approach presented here is focused ion beam/scanning electron microscopy (FIB/SEM) tomography, in which a sample is repeatedly milled with a focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrary small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. We show that resolution of this approach is considerably improved when the secondary electron signal is used. However, the most important prerequisite for three-dimensional imaging is good specimen preparation. For all three imaging methods, cryo-fixed (high-pressure frozen) and freeze-substituted samples have been used.

Elevated liver fibrosis index FIB-4 is not reliable for HCC risk stratification in predominantly non-Asian CHB patients

PubMed Central

Demir, Münevver; Grünewald, Friederike; Lang, Sonja; Schramm, Christoph; Bowe, Andrea; Mück, Vera; Kütting, Fabian; Goeser, Tobias; Steffen, Hans-Michael

2016-01-01

Abstract We aimed to validate the liver fibrosis index FIB-4 as a model for risk stratification of hepatocellular carcinoma development in predominantly non-Asian patients with chronic hepatitis B infection seen at a tertiary referral center in Germany. We retrospectively analyzed 373 adult patients with chronic hepatitis B infection. Patient demographics, hepatitis B markers, antiviral treatment, laboratory parameters, results from liver imaging and histology were recorded. Patients were divided into 2 groups according to their FIB-4 levels and their hazard ratios for developing hepatocellular carcinoma were analyzed adjusted for age, sex, body mass index, alcohol consumption, and antiviral medication. Median follow-up was 8.7 years (range 1–21.3 years), 93% of patients were of non-Asian origin, and 64% were male. Compared with patients with a low FIB-4 (<1.25) patients with FIB-4 ≥1.25 showed a hazard ratio for incidence of hepatocellular carcinoma of 3.03 (95% confidence interval (CI): 1.24–7.41) and an adjusted hazard ratio of 1.75 (95% CI: 0.64–4.74). Notably, 68% of patients with liver cirrhosis and 68% of those who developed HCC during observation had a low FIB-4 (<1.25). We could not confirm that a FIB-4 value ≥1.25 is a reliable clinical indicator for incidence of hepatocellular carcinoma in predominantly non-Asian patients with chronic hepatitis B. Further studies in geographically and ethnically diverse populations are needed to prove its utility as a predictive tool. PMID:27661015

3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

PubMed Central

Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

2012-01-01

Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

A comparison of legionella and other bacteria concentrations in cooling tower water

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

Cappabianca, R.M.; Jurinski, N.B.; Jurinski, J.B.

1994-05-01

A field study was conducted in which water samples collected from air conditioning cooling water reservoirs of high-rise buildings throughout an urban area were assayed for Legionella and for total bacteria. Buildings included within the study had ongoing biocidal treatment programs for the cooling towers. Separate sample analyses were performed to measure the viable colony concentrations of total bacteria and of Legionella in the process waters. The occurrence and viable counts of Legionella in 304 environmental water samples were determined by inoculating them onto plates of buffered charcoal yeast extract (BCYE) agar medium (a presumptive screening method). The samples weremore » collected during summer months between July and September. BCYE plate cultures of 50 (16.4%) of the samples yielded Legionella with viable counts ranging from 2 to 608 colony forming units per milliliter. In the water samples, 281 (92.4%) yielded viable counts of bacteria that ranged from 9 to 1.2 x 10{sup 6} per milliliter. This study demonstrates that Legionella are commonly present in the water of air conditioning cooling towers and that there is no significant correlation between concurrently sampled culture plate counts of Legionella and total bacteria plate counts. Correspondingly, there is no demonstrated validity for use of total bacterial counts as an inferential surrogate for the concentration of Legionella in the water. 19 refs., 3 figs., 1 tab.« less

Impacts of beach wrack removal via grooming on surf zone water quality.

PubMed

Russell, Todd L; Sassoubre, Lauren M; Zhou, Christina; French-Owen, Darien; Hassaballah, Abdulrahman; Boehm, Alexandria B

2014-02-18

Fecal indicator bacteria (FIB) are used to assess the microbial water quality of recreational waters. Increasingly, nonfecal sources of FIB have been implicated as causes of poor microbial water quality in the coastal environment. These sources are challenging to quantify and difficult to remediate. The present study investigates one nonfecal FIB source, beach wrack (decaying aquatic plants), and its impacts on water quality along the Central California coast. The prevalence of FIB on wrack was studied using a multibeach survey, collecting wrack throughout Central California. The impacts of beach grooming, to remove wrack, were investigated at Cowell Beach in Santa Cruz, California using a long-term survey (two summers, one with and one without grooming) and a 48 h survey during the first ever intensive grooming event. FIB were prevalent on wrack but highly variable spatially and temporally along the nine beaches sampled in Central California. Beach grooming was generally associated with either no change or a slight increase in coastal FIB concentrations and increases in surf zone turbidity and silicate, phosphate, and dissolved inorganic nitrogen concentrations. The findings suggest that beach grooming for wrack removal is not justified as a microbial pollution remediation strategy.

Clinical significance of the FIB-4 index for non-B non-C hepatocellular carcinoma treated with surgical resection.

PubMed

Nishikawa, Hiroki; Osaki, Yukio; Komekado, Hideyuki; Sakamoto, Azusa; Saito, Sumio; Nishijima, Norihiro; Nasu, Akihiro; Arimoto, Akira; Kita, Ryuichi; Kimura, Toru

2015-01-01

The aims of the present study were to examine the relationship between the preoperative FIB-4 index and background liver fibrosis in non-tumor parts obtained from surgical specimens and to investigate whether the FIB-4 index can be a useful predictor for non-B non-C hepatocellular carcinoma (NBNC-HCC) patients treated with surgical resection (SR). A total of 118 patients with NBNC-HCC treated with SR with curative intent were analyzed. Receiver operating characteristic (ROC) curve analysis was performed for calculating the area under the ROC (AUROC) for the FIB-4 index, aspartate aminotransferase (AST) to platelet ratio index, AST to alanine aminotransferase ratio, serum albumin, total bilirubin and platelet count for cirrhosis. We also examined predictors linked to overall survival (OS) and recurrence-free survival (RFS) after SR. The mean patient age was 68.9±9.0 years (93 males and 25 females) with a median observation period of 3.2 years. In extracted surgical specimens, background liver cirrhosis (F4) was observed in 39 patients (33.1%). The mean maximum tumor size was 5.7±3.2 cm. The mean body mass index was 24.3±3.9 kg/m2. The FIB-4 index yielded the highest AUROC for cirrhosis with a level of 0.887 at an optimal cut-off value of 2.97 (sensitivity, 92.3; specificity, 69.6%). In the multivariate analysis, serum α-fetoprotein >40 ng/ml (P=0.026) was the only significant independent predictor linked to OS, while tumor number (P=0.002) and FIB-4 index >2.97 (P=0.044) were significant factors linked to RFS. In conclusion, preoperative FIB-4 index can be a useful predictor for NBNC-HCC patients who undergo SR.

Spin-coated epoxy resin embedding technique enables facile SEM/FIB thickness determination of porous metal oxide ultra-thin films.

PubMed

Peña, B; Owen, G Rh; Dettelbach, K E; Berlinguette, C P

2018-01-25

A facile nonsubjective method was designed to measure porous nonconductive iron oxide film thickness using a combination of a focused ion beam (FIB) and scanning electron microscopy. Iron oxide films are inherently nonconductive and porous, therefore the objective of this investigation was to optimize a methodology that would increase the conductivity of the film to facilitate high resolution imaging with a scanning electron microscopy and to preserve the porous nature of the film that could potentially be damaged by the energy of the FIB. Sputter coating the sample with a thin layer of iridium before creating the cross section with the FIB decreased sample charging and drifting, but differentiating the iron layer from the iridium coating with backscattered electron imaging was not definitive, making accurate assumptions of the delineation between the two metals difficult. Moreover, the porous nature of the film was lost due to beam damage following the FIB process. A thin layer plastication technique was therefore used to embed the porous film in epoxy resin that would provide support for the film during the FIB process. However, the thickness of the resin created using conventional thin layer plastication processing varied across the sample, making the measuring process only possible in areas where the resin layer was at its thinnest. Such variation required navigating the area for ideal milling areas, which increased the subjectivity of the process. We present a method to create uniform thin resin layers, of controlled thickness, that are ideal for quantifying the thickness of porous nonconductive films with FIB/scanning electron microscopy. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Production of NO2/-/ and N2O by nitrifying bacteria at reduced concentrations of oxygen

NASA Technical Reports Server (NTRS)

Goreau, T. J.; Kaplan, W. A.; Wofsy, S. C.; Mcelroy, M. B.; Valois, F. W.; Watson, S. W.

1980-01-01

The influence of oxygen concentration on the production of NO2(-) and N2O by nitrifying marine bacteria of the genus Nitrosomonas is investigated. Pure cultures of the ammonium-oxiding bacteria isolated from the Western Tropical Atlantic Ocean were grown at oxygen partial pressures from 0.005 to 0.2 atm, and concentrations of N2O in the air above the growth medium and dissolved NO2(-) were determined. Decreasing oxygen concentrations are observed to induce a marked decrease in NO2(-) production rates and increase in N2O evolution, leading to an increase of the relative yield of N2O with respect to NO2(-) from 0.3% to nearly 10%. Similar yields of N2O at atmospheric oxygen levels are found for nitrifying bacteria of the genera Nitrosomonas, Nitrosolobus, Nitrosospira and Nitrosococcus, while nitrite-oxydizing bacteria and a dinoflagellate did not produce detectable quantities of N2O. Results support the view that nitrification is a major source of N2O in the environment.

Spatial and temporal microbial pollution patterns in a tropical estuary during high and low river flow conditions.

PubMed

Wiegner, T N; Edens, C J; Abaya, L M; Carlson, K M; Lyon-Colbert, A; Molloy, S L

2017-01-30

Spatial and temporal patterns of coastal microbial pollution are not well documented. Our study examined these patterns through measurements of fecal indicator bacteria (FIB), nutrients, and physiochemical parameters in Hilo Bay, Hawai'i, during high and low river flow. >40% of samples tested positive for the human-associated Bacteroides marker, with highest percentages near rivers. Other FIB were also higher near rivers, but only Clostridium perfringens concentrations were related to discharge. During storms, FIB concentrations were three times to an order of magnitude higher, and increased with decreasing salinity and water temperature, and increasing turbidity. These relationships and high spatial resolution data for these parameters were used to create Enterococcus spp. and C. perfringens maps that predicted exceedances with 64% and 95% accuracy, respectively. Mapping microbial pollution patterns and predicting exceedances is a valuable tool that can improve water quality monitoring and aid in visualizing FIB hotspots for management actions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Attempt of correlative observation of morphological synaptic connectivity by combining confocal laser-scanning microscope and FIB-SEM for immunohistochemical staining technique.

PubMed

Sonomura, Takahiro; Furuta, Takahiro; Nakatani, Ikuko; Yamamoto, Yo; Honma, Satoru; Kaneko, Takeshi

2014-11-01

Ten years have passed since a serial block-face scanning electron microscopy (SBF-SEM) method was developed [1]. In this innovative method, samples were automatically sectioned with an ultramicrotome placed inside a scanning electron microscope column, and the block surfaces were imaged one after another by SEM to capture back-scattered electrons. The contrast-inverted images obtained by the SBF-SEM were very similar to those acquired using conventional TEM. SFB-SEM has made easy to acquire image stacks of the transmission electron microscopy (TEM) in the mesoscale, which is taken with the confocal laser-scanning microcopy(CF-LSM).Furthermore, serial-section SEM has been combined with the focused ion beam (FIB) milling method [2]. FIB-incorporated SEM (FIB-SEM) has enabled the acquisition of three-dimensional images with a higher z-axis resolution com- pared to ultramicrotome-equipped SEM.We tried immunocytochemistry for FIB-SEM and correlated this immunoreactivity with that in CF-LSM. Dendrites of neurons in the rat neostriatum were visualized using a recombinant viral vector. Moreover, the thalamostriatal afferent terminals were immunolabeled with Cy5 fluorescence for vesicular glutamate transporter 2 (VGluT2). After detection of the sites of terminals apposed to the dendrites by using CF-LSM, GFP and VGluT2 immunoreactivities were further developed for EM by using immunogold/silver enhancement and immunoperoxidase/diaminobenzidine (DAB) methods, respectively.We showed that conventional immuno-cytochemical staining for TEM was applicable to FIB-SEM. Furthermore, several synaptic contacts, which were thought to exist on the basis of CF-LSM findings, were confirmed with FIB-SEM, revealing the usefulness of the combined method of CF-LSM and FIB-SEM. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Test of direct and indirect effects of agrochemicals on the survival of fecal indicator bacteria.

PubMed

Staley, Zachery R; Rohr, Jason R; Harwood, Valerie J

2011-12-01

Water bodies often receive agrochemicals and animal waste carrying fecal indicator bacteria (FIB) and zoonotic pathogens, but we know little about the effects of agrochemicals on these microbes. We assessed the direct effects of the pesticides atrazine, malathion, and chlorothalonil and inorganic fertilizer on Escherichia coli and enterococcal survival in simplified microcosms held in the dark. E. coli strain composition in sediments and water column were positively correlated, but none of the agrochemicals had significant direct effects on E. coli strain composition or on densities of culturable FIBs. In a companion study, microcosms with nondisinfected pond water and sediments were exposed to or shielded from sunlight to examine the potential indirect effects of atrazine and inorganic fertilizer on E. coli. The herbicide atrazine had no effect on E. coli in dark-exposed microcosms containing natural microbial and algal communities. However, in light-exposed microcosms, atrazine significantly lowered E. coli densities in the water column and significantly increased densities in the sediment compared to controls. This effect appears to be mediated by the effects of atrazine on algae, given that atrazine significantly reduced phytoplankton, which was a positive and negative predictor of E. coli densities in the water column and sediment, respectively. These data suggest that atrazine does not directly affect the survival of FIB, rather that it indirectly alters the distribution and abundance of E. coli by altering phytoplankton and periphyton communities. These results improve our understanding of the influence of agricultural practices on FIB densities in water bodies impacted by agricultural runoff.

Origin and spatial-temporal distribution of faecal bacteria in a bay of Lake Geneva, Switzerland.

PubMed

Poté, John; Goldscheider, Nico; Haller, Laurence; Zopfi, Jakob; Khajehnouri, Fereidoun; Wildi, Walter

2009-07-01

The origin and distribution of microbial contamination in Lake Geneva's most polluted bay were assessed using faecal indicator bacteria (FIB). The lake is used as drinking water, for recreation and fishing. During 1 year, water samples were taken at 23 points in the bay and three contamination sources: a wastewater treatment plant (WWTP), a river and a storm water outlet. Analyses included Escherichia coli, enterococci (ENT), total coliforms (TC), and heterotrophic plate counts (HPC). E. coli input flux rates from the WWTP can reach 2.5 x 10(10) CFU/s; those from the river are one to three orders of magnitude lower. Different pathogenic Salmonella serotypes were identified in water from these sources. FIB levels in the bay are highly variable. Results demonstrate that (1) the WWTP outlet at 30 m depth impacts near-surface water quality during holomixis in winter; (2) when the lake is stratified, the effluent water is generally trapped below the thermocline; (3) during major floods, upwelling across the thermocline may occur; (4) the river permanently contributes to contamination, mainly near the river mouth and during floods, when the storm water outlet contributes additionally; (5) the lowest FIB levels in the near-surface water occur during low-flow periods in the bathing season.

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China.

PubMed

Liao, Rui; Fu, Yi-Peng; Wang, Ting; Deng, Zhi-Gang; Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-03

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy.

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China

PubMed Central

Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-01

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy. PMID:27662665

Evaluation of APRI and FIB-4 scoring systems for non-invasive assessment of hepatic fibrosis in chronic hepatitis B patients.

PubMed

Kim, W Ray; Berg, Thomas; Asselah, Tarik; Flisiak, Robert; Fung, Scott; Gordon, Stuart C; Janssen, Harry L A; Lampertico, Pietro; Lau, Daryl; Bornstein, Jeffrey D; Schall, Raul E Aguilar; Dinh, Phillip; Yee, Leland J; Martins, Eduardo B; Lim, Seng Gee; Loomba, Rohit; Petersen, Jörg; Buti, Maria; Marcellin, Patrick

2016-04-01

While the gold standard in the assessment of liver fibrosis remains liver biopsy, non-invasive methods have been increasingly used for chronic hepatitis B (CHB). This study aimed to evaluate the performance of two commonly used non-invasive scoring systems (aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4)) to predict fibrosis stage in CHB patients. Demographic, histologic and clinical laboratory data from two trials investigating tenofovir disoproxil fumarate in CHB were analyzed. Predicted fibrosis stage, based on established scales and cut-off values for APRI and FIB-4 scores, was compared with Ishak scores obtained from liver biopsy at baseline and at 240 week follow-up. In the 575 patients with a baseline liver biopsy, APRI and FIB-4 scores correlated with Ishak stage (p<0.01); however extensive overlap in the distribution of both scores across Ishak stages prevented accurate determination of fibrosis. The majority (81-89%) of patients with advanced fibrosis or cirrhosis were missed by the scores. Similarly, 71% patients without fibrosis were misclassified as having clinically significant fibrosis. APRI and FIB-4 scores at week 240 tended to be low and underestimate fibrosis stage in the patients with liver biopsies after 240 weeks of therapy. APRI or FIB-4 reduction did not correlate with fibrosis regression after 240 weeks of antiviral therapy. APRI and FIB-4 scores are not suitable for use in clinical practice in CHB patients for assessment of hepatic fibrosis according to Ishak stage, especially in gauging improvements in liver fibrosis following therapy. Copyright © 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Comparison of the prognostic value of liver biopsy and FIB-4 index in patients coinfected with HIV and hepatitis C virus.

PubMed

Berenguer, Juan; Zamora, Francisco X; Aldámiz-Echevarría, Teresa; Von Wichmann, Miguel A; Crespo, Manel; López-Aldeguer, José; Carrero, Ana; Montes, Marisa; Quereda, Carmen; Téllez, María J; Galindo, María J; Sanz, José; Santos, Ignacio; Guardiola, Josep M; Barros, Carlos; Ortega, Enrique; Pulido, Federico; Rubio, Rafael; Mallolas, Josep; Tural, Cristina; Jusdado, Juan J; Pérez, Gloria; Díez, Cristina; Álvarez-Pellicer, Julio; Esteban, Herminia; Bellón, José M; González-García, Juan

2015-03-15

We compared the prognostic value of liver biopsy (LB) and FIB-4 index in patients with human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfection. We studied patients from the Grupo de Estudio del SIDA 3603 study cohort, in whom fibrosis was evaluated at baseline using both LB (Metavir score) and FIB-4 index. We assessed overall death (OD) and liver-related events (LREs), defined as decompensation or hepatocellular carcinoma, whichever occurred first. We used receiver operating characteristic (ROC) curves to determine the ability of LB and FIB-4 to predict outcomes. We also assessed the association between advanced fibrosis-LB (F3 or greater) or FIB-4 (≥3.25)-and outcomes using multivariate Cox regression analysis. The study sample comprised 903 patients (328 with sustained virologic response [SVR]). Baseline fibrosis by LB was as follows: F0, n = 71; F1, n = 242; F2, n = 236; F3, n = 236; F4, n = 118. Fibrosis by FIB-4 was as follows: ≤1, n = 148; >1 to <3.25, n = 597; ≥3.25, n = 158. After a median follow-up of 62 months, there were 46 deaths and 71 LREs. The area under the ROC curves for OD/LREs was 0.648 and 0.742 for LB and FIB-4, respectively (P = .006). Similar results were found for patients without SVR and for OD and LREs separately. The adjusted hazard ratios of OD or LRE were 1.740 (95% confidence interval [CI], 1.119-2.7.06; P = .014) for advanced fibrosis assessed by LB and 3.896 (95% CI, 2.463-6.160; P < .001) assessed by FIB-4. FIB-4 outperformed LB as a predictor of OD and LRE. These findings are of relevance for clinical practice and research and call into question the role of LB as a gold standard for assessing prognosis in HIV/HCV coinfection. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Faecal indicator bacteria enumeration in beach sand: a comparison study of extraction methods in medium to coarse sands.

PubMed

Boehm, A B; Griffith, J; McGee, C; Edge, T A; Solo-Gabriele, H M; Whitman, R; Cao, Y; Getrich, M; Jay, J A; Ferguson, D; Goodwin, K D; Lee, C M; Madison, M; Weisberg, S B

2009-11-01

The absence of standardized methods for quantifying faecal indicator bacteria (FIB) in sand hinders comparison of results across studies. The purpose of the study was to compare methods for extraction of faecal bacteria from sands and recommend a standardized extraction technique. Twenty-two methods of extracting enterococci and Escherichia coli from sand were evaluated, including multiple permutations of hand shaking, mechanical shaking, blending, sonication, number of rinses, settling time, eluant-to-sand ratio, eluant composition, prefiltration and type of decantation. Tests were performed on sands from California, Florida and Lake Michigan. Most extraction parameters did not significantly affect bacterial enumeration. anova revealed significant effects of eluant composition and blending; with both sodium metaphosphate buffer and blending producing reduced counts. The simplest extraction method that produced the highest FIB recoveries consisted of 2 min of hand shaking in phosphate-buffered saline or deionized water, a 30-s settling time, one-rinse step and a 10 : 1 eluant volume to sand weight ratio. This result was consistent across the sand compositions tested in this study but could vary for other sand types. Method standardization will improve the understanding of how sands affect surface water quality.

Effects of low concentrations of the phenylurea herbicide diuron on biofilm algae and bacteria.

PubMed

Ricart, Marta; Barceló, Damià; Geiszinger, Anita; Guasch, Helena; de Alda, Miren López; Romaní, Anna M; Vidal, Gemma; Villagrasa, Marta; Sabater, Sergi

2009-09-01

A system of recirculating channels was used in this study to examine the long-term effects (29d) of environmentally realistic concentrations of the herbicide diuron (from 0.07 to 7 microg L(-1)) on biofilm communities. The autotrophic activity of biofilms was affected by this herbicide, as reflected by a marked decrease in the photosynthetic efficiency. Diuron exposure also increased chlorophyll-a content and reduced the biovolume of diatom taxa at low concentrations. The effects on bacteria were also remarkable. Bacterial abundance was reduced after a week of exposure to the herbicide at a range of concentrations. Effects were on the number of live bacteria and on the increase in the leucine-aminopeptidase activity. It is suggested that inputs of herbicides to the river ecosystem at low concentrations may cause a chain of effects in the biofilm, which include inhibitory effects on algae but also indirect effects on the relationships between biofilm components.

Microstructural analysis of 800H steel exposed at test operation in HTHL by using FIB-SEM and HRTEM techniques

NASA Astrophysics Data System (ADS)

Marušáková, Daniela; Bublíková, Petra; Berka, Jan; Vávrovcová, Zuzana; Burda, Jaroslav

2017-09-01

To understand the degradation process of metal materials which are used in power engineering, appropriate evaluation procedure is necessary to ensure. In that order, the degradation of alloy 800H during the first period of test operation in High Temperature Helium Loop (HTHL) was tested. Experiment was carried out in atmosphere of pure technical helium with purity 4.6 containing only residual concentration of moisture up to 300 vppm. Parameters during the operation test were not constant, process was interrupted several times. The maximum temperature on specimens during this period was 750 °C, average temperature was 460 °C, gas pressure ranged from 3 to 6 MPa and gas flow from 3 to 9 gs-1. Total duration of the test was 264 h. After the exposure the degradation of specimens was investigated by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). Using the technique of Focused Ion Beam (FIB) integrated within SEM the transparent samples with quality surface parameters were obtained for TEM analysis. FIB technique in combination with High Resolution TEM ensured the guaranteed methodology of exposed sample preparation and precise description of changes in this kind of material.

Several methods for concentrating bacteria in fluid samples

NASA Technical Reports Server (NTRS)

Thomas, R. R.

1976-01-01

The sensitivities of the firefly luciferase - ATP flow system and luminol flow system were established as 300,000 E. coli per milliliter and 10,000 E. coli per milliliter respectively. To achieve the detection limit of 1,000 bacteria per milliliter previously established, a method of concentrating microorganisms using a sartorius membrane filter system is investigated. Catalase in 50% ethanol is found to be a stable luminol standard and can be used up to 24 hours with only a 10% loss of activity. The luminol reagent is also stable over a 24 hour period. A method of preparing relatively inexpensive luciferase from desiccated firefly tails is developed.

Decay Of Bacterial Pathogens, Fecal Indicators, And Real-Time Quantitative PCR Genetic Markers In Manure-Amended Soils

EPA Science Inventory

This study examined persistence and decay of bacterial pathogens, fecal indicator bacteria (FIB), and emerging real-time quantitative PCR (qPCR) genetic markers for rapid detection of fecal pollution in manure-amended agricultural soils. Known concentrations of transformed green...

Water Quality Conditions Associated with Cattle Grazing and Recreation on National Forest Lands

PubMed Central

Roche, Leslie M.; Kromschroeder, Lea; Atwill, Edward R.; Dahlgren, Randy A.; Tate, Kenneth W.

2013-01-01

There is substantial concern that microbial and nutrient pollution by cattle on public lands degrades water quality, threatening human and ecological health. Given the importance of clean water on multiple-use landscapes, additional research is required to document and examine potential water quality issues across common resource use activities. During the 2011 grazing-recreation season, we conducted a cross sectional survey of water quality conditions associated with cattle grazing and/or recreation on 12 public lands grazing allotments in California. Our specific study objectives were to 1) quantify fecal indicator bacteria (FIB; fecal coliform and E. coli), total nitrogen, nitrate, ammonium, total phosphorus, and soluble-reactive phosphorus concentrations in surface waters; 2) compare results to a) water quality regulatory benchmarks, b) recommended maximum nutrient concentrations, and c) estimates of nutrient background concentrations; and 3) examine relationships between water quality, environmental conditions, cattle grazing, and recreation. Nutrient concentrations observed throughout the grazing-recreation season were at least one order of magnitude below levels of ecological concern, and were similar to U.S. Environmental Protection Agency (USEPA) estimates for background water quality conditions in the region. The relative percentage of FIB regulatory benchmark exceedances widely varied under individual regional and national water quality standards. Relative to USEPA’s national E. coli FIB benchmarks–the most contemporary and relevant standards for this study–over 90% of the 743 samples collected were below recommended criteria values. FIB concentrations were significantly greater when stream flow was low or stagnant, water was turbid, and when cattle were actively observed at sampling. Recreation sites had the lowest mean FIB, total nitrogen, and soluble-reactive phosphorus concentrations, and there were no significant differences in FIB and

Cross-sectional TEM specimen preparation for W/B{sub 4}C multilayer sample using FIB

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

Mondal, Puspen, E-mail: puspen@rrcat.gov.in; Pradhan, P. C.; Tiwari, Pragya

2016-05-23

A recent emergence of a cross-beam scanning electron microscopy (SEM)/focused-ion-beam (FIB) system have given choice to fabricate cross-sectional transmission electron microscopy (TEM) specimen of thin film multilayer sample. A 300 layer pair thin film multilayer sample of W/B{sub 4}C was used to demonstrate the specimen lift-out technique in very short time as compared to conventional cross-sectional sample preparation technique. To get large area electron transparent sample, sample prepared by FIB is followed by Ar{sup +} ion polishing at 2 kV with grazing incident. The prepared cross-sectional sample was characterized by transmission electron microscope.

A novel approach to TEM preparation with a (7-axis stage) triple-beam FIB-SEM system

NASA Astrophysics Data System (ADS)

Clarke, Jamil J.

2015-10-01

Preparation of lamellae from bulk to grid for Cs-corrected Transmission Electron Microscope (TEM) observation has mostly become routine work on the latest FIB-SEM systems, with standardized techniques that often are left to automation for the initial steps. The finalization of lamellae however, has mostly become, non-routine, non-repeatable and often driven by user experience level in most cases to produce high quality damage-less cross section. Materials processing of the latest technologies, with ever-shrinking Nano-sized structures pose challenges to modern FIB-SEM systems. This can often lead to specialized techniques and hyper-specific functions for producing ultra-thin high quality lamellae that often are lab specific, preventing practical use of such techniques across multiple materials and applications. Several factors that should be incorporated in processing fine structured materials successfully include how the use of electron and ion scan conditions can affect a thin section during ion milling, the type of ion species applied for material processing during the finalization of lamellae with gallium ions or of a smaller ion species type such as Ar/Xe, sample orientation of the lamella during the thinning process which is linked to ion beam incident angle as a direct relationship in the creation of waterfall effects or curtain effects, and how software can be employed to aid in the reduction of these artifacts with reproducible results regardless of FIB-SEM experience for site-specific lift outs. A traditional TEM preparation was performed of a fine structure specimen in pursuit of a process technique to produce a high quality TEM lamella which would address all of the factors mentioned. These new capabilities have been refined and improved upon during the FIB-SEM design and development stages with an end result of a new approach that yields an improvement in quality by the reduction of common ion milling artifacts such as curtain effects, amorphous

Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

PubMed

Pouillot, Régis; Chen, Yuhuan; Hoelzer, Karin

2015-02-01

When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise. Published by Elsevier Ltd.

A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions.

PubMed

Rochelle-Newall, Emma; Nguyen, Thi Mai Huong; Le, Thi Phuong Quynh; Sengtaheuanghoung, Oloth; Ribolzi, Olivier

2015-01-01

Given the high numbers of deaths and the debilitating nature of diseases caused by the use of unclean water it is imperative that we have an understanding of the factors that control the dispersion of water borne pathogens and their respective indicators. This is all the more important in developing countries where significant proportions of the population often have little or no access to clean drinking water supplies. Moreover, and notwithstanding the importance of these bacteria in terms of public health, at present little work exists on the persistence, transfer and proliferation of these pathogens and their respective indicator organisms, e.g., fecal indicator bacteria (FIB) such as Escherichia coli and fecal coliforms in humid tropical systems, such as are found in South East Asia or in the tropical regions of Africa. Both FIB and the waterborne pathogens they are supposed to indicate are particularly susceptible to shifts in water flow and quality and the predicted increases in rainfall and floods due to climate change will only exacerbate the problems of contamination. This will be furthermore compounded by the increasing urbanization and agricultural intensification that developing regions are experiencing. Therefore, recognizing and understanding the link between human activities, natural process and microbial functioning and their ultimate impacts on human health are prerequisites for reducing the risks to the exposed populations. Most of the existing work in tropical systems has been based on the application of temperate indicator organisms, models and mechanisms regardless of their applicability or appropriateness for tropical environments. Here, we present a short review on the factors that control FIB dynamics in temperate systems and discuss their applicability to tropical environments. We then highlight some of the knowledge gaps in order to stimulate future research in this field in the tropics.

A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions

PubMed Central

Rochelle-Newall, Emma; Nguyen, Thi Mai Huong; Le, Thi Phuong Quynh; Sengtaheuanghoung, Oloth; Ribolzi, Olivier

2015-01-01

Given the high numbers of deaths and the debilitating nature of diseases caused by the use of unclean water it is imperative that we have an understanding of the factors that control the dispersion of water borne pathogens and their respective indicators. This is all the more important in developing countries where significant proportions of the population often have little or no access to clean drinking water supplies. Moreover, and notwithstanding the importance of these bacteria in terms of public health, at present little work exists on the persistence, transfer and proliferation of these pathogens and their respective indicator organisms, e.g., fecal indicator bacteria (FIB) such as Escherichia coli and fecal coliforms in humid tropical systems, such as are found in South East Asia or in the tropical regions of Africa. Both FIB and the waterborne pathogens they are supposed to indicate are particularly susceptible to shifts in water flow and quality and the predicted increases in rainfall and floods due to climate change will only exacerbate the problems of contamination. This will be furthermore compounded by the increasing urbanization and agricultural intensification that developing regions are experiencing. Therefore, recognizing and understanding the link between human activities, natural process and microbial functioning and their ultimate impacts on human health are prerequisites for reducing the risks to the exposed populations. Most of the existing work in tropical systems has been based on the application of temperate indicator organisms, models and mechanisms regardless of their applicability or appropriateness for tropical environments. Here, we present a short review on the factors that control FIB dynamics in temperate systems and discuss their applicability to tropical environments. We then highlight some of the knowledge gaps in order to stimulate future research in this field in the tropics. PMID:25941519

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method

PubMed Central

Chen, Bor-Sen

2016-01-01

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella’s rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the “brake component” in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each “brake component” were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the “brake component”. Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate “brake component” in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains. PMID:27096615

Virtual Beach 3: User's Guide

EPA Science Inventory

Virtual Beach version 3 (VB3) is a decision support tool that constructs site-specific statistical models to predict fecal indicator bacteria (FIB) concentrations at recreational beaches. VB3 is primarily designed for beach managers responsible for making decisions regarding beac...

Comparing Data Input Requirements of Statistical vs. Process-based Watershed Models Applied for Prediction of Fecal Indicator and Pathogen Levels in Recreational Beaches

EPA Science Inventory

Same day prediction of fecal indicator bacteria (FIB) concentrations and bather protection from the risk of exposure to pathogens are two important goals of implementing a modeling program at recreational beaches. Sampling efforts for modelling applications can be expensive and t...

Pilot study of using UAV to reveal spatial patterns of indicator bacteria concentrations in ponds and reservoirs used for irrigation

USDA-ARS?s Scientific Manuscript database

Determination of indicator bacteria concentrations in irrigation water recently became mandatory for farmers. These concentrations are known to have large spatial variability in ponds and reservoirs. This variability is partially attributed to affinity of indicator bacteria to algae accumulations. W...

Precise and economic FIB/SEM for CLEM: with 2 nm voxels through mitosis.

PubMed

Luckner, Manja; Wanner, Gerhard

2018-05-23

A portfolio is presented documenting economic, high-resolution correlative focused ion beam scanning electron microscopy (FIB/SEM) in routine, comprising: (i) the use of custom-labeled slides and coverslips, (ii) embedding of cells in thin, or ultra-thin resin layers for correlative light and electron microscopy (CLEM) and (iii) the claim to reach the highest resolution possible with FIB/SEM in xyz. Regions of interest (ROIs) defined in light microscope (LM), can be relocated quickly and precisely in SEM. As proof of principle, HeLa cells were investigated in 3D context at all stages of the cell cycle, documenting ultrastructural changes during mitosis: nuclear envelope breakdown and reassembly, Golgi degradation and reconstitution and the formation of the midzone and midbody.

Validation of the FIB-4 index for evaluation of fibrosis in patients with recurrent hepatitis C after living donor liver transplantation: A single center experience.

PubMed

Kitajima, Toshihiro; Kaido, Toshimi; Hamaguchi, Yuhei; Yagi, Shintaro; Taura, Kojiro; Fujimoto, Yasuhiro; Hatano, Etsuro; Okajima, Hideaki; Haga, Hironori; Uemoto, Shinji

2016-07-01

The FIB-4 index has been proposed as a simple, non-invasive surrogate marker of liver fibrosis in patients with hepatitis C virus (HCV). However, the utility of FIB-4 in HCV positive patients after living donor liver transplantation (LDLT) has not been assessed. The aim of this study was to evaluate the efficacy of FIB-4 in the detection of significant liver graft fibrosis caused by recurrent HCV infection after LDLT compared with other simple fibrosis markers. A total of 259 liver biopsies (LB) with evidence of recurrent HCV were taken from 110 HCV positive LDLT patients who had undergone concomitant splenectomy before administration of antiviral therapy. In LB performed at 3 months or later after LT (n = 202, subject group), FIB-4 was compared between fibrosis stages and the accuracy of FIB-4 in predicting significant fibrosis (METAVIR, F ≥ 2) was assessed compared with aspartate aminotransferase (AST) to alanine aminotransferase (ALT) ratio, age-platelet index, and AST to platelet ratio index (APRI). FIB-4 was significantly different between all fibrosis stages (F0 and F1-F4, P = 0.022; F0/1 and F2-F4, P < 0.0005; and F0-F2 and F3F4, P = 0.034) and provided the best area under the receiver-operator curve (AUROC) compared with other markers (FIB-4, 0.711; APRI, 0.693; age-platelet index, 0.663; and AST to ALT ratio, 0.562). The optimal cut-off value to identify significant fibrosis was 2.20 with 65% sensitivity and 69% specificity. FIB-4 is a more reliable marker for diagnosing significant liver fibrosis than APRI, age-platelet index, and AST to ALT ratio in LDLT patients with HCV. © 2015 The Japan Society of Hepatology.

FIB/SEM technology and Alzheimer's disease: three-dimensional analysis of human cortical synapses.

PubMed

Blazquez-Llorca, Lidia; Merchán-Pérez, Ángel; Rodríguez, José-Rodrigo; Gascón, Jorge; DeFelipe, Javier

2013-01-01

The quantification and measurement of synapses is a major goal in the study of brain organization in both health and disease. Serial section electron microscopy (EM) is the ideal method since it permits the direct quantification of crucial features such as the number of synapses per unit volume or the distribution and size of synapses. However, a major limitation is that obtaining long series of ultrathin sections is extremely time-consuming and difficult. Consequently, quantitative EM studies are scarce and the most common method employed to estimate synaptic density in the human brain is indirect, by counting at the light microscopic level immunoreactive puncta using synaptic markers. The recent development of automatic EM methods in experimental animals, such as the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM), are opening new avenues. Here we explored the utility of FIB/SEM to examine the cerebral cortex of Alzheimer's disease patients. We found that FIB/SEM is an excellent tool to study in detail the ultrastructure and alterations of the synaptic organization of the human brain. Using this technology, it is possible to reconstruct different types of plaques and the surrounding neuropil to find new aspects of the pathological process associated with the disease, namely; to count the exact number and types of synapses in different regions of the plaques, to study the spatial distribution of synapses, and to analyze the morphology and nature of the various types of dystrophic neurites and amyloid deposits.

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake.

PubMed

Staley, Christopher; Reckhow, Kenneth H; Lukasik, Jerzy; Harwood, Valerie J

2012-11-01

We investigated the potential for a variety of environmental reservoirs to harbor or contribute fecal indicator bacteria (FIB), DNA markers of human fecal contamination, and human pathogens to a freshwater lake. We hypothesized that submerged aquatic vegetation (SAV), sediments, and stormwater act as reservoirs and/or provide inputs of FIB and human pathogens to this inland water. Analysis included microbial source tracking (MST) markers of sewage contamination (Enterococcus faecium esp gene, human-associated Bacteroides HF183, and human polyomaviruses), pathogens (Salmonella, Cryptosporidium, Giardia, and enteric viruses), and FIB (fecal coliforms, Escherichia coli, and enterococci). Bayesian analysis was used to assess relationships among microbial and physicochemical variables. FIB in the water were correlated with concentrations in SAV and sediment. Furthermore, the correlation of antecedent rainfall and major rain events with FIB concentrations and detection of human markers and pathogens points toward multiple reservoirs for microbial contaminants in this system. Although pathogens and human-source markers were detected in 55% and 21% of samples, respectively, markers rarely coincided with pathogen detection. Bayesian analysis revealed that low concentrations (<45 CFU × 100 ml(-1)) of fecal coliforms were associated with 93% probability that pathogens would not be detected; furthermore the Bayes net model showed associations between elevated temperature and rainfall with fecal coliform and enterococci concentrations, but not E. coli. These data indicate that many under-studied matrices (e.g. SAV, sediment, stormwater) are important reservoirs for FIB and potentially human pathogens and demonstrate the usefulness of Bayes net analysis for water quality assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

AST-platelet ratio index, Forns index and FIB-4 in the prediction of significant fibrosis and cirrhosis in patients with chronic hepatitis C.

PubMed

Güzelbulut, Fatih; Çetınkaya, Züleyha Akkan; Sezıklı, Mesut; Yaşar, Bülent; Ozkara, Selvinaz; Övünç, Ayşe Oya Kurdaş

2011-06-01

The aim of this study was to evaluate the diagnostic accuracy of aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 for the assessment of hepatic fibrosis in chronic hepatitis C patients by comparison with liver biopsy. We retrospectively reviewed our computerized data of chronic hepatitis C patients who admitted to the Gastroenterology Clinic between 2004 and 2008. Treatment-naive chronic hepatitis C patients who had undergone liver biopsy and had laboratory test results allowing the calculation of aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 were included in this study. The degree of fibrosis was scored according to the METAVIR staging system. Significant fibrosis was defined as F2-4 and cirrhosis as F4. Aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 were calculated based on the original studies. Tests results were compared between groups F0-1 (no or mild fibrosis) versus F2-4 (significant fibrosis) and F03 (no cirrhosis) versus F4 (cirrhosis). One hundred and fifty patients with chronic hepatitis C were included in this study. The areas under the ROC curves of the Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 to predict significant fibrosis were 0.795, 0.774 and 0.764, respectively. The area under the ROC curves of the Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 to predict cirrhosis were 0.879, 0.839 and 0.874, respectively. The Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 were accurate noninvasive blood tests to predict the presence or absence of significant fibrosis and cirrhosis in half of the chronic hepatitis C patients. The Forns index was slightly better than the aspartate aminotransferase-platelet ratio index and FIB-4 in the prediction of significant fibrosis and cirrhosis.

Effects of ceiling-mounted HEPA-UV air filters on airborne bacteria concentrations in an indoor therapy pool building.

PubMed

Kujundzic, Elmira; Zander, David A; Hernandez, Mark; Angenent, Largus T; Henderson, David E; Miller, Shelly L

2005-02-01

The purpose of this study was to assess the effectiveness of a new generation of high-volume, ceiling-mounted high-efficiency particulate air (HEPA)-ultraviolet (UV) air filters (HUVAFs) for their ability to remove or inactivate bacterial aerosol. In an environmentally controlled full-scale laboratory chamber (87 m3), and an indoor therapy pool building, the mitigation ability of air filters was assessed by comparing concentrations of total bacteria, culturable bacteria, and airborne endotoxin with and without the air filters operating under otherwise similar conditions. Controlled chamber tests with pure cultures of aerosolized Mycobacterium parafortuitum cells showed that the HUVAF unit tested provided an equivalent air-exchange rate of 11 hr(-1). Using this equivalent air-exchange rate as a design basis, three HUVAFs were installed in an indoor therapy pool building for bioaerosol mitigation, and their effectiveness was studied over a 2-year period. The HUVAFs reduced concentrations of culturable bacteria by 69 and 80% during monitoring periods executed in respective years. The HUVAFs reduced concentrations of total bacteria by 12 and 76% during the same monitoring period, respectively. Airborne endotoxin concentrations were not affected by the HUVAF operation.

Long-term prognosis of patients with chronic hepatitis C who did not receive interferon-based therapy: causes of death and analysis based on the FIB-4 index.

PubMed

Tada, Toshifumi; Kumada, Takashi; Toyoda, Hidenori; Kiriyama, Seiki; Tanikawa, Makoto; Hisanaga, Yasuhiro; Kanamori, Akira; Kitabatake, Shusuke; Yama, Tsuyoki; Tanaka, Junko

2016-04-01

Interferon (IFN)-based therapy has been reported to reduce the liver-related mortality rate in patients with chronic hepatitis C virus (HCV) infection. However, predictors of survival and causes of death, including non-liver-related causes, have not been sufficiently investigated in chronic HCV patients who have not received IFN-based therapy. A total of 1723 patients with chronic HCV infection who were not treated with IFN-based therapy were enrolled. Survival from liver-related diseases and non-liver-related diseases and causes of death were analyzed on the basis of the fibrosis-4 (FIB-4) index, an index of liver fibrosis. The median follow-up duration was 10.3 years. Of 465 patients who died during the follow-up period, 48.4 % died of liver-related diseases; of the remainder, 51.6 % died of non-liver-related diseases. On the basis of FIB-4 index, the liver-related mortality rate increased as the FIB-4 index increased: 16.1 % in the FIB-4 index < 1.45 group, 36.7 % in the 1.45 ≤ FIB-4 index ≤ 3.25 group, and 58.7 % in the FIB-4 index > 3.25 group (p < 0.001). Conversely, the non-liver-related mortality rate decreased as the FIB-4 index increased: 83.9, 63.3, and 41.3 %, respectively (p = 0.001). In the multivariate analysis, a FIB-4 index greater than 3.25 was identified as a risk factor independently associated with both liver-related death (hazard ratio 13.020; 95 % confidence interval 4.155-40.770) and non-liver-related death (hazard ratio 1.667; 95 % confidence interval 1.188-2.340). Patients with chronic HCV infection and an elevated FIB-4 index may benefit from monitoring not only for the development of liver-related diseases but also for the development of non-liver-related diseases.

Can transient elastography, Fib-4, Forns Index, and Lok Score predict esophageal varices in HCV-related cirrhotic patients?

PubMed

Hassan, Eman M; Omran, Dalia A; El Beshlawey, Mohamad L; Abdo, Mahmoud; El Askary, Ahmad

2014-02-01

Gastroesophageal varices are present in approximately 50% of patients with liver cirrhosis. The aim of this study was to evaluate liver stiffness measurement (LSM), Fib-4, Forns Index and Lok Score as noninvasive predictors of esophageal varices (EV). This prospective study included 65 patients with HCV-related liver cirrhosis. All patients underwent routine laboratory tests, transient elastograhy (TE) and esophagogastroduodenoscopy. FIB-4, Forns Index and Lok Score were calculated. The diagnostic performances of these methods were assessed using sensitivity, specificity, positive predictive value, negative predictive value, accuracy and receiver operating characteristic curves. All predictors (LSM, FIB-4, Forns Index and Lok Score) demonstrated statistically significant correlation with the presence and the grade of EV. TE could diagnose EV at a cutoff value of 18.2kPa. Fib-4, Forns Index, and Lok Score could diagnose EV at cutoff values of 2.8, 6.61 and 0.63, respectively. For prediction of large varices (grade 2, 3), LSM showed the highest accuracy (80%) with a cutoff of 22.4kPa and AUROC of 0.801. Its sensitivity was 84%, specificity 72%, PPV 84% and NPV 72%. The diagnostic accuracies of FIB-4, Forns Index and Lok Score were 70%, 70% and76%, respectively, at cutoffs of 3.3, 6.9 and 0.7, respectively. For diagnosis of large esophageal varices, adding TE to each of the other diagnostic indices (serum fibrosis scores) increased their sensitivities with little decrease in their specificities. Moreover, this combination decreased the LR- in all tests. Noninvasive predictors can restrict endoscopic screening. This is very important as non invasiveness is now a major goal in hepatology. Copyright © 2013 Elsevier España, S.L. and AEEH y AEG. All rights reserved.

Investigation of properties of nanobridge Josephson junctions and superconducting tracks fabricated by FIB

NASA Astrophysics Data System (ADS)

Li, B.; Godfrey, T.; Cox, D.; Li, T.; Gallop, J.; Galer, S.; Nisbet, A.; Romans, Ed; Hao, L.

2018-02-01

An important requirement across a range of sensitive detectors is to determine accurately the energy deposited by the impact of a particle in a small volume. The particle may be anything from a visible photon through to an X-ray or massive charged particle. We have been developing nanobridge Josephson junctions based SQUIDs and nanoSQUID devices covering the entire range of particle detection energies from 1eV to MeV. In this paper we discuss some developments in nanobridge Josephson junctions fabrication using focussed ion beam (FIB) and how these developments impact future applications. We focus on tuning of the transition temperature of a superconducting thin-film absorber, with the aim to match the absorber Tc to the working temperature range of the SQUID and also on using a new Xe FIB to improve Josephson junction and superconducting film quality.

SOME STATISTICAL ISSUES RELATED TO MULTIPLE LINEAR REGRESSION MODELING OF BEACH BACTERIA CONCENTRATIONS

EPA Science Inventory

As a fast and effective technique, the multiple linear regression (MLR) method has been widely used in modeling and prediction of beach bacteria concentrations. Among previous works on this subject, however, several issues were insufficiently or inconsistently addressed. Those is...

Diagnostic Usefulness of APRI and FIB-4 for the Prediction of Liver Fibrosis After Liver Transplantation in Patients Infected with Hepatitis C Virus.

PubMed

Imai, H; Kamei, H; Onishi, Y; Ishizu, Y; Ishigami, M; Goto, H; Ogura, Y

2018-06-01

Aspartate transaminase-to-platelet ratio index (APRI) and fibrosis-4 (FIB-4) are well known as representative indirect serum biomarkers related to liver fibrosis. The usefulness of these markers for the diagnosis of liver fibrosis after liver transplantation (LT) in hepatitis C virus (HCV)-infected patients and the influence of splenectomy were investigated. From June 2003 to May 2014, 31 HCV-infected patients who underwent LT and postoperative follow-up liver biopsies were included in this study. The association between liver fibrosis and serum biomarkers and the influence of splenectomy on APRI and FIB-4 were also investigated. A total of 195 biopsy specimens were collected, and liver fibrosis was identified as: F0, 59.7%; F1, 34.1%; and F2, 6.3%. Both APRI and FIB-4 were significantly higher in patients who showed F1 and F2 in liver biopsy specimen than F0 (P values, .009 and .022, respectively); sensitivity and specificity of APRI were, respectively, 63.4% and 66.7%, and those of FIB-4 were 57.7% and 69.6%. In 11 patients (35.5%) who underwent splenectomy at the time of LT, the cutoff values for APRI and FIB-4 were 0.61 and 1.41, which were significantly lower than the corresponding values (1.00 and 3.64) of patients without splenectomy. APRI and FIB-4 could effectively estimate liver fibrosis after LT for HCV-related liver disease. For LT patients with splenectomy, APRI and FIB-4 were also useful to estimate liver fibrosis, but the standard values should be adjusted lower than those for patients without splenectomy. Copyright © 2018 Elsevier Inc. All rights reserved.

High FIB-4 index as an independent risk factor of prevalent chronic kidney disease in patients with nonalcoholic fatty liver disease.

PubMed

Xu, Huang-Wei; Hsu, Yung-Chien; Chang, Chia-Hao; Wei, Kuo-Liang; Lin, Chun-Liang

2016-03-01

Growing evidence suggests that non-alcoholic fatty liver disease (NAFLD) is linked to an increased risk for chronic kidney disease (CKD); liver fibrosis with biopsy-proven NAFLD has also been shown to associate with an increased risk of CKD. This study compares the diagnostic performance of simple noninvasive tests in identifying prevalent CKD among individuals with ultrasonography-diagnosed NAFLD. A total of 755 with ultrasonography-diagnosed NAFLD were included. Estimated glomerular filtration rate and noninvasive markers for hepatic fibrosis: aspartate transaminase to alanine transaminase ratio (AAR), aspartate transaminase to platelet ratio index (APRI), FIB-4 score, NAFLD fibrosis score (NFS) and BARD score were assessed. Binary logistic regression to generate a propensity score and receiver operating characteristic curves were developed for each of the noninvasive markers for predicting CKD, and the area under the receiver operating characteristic curve was greatest for FIB-4 score (0.750), followed by NFS (0.710), AAR (0.594), APRI (0.587), and BARD score (0.561). A cut-off value of 1.100 for FIB-4 score gave a sensitivity of 68.85% and a specificity of 71.07% for predicting CKD. The positive predictive value and negative predictive value were 37.50 and 90.05%, respectively. In multiple logistic regression analysis, only FIB-4 score ≧1.100 (OR 2.660, 95% CI 1.201-5.889; p = .016), older age, higher diastolic blood pressure and higher uric acid were independent predictors of CKD. High noninvasive fibrosis score is associated with an increased risk of prevalent CKD; the FIB-4 is the better predictor. With a cut-off value of 1.100 for FIB-4, it is useful in excluding the presence of CKD in patients with NAFLD.

Reductions in Gull Populations Improve Beachwater Quality.

EPA Science Inventory

BACKGROUND. Gulls are often cited as an important source of fecal pollution to surface waters, and fecal indicator bacteria (FIB) concentrations have been shown to be significantly correlated with gull populations. However, it is unclear whether gull contamination poses a risk to...

FIB/SEM and SEM/EDS microstructural analysis of metal-ceramic and zirconia-ceramic interfaces.

PubMed

Massimi, F; Merlati, G; Sebastiani, M; Battaini, P; Menghini, P; Bemporad, E

2012-01-10

Recently introduced FIB/SEM analysis in microscopy seems to provide a high-resolution characterization of the samples by 3D (FIB) cross-sectioning and (SEM) high resolution imaging. The aim of this study was to apply the FIB/SEM and SEM/EDS analysis to the interfaces of a metal-ceramic vs. two zirconia-ceramic systems. Plate samples of three different prosthetic systems were prepared in the dental lab following the manufacturers' instructions, where metal-ceramic was the result of a ceramic veneering (porcelain-fused-to-metal) and the two zirconia-ceramic systems were produced by the dedicated CAD-CAM procedures of the zirconia cores (both with final sintering) and then veneered by layered or heat pressed ceramics. In a FIB/SEM equipment (also called DualBeam), a thin layer of platinum (1 μm) was deposited on samples surface crossing the interfaces, in order to protect them during milling. Then, increasingly deeper trenches were milled by a focused ion beam, first using a relatively higher and later using a lower ion current (from 9 nA to 0.28 nA, 30KV). Finally, FEG-SEM (5KV) micrographs (1000-50,000X) were acquired. In a SEM the analysis of the morphology and internal microstructure was performed by 13KV secondary and backscattered electrons signals (in all the samples). The compositional maps were then performed by EDS probe only in the metal-ceramic system (20kV). Despite the presence of many voids in all the ceramic layers, it was possible to identify: (1) the grain structures of the metallic and zirconia substrates, (2) the thin oxide layer at the metal-ceramic interface and its interactions with the first ceramic layer (wash technique), (3) the roughness of the two different zirconia cores and their interactions with the ceramic interface, where the presence of zirconia grains in the ceramic layer was reported in two system possibly due to sandblasting before ceramic firing.

Comparing Child-Pugh, MELD, and FIB-4 to Predict Clinical Outcomes in Hepatitis C Virus-Infected Persons: Results From ERCHIVES.

PubMed

Butt, Adeel A; Ren, Yanjie; Lo Re, Vincent; Taddei, Tamar H; Kaplan, David E

2017-07-01

Identifying hepatitis C virus (HCV)-positive persons at high risk of early complications can help prioritize treatment decisions. We conducted this study to compare Child-Turcotte-Pugh (CP), MELD, and FIB-4 scores for predicting clinical outcomes and to identify those at low risk of complications. Within electronically retrieved cohort of HCV-infected veterans, we identified HCV-positive persons and excluded those with human immunodeficiency virus (HIV), hepatitis B surface antigen (HBsAg), prevalent hepatic decompensation (HD), hepatocellular carcinoma (HCC), and those treated for HCV. We calculated incidence rates for HD, HCC, and all-cause mortality at 1, 3, and 5 years after HCV diagnosis. Using receiver operating characteristic (ROC) curves, we determined the optimal cut-off values for each score for these outcomes. Among 21 116 persons evaluated, 89.7% were CP Class-A, 79.9% had MELD<9, and 43.4% had FIB-4<1.45. AUROC for HD at 1, 3, and 5 years was higher for FIB-4 (0.84-0.86) compared with MELD (0.70-0.76) (P < .001). AUROC for HCC at 1, 3, and 5 years was 0.81-0.82 for FIB-4 but 0.61-0.68 for CP and MELD scores. (P < .001) AUROC for all-cause mortality at 3 and 5 years was 0.65-0.68. The optimal cut-off scores to identify persons at low risk of complications were as follows: CP <5; MELD <8; FIB-4 <3 for HD and HCC, and <2 for all-cause mortality, below which <1.5% developed HD and HCC and ≤2.5% died at 3 years. FIB-4 score is a better predictor of HD and HCC in HCV-positive persons. A score of <3 is associated with a low risk of HD and HCC 1 and 3 years after HCV diagnosis. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com

Faecal indicator bacteria enumeration in beach sand: A comparison study of extraction methods in medium to coarse sands

USGS Publications Warehouse

Boehm, A.B.; Griffith, J.; McGee, C.; Edge, T.A.; Solo-Gabriele, H. M.; Whitman, R.; Cao, Y.; Getrich, M.; Jay, J.A.; Ferguson, D.; Goodwin, K.D.; Lee, C.M.; Madison, M.; Weisberg, S.B.

2009-01-01

Aims: The absence of standardized methods for quantifying faecal indicator bacteria (FIB) in sand hinders comparison of results across studies. The purpose of the study was to compare methods for extraction of faecal bacteria from sands and recommend a standardized extraction technique. Methods and Results: Twenty-two methods of extracting enterococci and Escherichia coli from sand were evaluated, including multiple permutations of hand shaking, mechanical shaking, blending, sonication, number of rinses, settling time, eluant-to-sand ratio, eluant composition, prefiltration and type of decantation. Tests were performed on sands from California, Florida and Lake Michigan. Most extraction parameters did not significantly affect bacterial enumeration. anova revealed significant effects of eluant composition and blending; with both sodium metaphosphate buffer and blending producing reduced counts. Conclusions: The simplest extraction method that produced the highest FIB recoveries consisted of 2 min of hand shaking in phosphate-buffered saline or deionized water, a 30-s settling time, one-rinse step and a 10 : 1 eluant volume to sand weight ratio. This result was consistent across the sand compositions tested in this study but could vary for other sand types. Significance and Impact of the Study: Method standardization will improve the understanding of how sands affect surface water quality. ?? 2009 The Society for Applied Microbiology.

Does Incorporating Change in APRI or FIB-4 Indices Over Time Improve the Accuracy of a Single Index for Identifying Liver Fibrosis in Persons With Chronic Hepatitis C Virus Infection?

PubMed

Gounder, Prabhu P; Haering, Celia; Bruden, Dana J T; Townshend-Bulson, Lisa; Simons, Brenna C; Spradling, Philip R; McMahon, Brian J

2018-01-01

The aspartate aminotransferase-to-platelet ratio index (APRI) and a fibrosis index calculated using platelets (FIB-4) have been proposed as noninvasive markers of liver fibrosis. To determine APRI/FIB-4 accuracy for predicting histologic liver fibrosis and evaluate whether incorporating change in index improves test accuracy in hepatitis C virus (HCV)-infected Alaska Native persons. Using liver histology as the gold standard, we determined the test characteristics of APRI to predict Metavir ≥F2 fibrosis and FIB-4 to predict Metavir ≥F3 fibrosis. Index discrimination was measured as the area under the receiver operator characteristic curve. We fit a logistic regression model to determine whether incorporating change in APRI/FIB-4 over time improved index discrimination. Among 283 participants, 46% were female, 48% had a body mass index >30, 11% had diabetes mellitus, 8% reported current heavy alcohol use. Participants were infected with HCV genotypes 1 (68%), 2 (17%), or 3 (15%). On liver histology, 30% of study participants had ≥F2 fibrosis and 15% had ≥F3 fibrosis. The positive predictive value of an APRI>1.5/FIB-4>3.25 for identifying fibrosis was 77%/78%. The negative predictive value of an APRI<0.5/FIB-4<1.45 was 91%/87%. The area under the receiver operator characteristic curve of an APRI/FIB-4 for identifying fibrosis was 0.82/0.84. Incorporating change in APRI/FIB-4 did not improve index discrimination. The accuracy of APRI/FIB-4 for identifying liver fibrosis in HCV-infected Alaska Native persons is similar to that reported in other populations and could help prioritize patients for treatment living in areas without access to liver biopsy. Change in APRI/FIB-4 was not predictive of degree of fibrosis.

Liver stiffness measurement, better than APRI, Fibroindex, Fib-4, and NBI gastroscopy, predicts portal hypertension in patients with cirrhosis.

PubMed

Zhang, Wei; Wang, Liqiong; Wang, Lei; Li, Gang; Huang, Aoshuang; Yin, Ping; Yang, Zhenhua; Ling, Changquan; Wang, Lingtai

2015-03-01

Liver stiffness measurement (LSM) is frequently used as non-invasive alternative for liver fibrosis including cirrhosis, which can lead to portal hypertension. This study was conducted to evaluate the predictive value of LSM in cirrhosis-induced portal hypertension patients. Between July 2011 and December 2013, 153 participants were enrolled into a single-center, prospective, cross-sectional study. Each subject received both gastroscopy and LSM. Baseline biochemical, APRI, Fibroindex, and Fib-4 were also performed. LSM of cirrhosis patients with portal hypertension was significantly higher compared to those without portal hypertension (P < 0.05). A LSM ≥ 13.6 kPa had a sensitivity of 83.87 % and a specificity of 72.53 % with an accuracy of 77.1 for the prediction of portal hypertension, which are higher than those of APRI, Fib-4, and Fibroscan separately. A combination of Fibroscan combined with Fib-4 achieved a maximum AUC of 0.833 and accuracy of 77.8. Discriminant and internal validation analysis showed that Fibroscan plus APRI obtained a lower false negative rate compared to Fibroscan plus Fib-4 and Fibroscan plus Fibroindex (9.68, 17.74, and 11.29 %, respectively). A good relationship was found between LSM and NBI mean optical density both by linear and polynomial correlation analysis (r = 0.5533 and r = 0.7349, both P < 0.001). There was a trend toward a better performance of LSM for assessing portal hypertension compared with NBI gastroscopy mean optical density (P = 0.028 and P = 0.05, respectively). Better than APRI, Fibroindex, Fib-4, and NBI gastroscopy, LSM can predict portal hypertension in cirrhosis patients. A LSM of 13.6 kPa can be considered to be the predictive value for portal hypertension.

Migration of Chemotactic Bacteria in Soft Agar: Role of Gel Concentration

PubMed Central

Croze, Ottavio A.; Ferguson, Gail P.; Cates, Michael E.; Poon, Wilson C.K.

2011-01-01

We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15–0.5% (w/v). For C≲0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4–0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15–0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays. PMID:21806920

Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

PubMed

Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

1982-11-01

Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

Diagnostic accuracy of APRI, FIB-4 and Forns for the detection of liver cirrhosis in HIV/HCV-coinfected patients.

PubMed

Merli, Marco; Galli, Laura; Castagna, Antonella; Salpietro, Stefania; Gianotti, Nicola; Messina, Emanuela; Poli, Andrea; Morsica, Giulia; Bagaglio, Sabrina; Cernuschi, Massimo; Bigoloni, Alba; Uberti-Foppa, Caterina; Lazzarin, Adriano; Hasson, Hamid

2016-04-01

We determined the diagnostic accuracy and optimal cut off of three indirect fibrosis biomarkers (APRI, FIB-4, Forns) compared with liver stiffness (LS) for the detection of liver cirrhosis in HIV/HCV-coinfected patients. An observational retrospective study on HIV/HCV-coinfected patients with concomitant LS measurement and APRI, FIB-4 and Forns was performed. The presence of liver cirrhosis was defined as a LS ≥13 KPa. The diagnostic accuracy and optimal cut-off values, compared with LS categorization (<13 vs ≥13 KPa), were determined by receiver operating characteristics (ROC) curves. The study sample included 646 patients. The area-under-the ROC curve (95% confidence interval) for the detection of liver cirrhosis were 0.84 (0.81-0.88), 0.87 (0.84-0.91) and 0.87 (0.84-0.90) for APRI, FIB-4 and Forns, respectively. According to the optimal cut off values for liver cirrhosis (≥0.97 for APRI, ≥2.02 for FIB-4 and ≥7.8 for Forns), 80%, 80% and 82% of subjects were correctly classified by the three indirect fibrosis biomarkers, respectively. Misclassifications were mostly due to false positive cases. The study suggests that indirect fibrosis biomarkers can help clinicians to exclude liver cirrhosis in the management of HIV/HCV co-infected patients, reducing the frequency of more expensive or invasive assessments.

Large volume serial section tomography by Xe Plasma FIB dual beam microscopy.

PubMed

Burnett, T L; Kelley, R; Winiarski, B; Contreras, L; Daly, M; Gholinia, A; Burke, M G; Withers, P J

2016-02-01

Ga(+) Focused Ion Beam-Scanning Electron Microscopes (FIB-SEM) have revolutionised the level of microstructural information that can be recovered in 3D by block face serial section tomography (SST), as well as enabling the site-specific removal of smaller regions for subsequent transmission electron microscope (TEM) examination. However, Ga(+) FIB material removal rates limit the volumes and depths that can be probed to dimensions in the tens of microns range. Emerging Xe(+) Plasma Focused Ion Beam-Scanning Electron Microscope (PFIB-SEM) systems promise faster removal rates. Here we examine the potential of the method for large volume serial section tomography as applied to bainitic steel and WC-Co hard metals. Our studies demonstrate that with careful control of milling parameters precise automated serial sectioning can be achieved with low levels of milling artefacts at removal rates some 60× faster. Volumes that are hundreds of microns in dimension have been collected using fully automated SST routines in feasible timescales (<24h) showing good grain orientation contrast and capturing microstructural features at the tens of nanometres to the tens of microns scale. Accompanying electron back scattered diffraction (EBSD) maps show high indexing rates suggesting low levels of surface damage. Further, under high current Ga(+) FIB milling WC-Co is prone to amorphisation of WC surface layers and phase transformation of the Co phase, neither of which have been observed at PFIB currents as high as 60nA at 30kV. Xe(+) PFIB dual beam microscopes promise to radically extend our capability for 3D tomography, 3D EDX, 3D EBSD as well as correlative tomography. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Infection with hepatitis viruses, FIB-4 index and risk of hepatocellular carcinoma in southern Italy: a population-based cohort study.

PubMed

Fusco, Mario; Piselli, Pierluca; Virdone, Saverio; Di Cicco, Pietro; Scognamiglio, Paola; De Paoli, Paolo; Ciullo, Valerio; Verdirosi, Diana; D'Orazio, Michele; Dal Maso, Luigino; Girardi, Enrico; Franceschi, Silvia; Serraino, Diego

2016-01-01

The incidence of hepatocellular carcinoma (HCC) and its association with hepatitis C (HCV) and hepatitis B virus (HBV) infections, FIB-4 index and liver enzymes was assessed in an area of the province of Naples covered by a population-based cancer registry. We conducted a cohort investigation on 4492 individuals previously enrolled in a population-based seroprevalent survey on HCV and HBV infections. The diagnosis of HCC was assessed through a record linkage with the cancer registry. Hepatic metabolic activity was measured through serum alanine transaminase, aspartate aminotransferase, gamma-glutamyl-transferase, and platelet. The FIB-4 index was used as a marker of fibrosis. We computed HCC incidence rates (IR) for 100,000 (10 5 ) person-years of observation, and multivariable hazard ratios (HR) with 95 % confidence intervals (CI) to assess risk factors for HCC. Twenty two cases of HCC were diagnosed during follow-up (IR = 63.3 cases/10 5 ). Significantly increased HCC risks were documented in individuals with higher than normal liver enzymes and low platelet count; in the 239 HCV RNA-positives (HR = 61.8, 95 % CI:13.3-286); and in the 95 HBsAg-positives (HR = 75.0) -as compared to uninfected individuals. The highest FIB-4 score was associated with a 17.6-fold increased HCC risk. An elevated FIB-4 index turned out to be an important predictor of HCC occurrence. Although the standard method to assess hepatic fibrosis in chronic hepatitis remains the histologic staging of liver biopsy specimen, the assessment of FIB-4 in HCV RNA-positive individuals may help in identifying the highest HCC-risk individuals who need anti-HCV treatment most urgently.

Mapping Strain Gradients in the FIB-Structured InGaN/GaN Multilayered Films with 3D X-ray Microbeam

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

Barabash, Rozaliya; Gao, Yanfei; Ice, Gene E

2010-01-01

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Mapping strain gradients in the FIB-structured InGaN/GaN multilayered films with 3D x-ray microbeam.

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

Barabash, R. I.; Gao, Y. F.; Ice, G. E.

2010-11-25

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Speculation of the Time-Dependent Change of FIB4 Index in Patients with Nonalcoholic Fatty Liver Disease: A Retrospective Study.

PubMed

Miyata, Hiroshi; Miyata, Satoru

2018-01-01

To speculate on the time-dependent change of FIB4 index in patients with nonalcoholic fatty liver disease (NAFLD) and its increase-decrease rate per year, simply and accurately. In all 23 patients with NAFLD with the value of FIB4 index over 1.30 at the peak, the period from the first to each examination date was calculated and this period (years) was regarded as x . Next, the mean value of FIB4 index during the past year to each examination date was regarded as y . In every y , the minimum and the maximum y value were found out. Between x corresponding to this minimum y and x corresponding to this maximum y , the correlation between x and y was analyzed as the main subject. Then, the slope of each correlation was investigated, because it should indicate increase-decrease rate per year. In all 23 patients, the correlations as the main subject were recognized and the mean absolute value of correlation coefficient ( r ) was 0.91 ± 0.08. As for the slope, the mean absolute value was 0.1371 ± 0.1147 (/year). Simply and accurately, the time-dependent change of FIB4 index and its increase-decrease rate per year could be approximately speculated.

Microstructural characterization of Ti-6Al-4V metal chips by focused ion beam (FIB) and transmission electron microscopy (TEM)

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

Schneider, Judy; Dong, Lei; Howe, Jane Y

2011-01-01

The microstructure of the secondary deformation zone (SDZ) near the cutting surface in metal chips of Ti-6Al-4V formed during machining was investigated using focused ion beam (FIB) specimen preparation and transmission electron microscopy (TEM) imaging. Use of the FIB allowed precise extraction of the specimen across this region to reveal its inhomogeneous microstructure resulting from the non-uniform distribution of strain, strain rate, and temperature generated during the cutting process. Initial imaging from conventional TEM foil preparation revealed microstructures ranging from heavily textured to regions of fine grains. Using FIB preparation, the transverse microstructure could be interpreted as fine grains nearmore » the cutting surface which transitioned to coarse grains toward the free surface. At the cutting surface a 10 nm thick recrystallized layer was observed capping a 20 nm thick amorphous layer.« less

A Novel Hybrid Ultramicrotomy/FIB-SEM Technique: Preparation of Serial Electron-Transparent Thin Sections of a Hayabusa Grain

NASA Technical Reports Server (NTRS)

Berger, Eve L.; Keller, Lindsay P.

2014-01-01

The Japanese space agency's (JAXA) Hayabusa mission returned the first particulate samples (typically <100micron) from the surface of an asteroid (25143 Itokawa). These precious samples provide important insights into early Solar System processes, but their sizes pose tremendous challenges to coordinated analysis using a variety of nano- and micro-beam techniques. The ability to glean maximal information from individual particles has become increasingly important and depends critically on sample preparation. We developed a hybrid technique combining traditional ultramicrotomy with focused ion beam (FIB) techniques, allowing for more thorough in situ investigations of grain surfaces and interiors. Using this method, we increase the number of FIB-prepared sections that can be recovered from a particle with dimensions on the order of tens of microns. These sections can be subsequently analyzed using a variety of analytical techniques. Particle RA-QD02-0211 is a approx. 40×40×20 micron particle from Itokawa containing olivine and Fe sulfides. It was embedded in low viscosity epoxy and partly sectioned to a depth of approx 10 micron; sections are placed on Cu grids with thin amorphous films for transmission electron microscope (TEM) analyses. With the sample surface partly exposed, the epoxy bullet is trimmed to a height of approx. 5mm to accommodate the allowable dimensions for FIB work (FEI Quanta 600 3D dual beam FIB-SEM). Using a diamond trim knife, the epoxy surrounding the grain is removed on 3 sides (to within a few microns of the grain); the depth of material removed extends well below the bottom of the particle. The sample is attached to an SEM pin mount, the epoxy coated with conductive paint, and the entire assembly coated with approx. 40nm of carbon to eliminate sample charging during FIB work. A protective carbon cap is placed according to the plan for the 15 FIB sections. The central 'spine' of the cap runs perpendicular to the front of the sample, and

Comparison of FIB-4 index and aspartate aminotransferase to platelet ratio index on carcinogenesis in chronic hepatitis B treated with entecavir.

PubMed

Nishikawa, Hiroki; Nishijima, Norihiro; Enomoto, Hirayuki; Sakamoto, Azusa; Nasu, Akihiro; Komekado, Hideyuki; Nishimura, Takashi; Kita, Ryuichi; Kimura, Toru; Iijima, Hiroko; Nishiguchi, Shuhei; Osaki, Yukio

2017-01-01

We sought to compare the effects of FIB-4 index and aspartate aminotransferase to platelet ratio index (APRI) on hepatocellular carcinoma (HCC) incidence in chronic hepatitis B (CHB) patients undergoing entecavir (ETV) therapy. A total of 338 nucleosides analogue therapy naïve CHB patients initially treated with ETV were analyzed. The optimal cutoff points in each continuous variable were determined by receiver operating curve (ROC) analysis. The effects of FIB-4 index and APRI on HCC incidence were compared using time-dependent ROC analysis and factors linked to HCC incidence were also examined using univariate and multivariate analyses. There were 215 males and 123 females with the median age of 52 years and the median baseline HBV-DNA level of 6.6 log copies/ml. The median follow-up interval after the initiation of ETV therapy was 4.99 years. During the follow-up period, 33 patients (9.8%) developed HCC. The 3-, 5- 7-year cumulative HCC incidence rates in all cases were 4.4%, 9.2% and 13.5%, respectively. In the multivariate analysis, FIB-4 index revealed to be an independent predictor associated with HCC incidence, while APRI was not. In the time-dependent ROC analyses for all cases and for all subgroups analyses stratified by viral status or cirrhosis status, all area under the ROCs in each time point (2-, 3-, 4-, 5-, 6-, and 7-year) of FIB-4 index were higher than those of APRI. FIB-4 index rather than APRI can be a useful predictor associated with HCC development for CHB patients undergoing ETV therapy.

Ammonium removal using algae-bacteria consortia: the effect of ammonium concentration, algae biomass, and light.

PubMed

Jia, Huijun; Yuan, Qiuyan

2018-04-01

In this study, the effects of ammonium nitrogen concentration, algae biomass concentration, and light conditions (wavelength and intensity) on the ammonium removal efficiency of algae-bacteria consortia from wastewater were investigated. The results indicated that ammonium concentration and light intensity had a significant impact on nitrification. It was found that the highest ammonia concentration (430 mg N/L) in the influent resulted in the highest ammonia removal rate of 108 ± 3.6 mg N/L/days, which was two times higher than the influent with low ammonia concentration (40 mg N/L). At the lowest light intensity of 1000 Lux, algae biomass concentration, light wavelength, and light cycle did not show a significant effect on the performance of algal-bacterial consortium. Furthermore, the ammonia removal rate was approximately 83 ± 1.0 mg N/L/days, which was up to 40% faster than at the light intensity of 2500 Lux. It was concluded that the algae-bacteria consortia can effectively remove nitrogen from wastewater and the removal performance can be stabilized and enhanced using the low light intensity of 1000 Lux that is also a cost-effective strategy.

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.

Nitrogen Gas Field Ion Source (GFIS) Focused Ion Beam (FIB) Secondary Electron Imaging: A First Look.

PubMed

Schmidt, Marek E; Yasaka, Anto; Akabori, Masashi; Mizuta, Hiroshi

2017-08-01

The recent technological advance of the gas field ion source (GFIS) and its successful integration into systems has renewed the interest in the focused ion beam (FIB) technology. Due to the atomically small source size and the use of light ions, the limitations of the liquid metal ion source are solved as device dimensions are pushed further towards the single-digit nanometer size. Helium and neon ions are the most widely used, but a large portfolio of available ion species is desirable, to allow a wide range of applications. Among argon and hydrogen, $${\\rm N}_{2}^{{\\plus}} $$ ions offer unique characteristics due to their covalent bond and their use as dopant for various carbon-based materials including diamond. Here, we provide a first look at the $${\\rm N}_{2}^{{\\plus}} $$ GFIS-FIB enabled imaging of a large selection of microscopic structures, including gold on carbon test specimen, thin metal films on insulator and nanostructured carbon-based devices, which are among the most actively researched materials in the field of nanoelectronics. The results are compared with images acquired by He+ ions, and we show that $${\\rm N}_{2}^{{\\plus}} $$ GFIS-FIB can offer improved material contrast even at very low imaging dose and is more sensitive to the surface roughness.

Coordinated STEM/FIB/NanoSIMS Analyses of Presolar Silicates in Comet Dust and Primitive Meteorites

NASA Technical Reports Server (NTRS)

Keller, Lindsay; Nguyen, A.; Rahman, Z.; Messenger, S.

2012-01-01

Silicate grains were among the most abundant mineralogical building blocks of our Solar System. These grains were the detritus from earlier generations of stars that have been recycled in the early solar nebula. Rare sub-micrometer survivors of this processing have been identified in meteorites, micrometeorites and interplanetary dust particles (IDPs). These silicate grains are recognized as presolar in origin because of their extremely anomalous isotopic compositions that reflect nucleosynthetic processes in their stellar sources (evolved stars, novae and supernovae). We perform coordinated chemical, mineralogical and isotopic studies of these grains to determine their origins and histories. We examine the complex mineralogy and petrography of presolar silicates using imaging, diffraction and chemical data obtained from thin sections with the JSC JEOL 2500 field-emission STEM equipped with a Noran thin window energy dispersive x-ray (EDX) spectrometer and a Gatan Tridiem GIF. Quantitative element x-ray maps (spectrum images) are acquired by rastering a 4 nm incident probe whose dwell time is minimized to avoid beam damage and element diffusion during mapping. Successive image layers are acquired and combined in order to achieve approx 1% counting statistics for major elements. The IDP samples are prepared by ultramicrotomy of particles embedded in epoxy or elemental sulfur. After EDX mapping, the sections are subjected to C, N, and O isotopic imaging with the JSC NanoSIMS 50L ion microprobe. We prepare sections of some meteorite grains using the JSC FEI Quanta 3D focused ion beam (FIB) instrument. The specimen surface is protected from the FIB milling process by layers of electron beam-deposited C and Pt followed by an ion-deposited Pt layer. We also use the FIB to preferentially remove surrounding grains to reduce the background in subsequent NanoSIMS measurements. For mineralogical studies, we again employ the FIB instrument to deposit a protective cap over the

Labyrinths, columns and cavities: new internal features of pollen grain walls in the Acanthaceae detected by FIB-SEM.

PubMed

House, Alisoun; Balkwill, Kevin

2016-03-01

External pollen grain morphology has been widely used in the taxonomy and systematics of flowering plants, especially the Acanthaceae which are noted for pollen diversity. However internal pollen wall features have received far less attention due to the difficulty of examining the wall structure. Advancing technology in the field of microscopy has made it possible, with the use of a focused ion beam-scanning electron microscope (FIB-SEM), to view the structure of pollen grain walls in far greater detail and in three dimensions. In this study the wall structures of 13 species from the Acanthaceae were investigated for features of potential systematic relevance. FIB-SEM was applied to obtain precise cross sections of pollen grains at selected positions for examining the wall ultrastructure. Exploratory studies of the exine have thus far identified five basic structural types. The investigations also show that similar external pollen wall features may have a distinctly different internal structure. FIB-SEM studies have revealed diverse internal pollen wall features which may now be investigated for their systematic and functional significance.

Water quality prediction of marine recreational beaches receiving watershed baseflow and stormwater runoff in southern California, USA.

PubMed

He, Li-Ming Lee; He, Zhen-Li

2008-05-01

Beach advisories are issued to the public in California when the concentration of fecal indicator bacteria (FIB), including total coliform, fecal coliform (or Escherichia coli), and Enterococcus, exceed their recreational water health standards, or when the amount of a rainfall event is above the pre-determined threshold. However, it is not fully understood about how and to what degree stormwater runoff or baseflow exerts impacts on beach water quality. Furthermore, current laboratory methods used to determine the FIB levels take 18-96 h, which is too slow to keep pace with changes in FIB levels in water. Thus, a beach may not be posted when it is contaminated, and may be posted under advisory when bacterial levels have already decreased to within water quality standards. The study was designed to address the above critical issues. There were large temporal and spatial variations in FIB concentrations along two popular State Beaches in San Diego, CA, USA. The rainstorm-induced runoff from the watersheds exerts significant impacts on the marine recreational water quality of the beaches adjacent to lagoons during the first 24-48 h after a rain event. The large volume of stormwater runoff discharging to beaches caused high FIB concentrations in beach water not only at the lagoon outlet channel and the mixing zone, but also at the locations 90 m away from the channel northward or southward along the shoreline. The geomorphology of beach shoreline, distance from the outlet channel, wind strength, wind direction, tide height, wave height, rainfall, time lapse after a rainstorm, or channel flow rate played a role in affecting the distribution of FIB concentrations in beach water. Despite the great temporal and spatial variability of FIB concentrations along a shoreline, the artificial neural network-based models developed in this study are capable of successfully predicting FIB concentrations at different beaches, different locations, and different times under baseflow or

APRI and FIB-4 are good predictors of the stage of liver fibrosis in chronic hepatitis B: the Chronic Hepatitis Cohort Study (CHeCS).

PubMed

Teshale, E; Lu, M; Rupp, L B; Holmberg, S D; Moorman, A C; Spradling, P; Vijayadeva, V; Boscarino, J A; Schmidt, M A; Gordon, S C

2014-12-01

We aim to determine the predictive ability of APRI, FIB-4 and AST/ALT ratio for staging of liver fibrosis and to differentiate significant fibrosis (F2-F4) from none to minimal fibrosis (F0-F1) in chronic hepatitis B (CHB). Liver biopsy results were mapped to an F0-4 equivalent fibrosis stage. Mean APRI and FIB-4 scores were significantly higher for each successive fibrosis level from F1 to F4 (P < 0.05). Based on optimized cut-offs, the AUROCs in distinguishing F2-F4 from F0 to F1 were 0.81 (0.76-0.87) for APRI, 0.81 (0.75-0.86) for FIB-4 and 0.56 (0.49-0.64) for AST/ALT ratio. APRI and FIB-4 distinguished F2-F4 from F0 to F1 with good sensitivity and specificity and can be useful for treatment decisions and monitoring progression of fibrosis. © 2014 John Wiley & Sons Ltd.

Exploring the interior of cuticles and compressions of fossil plants by FIB-SEM milling and image microscopy.

PubMed

Sender, L M; Escapa, I; Benedetti, A; Cúneo, R; Diez, J B

2018-01-01

We present the first study of cuticles and compressions of fossil leaves by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Cavities preserved inside fossil leaf compressions corresponding to substomatal chambers have been observed for the first time and several new features were identified in the cross-section cuts. These results open a new way in the investigation of the three-dimensional structures of both micro- and nanostructural features of fossil plants. Moreover, the application of the FIB-SEM technique to both fossils and extant plant remains represent a new source of taxonomical, palaeoenvironmental and palaeoclimatic information. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.

PubMed

Oi, Takao; Enomoto, Sakiko; Nakao, Tomoyo; Arai, Shigeo; Yamane, Koji; Taniguchi, Mitsutaka

2017-07-01

Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll

Comparison of FIB-4 index and aspartate aminotransferase to platelet ratio index on carcinogenesis in chronic hepatitis B treated with entecavir

PubMed Central

Nishikawa, Hiroki; Nishijima, Norihiro; Enomoto, Hirayuki; Sakamoto, Azusa; Nasu, Akihiro; Komekado, Hideyuki; Nishimura, Takashi; Kita, Ryuichi; Kimura, Toru; Iijima, Hiroko; Nishiguchi, Shuhei; Osaki, Yukio

2017-01-01

Aims: We sought to compare the effects of FIB-4 index and aspartate aminotransferase to platelet ratio index (APRI) on hepatocellular carcinoma (HCC) incidence in chronic hepatitis B (CHB) patients undergoing entecavir (ETV) therapy. Patient and methods: A total of 338 nucleosides analogue therapy naïve CHB patients initially treated with ETV were analyzed. The optimal cutoff points in each continuous variable were determined by receiver operating curve (ROC) analysis. The effects of FIB-4 index and APRI on HCC incidence were compared using time-dependent ROC analysis and factors linked to HCC incidence were also examined using univariate and multivariate analyses. Results: There were 215 males and 123 females with the median age of 52 years and the median baseline HBV-DNA level of 6.6 log copies/ml. The median follow-up interval after the initiation of ETV therapy was 4.99 years. During the follow-up period, 33 patients (9.8%) developed HCC. The 3-, 5- 7-year cumulative HCC incidence rates in all cases were 4.4%, 9.2% and 13.5%, respectively. In the multivariate analysis, FIB-4 index revealed to be an independent predictor associated with HCC incidence, while APRI was not. In the time-dependent ROC analyses for all cases and for all subgroups analyses stratified by viral status or cirrhosis status, all area under the ROCs in each time point (2-, 3-, 4-, 5-, 6-, and 7-year) of FIB-4 index were higher than those of APRI. Conclusion: FIB-4 index rather than APRI can be a useful predictor associated with HCC development for CHB patients undergoing ETV therapy. PMID:28243319

Three dimensional (3D) microstructure-based finite element modeling of Al-SiC nanolaminates using focused ion beam (FIB) tomography

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

Mayer, Carl R.

Al-SiC nanolaminate composites show promise as high performance coating materials due to their combination of strength and toughness. Although a significant amount of modeling effort has been focused on materials with an idealized flat nanostructure, experimentally these materials exhibit complex undulating layer geometries. This work utilizes FIB tomography to characterize this nanostructure in 3D and finite element modeling to determine the effect that this complex structure has on the mechanical behavior of these materials. A sufficiently large volume was characterized such that a 1 × 2 μm micropillar could be generated from the dataset and compared directly to experimental results.more » The mechanical response from this nanostructure was then compared to pillar models using simplified structures with perfectly flat layers, layers with sinusoidal waviness, and layers with arc segment waviness. The arc segment based layer geometry showed the best agreement with the experimentally determined structure, indicating it would be the most appropriate geometry for future modeling efforts. - Highlights: •FIB tomography was used to determine the structure of an Al-SiC nanolaminate in 3D. •FEM was used to compare the deformation of the nanostructure to experimental results. •Idealized structures from literature were compared to the FIB determined structure. •Arc segment based structures approximated the FIB determined structure most closely.« less

Bacteriophages as indicators of faecal pollution and enteric virus removal.

PubMed

McMinn, B R; Ashbolt, N J; Korajkic, A

2017-07-01

Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants. Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal. © 2017 The Society for Applied Microbiology.

Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters.

PubMed

Ahmed, Warish; Zhang, Qian; Lobos, Aldo; Senkbeil, Jacob; Sadowsky, Michael J; Harwood, Valerie J; Saeidi, Nazanin; Marinoni, Oswald; Ishii, Satoshi

2018-07-01

Stormwater contamination can threaten the health of aquatic ecosystems and human exposed to runoff via nutrient and pathogen influxes. In this study, the concentrations of 11 bacterial pathogens and 47 antibiotic resistance genes (ARGs) were determined by using high-throughput microfluidic qPCR (MFQPCR) in several storm drain outfalls (SDOs) during dry and wet weather in Tampa Bay, Florida, USA. Data generated in this study were also compared with the levels of fecal indicator bacteria (FIB) and sewage-associated molecular markers (i.e., Bacteroides HF183 and crAssphage markers) in same SDOs collected in a recent study (Ahmed et al., 2018). Concentration of FIB, sewage-associated markers, bacterial pathogens and many ARGs in water samples were relatively high and SDOs may be potentially hotspots for microbial contamination in Tampa Bay. Mean concentrations of culturable E. coli and Enterococcus spp. were tenfold higher in wet compared to dry weather. The majority of microbiological contaminants followed this trend. E. coli eaeA, encoding the virulence factor intimin, was correlated with levels of 20 ARGs, and was more frequently detected in wet weather than dry weather samples. The bla KPC gene associated with carbapenem resistant Enterobacteriaceae and the beta-lactam resistant gene (bla NPS ) were only detected in wet weather samples. Frequency of integron genes Intl2 and Intl3 detection increased by 42% in wet weather samples. Culturable E. coli and Enterococcus spp. significantly correlated with 19 of 47 (40%) ARG tested. Sewage-associated markers crAssphage and HF183 significantly correlated (p < 0.05) with the following ARGs: intl1, sul1, tet(M), ampC, mexB, and tet(W). The presence of sewage-associated marker genes along with ARGs associated with sewage suggested that aging sewage infrastructure contributed to contaminant loading in the Bay. Further research should focus on collecting spatial and temporal data on the microbiological contaminants

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage in a laboratory culture experiment.

PubMed

Song, Woojin; Kim, Mincheol; Tripathi, Binu M; Kim, Hyoki; Adams, Jonathan M

2016-06-01

It is difficult to understand the processes that structure immensely complex bacterial communities in the soil environment, necessitating a simplifying experimental approach. Here, we set up a microcosm culturing experiment with soil bacteria, at a range of nutrient concentrations, and compared these over time to understand the relationship between soil bacterial community structure and time/nutrient concentration. DNA from each replicate was analysed using HiSeq2000 Illumina sequencing of the 16S rRNA gene. We found that each nutrient treatment, and each time point during the experiment, produces characteristic bacterial communities that occur predictably between replicates. It is clear that within the context of this experiment, many soil bacteria have distinct niches from one another, in terms of both nutrient concentration, and successional time point since a resource first became available. This fine niche differentiation may in part help to explain the coexistence of a diversity of bacteria in soils. In this experiment, we show that the unimodal relationship between nutrient concentration/time and species diversity often reported in communities of larger organisms is also evident in microbial communities. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gene and antigen markers of Shiga-toxin producing E. coli from Michigan and Indiana river water: Occurrence and relation to recreational water quality criteria

USGS Publications Warehouse

Duris, J.W.; Haack, S.K.; Fogarty, L.R.

2009-01-01

The relation of bacterial pathogen occurrence to fecal indicator bacteria (FIB) concentrations used for recreational water quality criteria (RWQC) is poorly understood. This study determined the occurrence of Shiga-toxin producing Escherichia coli (STEC) markers and their relation to FIB concentrations in Michigan and Indiana river water. Using 67 fecal coliform (FC) bacteria cultures from 41 river sites in multiple watersheds, we evaluated the occurrence of five STEC markers: the Escherichia coli (EC) O157 antigen and gene, and the STEC virulence genes eaeA, stx1, and stx2. Simple isolations from selected FC cultures yielded viable EC O157. By both antigen and gene assays, EC O157 was detected in a greater proportion of samples exceeding rather than meeting FC RWQC (P < 0.05), but was unrelated to EC and enterococci RWQC. The occurrence of all other STEC markers was unrelated to any FIB RWQC. The eaeA, stx2, and stx1 genes were found in 93.3, 13.3, and in 46.7% of samples meeting FC RWQC and in 91.7, 0.0, and 37.5% of samples meeting the EC RWQC. Although not statistically significant, the percentage of samples positive for each STEC marker except stx1 was lower in samples that met, as opposed to exceeded, FIB RWQC. Viable STEC were common members of the FC communities in river water throughout southern Michigan and northern Indiana, regardless of FIB RWQC. Our study indicates that further information on the occurrence of pathogens in recreational waters, and research on alternative indicators of their occurrence, may help inform water-resource management and public health decision-making. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Modeling Fecal Indicator Bacteria Like Salt in Newport Bay

NASA Astrophysics Data System (ADS)

Ciglar, A. M.; Rippy, M.; Grant, S. B.

2015-12-01

Newport Bay is a harbor and estuary located in Orange County, CA that provides many water sports and recreational activities for millions of southern California residents and tourists. The aim of this study is to quickly assess exceedances of FIB in the Newport Bay which pose a health risk to recreational users. The ability to quickly assess water quality is made possible with an advection-diffusion mass transport model that uses easily measurable parameters such as volumetric flow rate from tributaries. Current FIB assessment methods for Newport Bay take a minimum of 24 hours to evaluate health risk by either culturing for FIB or running a more complex fluid dynamics model. By this time the FIB may have already reached the ocean outlet thus no longer posing a risk in the bay or recreationists may have already come in close contact with contaminated waters. The advection-diffusion model can process and disseminate health risk information within a few hours of flow rate measurements, minimizing time between an FIB exceedance and public awareness about the event. Data used to calibrate and validate the model was collected from January 2006 through February 2007. Salinity data was used for calibration and FIB data was used for validation. Both steady-state and transient conditions were assessed to determine if dry weather patterns can be simplified to the steady-state condition.

Distribution and sources of surfzone bacteria at Huntington Beach before and after disinfection on an ocean outfall - A frequency-domain analysis

USGS Publications Warehouse

Noble, M.A.; Xu, J. P.; Robertson, G.L.; Rosenfeld, L.K.

2006-01-01

Fecal indicator bacteria (FIB) were measured approximately 5 days a week in ankle-depth water at 19 surfzone stations along Huntington Beach and Newport Beach, California, from 1998 to the end of 2003. These sampling periods span the time before and after treated sewage effluent, discharged into the coastal ocean from the local outfall, was disinfected. Bacterial samples were also taken in the vicinity of the outfall during the pre- and post-disinfection periods. Our analysis of the results from both data sets suggest that land-based sources, rather than the local outfall, were the source of the FIB responsible for the frequent closures and postings of local beaches in the summers of 2001 and 2002. Because the annual cycle is the dominant frequency in the fecal and total coliform data sets at most sampling stations, we infer that sources associated with local runoff were responsible for the majority of coliform contamination along wide stretches of the beach. The dominant fortnightly cycle in enterococci at many surfzone sampling stations suggests that the source for these relatively frequent bacteria contamination events in summer is related to the wetting and draining of the land due to the large tidal excursions found during spring tides. Along the most frequently closed section of the beach at stations 3N-15N, the fortnightly cycle is dominant in all FIBs. The strikingly different spatial and spectral patterns found in coliform and in enterococci suggest the presence of different sources, at least for large sections of beach. The presence of a relatively large enterococci fortnightly cycle along the beaches near Newport Harbor indicates that contamination sources similar to those found off Huntington Beach are present, though not at high enough levels to close the Newport beaches. ?? 2006 Elsevier Ltd. All rights reserved.

Distribution and sources of surfzone bacteria at Huntington Beach before and after disinfection on an ocean outfall-- a frequency-domain analysis.

PubMed

Noble, M A; Xu, J P; Robertson, G L; Rosenfeld, L K

2006-06-01

Fecal indicator bacteria (FIB) were measured approximately 5 days a week in ankle-depth water at 19 surfzone stations along Huntington Beach and Newport Beach, California, from 1998 to the end of 2003. These sampling periods span the time before and after treated sewage effluent, discharged into the coastal ocean from the local outfall, was disinfected. Bacterial samples were also taken in the vicinity of the outfall during the pre- and post-disinfection periods. Our analysis of the results from both data sets suggest that land-based sources, rather than the local outfall, were the source of the FIB responsible for the frequent closures and postings of local beaches in the summers of 2001 and 2002. Because the annual cycle is the dominant frequency in the fecal and total coliform data sets at most sampling stations, we infer that sources associated with local runoff were responsible for the majority of coliform contamination along wide stretches of the beach. The dominant fortnightly cycle in enterococci at many surfzone sampling stations suggests that the source for these relatively frequent bacteria contamination events in summer is related to the wetting and draining of the land due to the large tidal excursions found during spring tides. Along the most frequently closed section of the beach at stations 3N-15N, the fortnightly cycle is dominant in all FIBs. The strikingly different spatial and spectral patterns found in coliform and in enterococci suggest the presence of different sources, at least for large sections of beach. The presence of a relatively large enterococci fortnightly cycle along the beaches near Newport Harbor indicates that contamination sources similar to those found off Huntington Beach are present, though not at high enough levels to close the Newport beaches.

Three-dimensional analysis of somatic mitochondrial dynamics in fission-deficient injured motor neurons using FIB/SEM.

PubMed

Tamada, Hiromi; Kiryu-Seo, Sumiko; Hosokawa, Hiroki; Ohta, Keisuke; Ishihara, Naotada; Nomura, Masatoshi; Mihara, Katsuyoshi; Nakamura, Kei-Ichiro; Kiyama, Hiroshi

2017-08-01

Mitochondria undergo morphological changes through fusion and fission for their quality control, which are vital for neuronal function. In this study, we examined three-dimensional morphologies of mitochondria in motor neurons under normal, nerve injured, and nerve injured plus fission-impaired conditions using the focused ion beam/scanning electron microscopy (FIB/SEM), because the FIB/SEM technology is a powerful tool to demonstrate both 3D images of whole organelle and the intra-organellar structure simultaneously. Crossing of dynamin-related protein 1 (Drp1) gene-floxed mice with neuronal injury-specific Cre driver mice, Atf3:BAC Tg mice, allowed for Drp1 ablation specifically in injured neurons. FIB/SEM analysis demonstrated that somatic mitochondrial morphologies in motor neurons were not altered before or after nerve injury. However, the fission impairment resulted in prominent somatic mitochondrial enlargement, which initially induced complex morphologies with round regions and long tubular processes, subsequently causing a decrease in the number of processes and further enlargement of the round regions, which eventually resulted in big spheroidal mitochondria without processes. The abnormal mitochondria exhibited several degradative morphologies: local or total cristae collapse, vacuolization, and mitophagy. These suggest that mitochondrial fission is crucial for maintaining mitochondrial integrity in injured motor neurons, and multiple forms of mitochondria degradation may accelerate neuronal degradation. © 2017 Wiley Periodicals, Inc.

Post Irradiation TEM Investigation of ZrN Coated U(Mo) Particles Prepared with FIB

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

Van Renterghem, W.; Leenaers, A.; Van den Berghe, S.

2015-10-01

In the framework of the Selenium project, two dispersion fuel plates were fabricated with Si and ZrN coated fuel particles and irradiated in the Br2 reactor of SCK•CEN to high burn-up. The first analysis of the irradiated plate proved the reduced swelling of the fuel plate and interaction layer growth up to 70% burn-up. The question was raised how the structure of the interaction layer had been affected by the irradiation and how the structure of the fuel particles had evolved. Hereto, samples from the ZrN coated UMo particles were prepared for transmission electron microscopy (TEM) using focused ion beammore » milling (FIB) at INL. The FIB technique allowed to precisely select the area of the interaction layer and/or fuel to produce a sample that is TEM transparent over an area of 20 by 20 µm. In this contribution, the first TEM results will be presented from the 66% burn-up sample.« less

Free testosterone concentration is inversely associated with markers of liver fibrosis in men with type 2 diabetes mellitus.

PubMed

Miyauchi, Shozo; Miyake, Teruki; Miyazaki, Masumi; Eguchi, Toru; Niiya, Tetsuji; Yamamoto, Shin; Senba, Hidenori; Furukawa, Shinya; Matsuura, Bunzo; Hiasa, Yoichi

2017-12-28

The association between serum testosterone level and liver fibrosis in patients with non-alcoholic fatty liver disease is unclear. To clarify this association, we investigated the relationship between serum free testosterone concentration and markers of liver fibrosis in men with type 2 diabetes mellitus but no obvious features of alcohol consumption. This retrospective observational cross-sectional study enrolled 248 men with type 2 diabetes mellitus. The FIB-4 index was measured as a marker of liver fibrosis, and multiple linear regression analysis was performed to examine its association with serum free testosterone concentration. In addition, the 7S domain of type IV collagen (IV-7S) was examined in 140 of the 248 patients. The mean free testosterone concentration was 10.6 ± 6.8 pg/mL and the means of the FIB-4 index and IV-7S were 1.64 ± 1.19 and 4.02 ± 1.11 ng/mL, respectively. After adjusting for all relevant variables, serum free testosterone concentrations were inversely associated with both the FIB-4 index and IV-7S (β; -0.28, P < 0.0001, and β; -0.28, P = 0.002, respectively). Measuring serum free testosterone concentrations in men with type 2 diabetes mellitus may help to predict progression to advanced liver disease. Identifying patients at risk may help to prevent the development of cirrhosis and hepatocellular carcinoma.

Impact of age on the diagnostic performances and cut-offs of APRI and FIB-4 for significant fibrosis and cirrhosis in chronic hepatitis B.

PubMed

Li, Qiang; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-07-11

Assessing the diagnostic performances of APRI and FIB-4 using age as a categorical marker. 822 chronic hepatitis B (CHB) patients were included. Using METAVIR scoring system as a reference, the performances of APRI and FIB-4 were compared between patients aged≥30 and patients aged<30 years. The APRI AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.61 vs 0.70, p<0.001) and cirrhosis (0.64 vs 0.78, p<0.001). The FIB-4 AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.57 vs 0.65, p<0.001) and cirrhosis (0.63 vs 0.72, p<0.001). Using specificity≥90%, the APRI cut-off in patients aged<30 years was lower than patients aged≥30 years for significant fibrosis (1.0 vs 1.2) and cirrhosis (1.2 vs 1.5). Using sensitivity≥90%, the APRI cut-off in patients aged<30 years was also lower than patients aged≥30 years for significant fibrosis (0.2 vs 0.4) and cirrhosis (0.3 vs 0.5). Using specificity≥90%, the FIB-4 cut-off in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (1.2 vs 2.1) and cirrhosis (1.4 vs 2.6). Using sensitivity≥90%, the FIB-4 cut-off in patients aged<30 years was also lower than that in patients aged≥30 years for significant fibrosis (0.5 vs 0.8) and cirrhosis (0.8 vs 1.2). Evaluation of the diagnostic performances of APRI and FIB-4 should take age into consideration.

Impact of age on the diagnostic performances and cut-offs of APRI and FIB-4 for significant fibrosis and cirrhosis in chronic hepatitis B

PubMed Central

Li, Qiang; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-01-01

Aims Assessing the diagnostic performances of APRI and FIB-4 using age as a categorical marker. Methods 822 chronic hepatitis B (CHB) patients were included. Using METAVIR scoring system as a reference, the performances of APRI and FIB-4 were compared between patients aged≥30 and patients aged<30 years. Results The APRI AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.61 vs 0.70, p<0.001) and cirrhosis (0.64 vs 0.78, p<0.001). The FIB-4 AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.57 vs 0.65, p<0.001) and cirrhosis (0.63 vs 0.72, p<0.001). Using specificity≥90%, the APRI cut-off in patients aged<30 years was lower than patients aged≥30 years for significant fibrosis (1.0 vs 1.2) and cirrhosis (1.2 vs 1.5). Using sensitivity≥90%, the APRI cut-off in patients aged<30 years was also lower than patients aged≥30 years for significant fibrosis (0.2 vs 0.4) and cirrhosis (0.3 vs 0.5). Using specificity≥90%, the FIB-4 cut-off in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (1.2 vs 2.1) and cirrhosis (1.4 vs 2.6). Using sensitivity≥90%, the FIB-4 cut-off in patients aged<30 years was also lower than that in patients aged≥30 years for significant fibrosis (0.5 vs 0.8) and cirrhosis (0.8 vs 1.2). Conclusions Evaluation of the diagnostic performances of APRI and FIB-4 should take age into consideration. PMID:28514753

Prevalence of and Progression to Abnormal Non-Invasive Markers of Liver Disease (APRI and FIB-4) among US HIV-infected Youth

PubMed Central

Kapogiannis, Bill G.; Leister, Erin; Siberry, George K.; Van Dyke, Russell B.; Rudy, Bret; Flynn, Patricia; Williams, Paige L.

2015-01-01

Objective To longitudinally characterize non-invasive markers of liver disease in HIV-infected youth. Design HIV infection, without viral hepatitis co-infection, may contribute to liver disease. Non-invasive markers of liver disease [FIB-4 (Fibrosis-4) and APRI (aspartate aminotransferase-to-platelet ratio index)] have been evaluated in adults with concomitant HIV and hepatitis C, but are less studied in children. Methods In prospective cohorts of HIV-infected and HIV-uninfected youth, we used linear regression models to compare log-transformed FIB-4 and APRI measures by HIV status based on a single visit at ages 15–20 years. We also longitudinally modeled trends in these measures in HIV-infected youth with ≥2 visits to compare those with behavioral vs perinatal HIV infection (PHIV) using mixed effect linear regression, adjusting for age, gender, body mass index, and race/ethnicity. Results Of 1785 participants, 41% were male, 57% black non-Hispanic and 27% Hispanic. More HIV-infected than uninfected youth had an APRI score >0.5 (13% vs 3%, p<0.001). Among 1307 HIV-infected participants with longitudinal measures, FIB-4 scores increased 6% per year (p<0.001) among all HIV-infected youth, whereas APRI scores increased 2% per year (p=0.007) only among PHIV youth. The incidence rates (95% CI) of progression of APRI to >0.5 and >1.5 were 7.5 (6.5–8.7) and 1.4 (1.0–1.9) cases per 100 person-years of follow up, respectively. The incidence of progression of FIB-4 to >1.5 and >3.25 were 1.6 (1.2–2.2) and 0.3 (0.2–0.6) cases per 100 person-years, respectively. Conclusions APRI and FIB-4 scores were higher among HIV-infected youth. Progression to scores suggesting subclinical fibrosis or worse was common. PMID:26959353

Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Olson, Leif E.; Johnson, Heather E.

2011-01-01

The City of Wilmington, Delaware, is in the downstream part of the Brandywine Creek Basin, on the main stem of Brandywine Creek. Wilmington uses this stream, which drains a mixed-land-use area upstream, for its main drinking-water supply. Because the stream is used for drinking water, Wilmington is in need of information about the occurrence and distribution of specific fecally derived pathogenic bacteria (disease-causing bacteria) and their relations to commonly measured fecal-indicator bacteria (FIB), as well as information regarding the potential sources of the fecal pollution and pathogens in the basin. This study focused on five routinely sampled sites within the basin, one each on the West Branch and the East Branch of Brandywine Creek and at three on the main stem below the confluence of the West and East Branches. These sites were sampled monthly for 1 year. Targeted event samples were collected on two occasions during high flow and two occasions during normal flow. On the basis of this study, high flows in the Brandywine Creek Basin were related to increases in FIB densities, and in the frequency of selected pathogen and source markers, in the West Branch and main stem of Brandywine Creek, but not in the East Branch. Water exceeding the moderate fullbody-contact single-sample recreational water-quality criteria (RWQC) for Escherichia coli (E. coli) was more likely to contain selected markers for pathogenic E. coli (eaeA,stx1, and rfbO157 gene markers) and bovine fecal sources (E. hirae and LTIIa gene markers), whereas samples exceeding the enterococci RWQC were more likely to contain the same pathogenic markers but also were more likely to carry a marker indicative of human source (esp gene marker). On four sample dates, during high flow between October and March, the West Branch was the only observed potential contributor of selected pathogen and bovine source markers to the main stem of Brandywine Creek. Indeed, the stx2 marker, which indicates a highly

Effects of substrate concentrations on the growth of heterotrophic bacteria and algae in secondary facultative ponds.

PubMed

Kayombo, S; Mbwette, T S A; Katima, J H Y; Jorgensen, S E

2003-07-01

This paper presents the effect of substrate concentration on the growth of a mixed culture of algae and heterotrophic bacteria in secondary facultative ponds (SFPs) utilizing settled domestic sewage as a sole source of organic carbon. The growth of the mixed culture was studied at the concentrations ranging between 200 and 800 mg COD/l in a series of batch chemostat reactors. From the laboratory data, the specific growth rate (micro) was determined using the modified Gompertz model. The maximum specific growth rate ( micro(max)) and half saturation coefficients (K(s)) were calculated using the Monod kinetic equation. The maximum observed growth rate ( micro(max)) for heterotrophic bacteria was 3.8 day(-1) with K(s) of 200 mg COD/l. The micro(max) for algal biomass based on suspended volatile solids was 2.7 day(-1) with K(s) of 110 mg COD/l. The micro(max) of algae based on the chlorophyll-a was 3.5 day(-1) at K(s) of 50mg COD/l. The observed specific substrate removal by heterotrophic bacteria varied between the concentrations of substrate used and the average value was 0.82 (mg COD/mg biomass). The specific substrate utilization rate in the bioreactors was direct proportional to the specific growth rate. Hence, the determined Monod kinetic parameters are useful for the definition of the operation of SFPs.

A single method for recovery and concentration of enteric viruses and bacteria from fresh-cut vegetables.

PubMed

Sánchez, G; Elizaquível, P; Aznar, R

2012-01-03

Fresh-cut vegetables are prone to be contaminated with foodborne pathogens during growth, harvest, transport and further processing and handling. As most of these products are generally eaten raw or mildly treated, there is an increase in the number of outbreaks caused by viruses and bacteria associated with fresh vegetables. Foodborne pathogens are usually present at very low levels and have to be concentrated (i.e. viruses) or enriched (i.e. bacteria) to enhance their detection. With this aim, a rapid concentration method has been developed for the simultaneous recovery of hepatitis A virus (HAV), norovirus (NV), murine norovirus (MNV) as a surrogate for NV, Escherichia coli O157:H7, Listeria monocytogenes and Salmonella enterica. Initial experiments focused on evaluating the elution conditions suitable for virus release from vegetables. Finally, elution with buffered peptone water (BPW), using a Pulsifier, and concentration by polyethylene glycol (PEG) precipitation were the methods selected for the elution and concentration of both, enteric viruses and bacteria, from three different types of fresh-cut vegetables by quantitative PCR (qPCR) using specific primers. The average recoveries from inoculated parsley, spinach and salad, were ca. 9.2%, 43.5%, and 20.7% for NV, MNV, and HAV, respectively. Detection limits were 132 RT-PCR units (PCRU), 1.5 50% tissue culture infectious dose (TCID₅₀), and 6.6 TCID₅₀ for NV, MNV, and HAV, respectively. This protocol resulted in average recoveries of 57.4%, 64.5% and 64.6% in three vegetables for E. coli O157:H7, L. monocytogenes and Salmonella with corresponding detection limits of 10³, 10² and 10³ CFU/g, respectively. Based on these results, it can be concluded that the procedure herein is suitable to recover, detect and quantify enteric viruses and foodborne pathogenic bacteria within 5 h and can be applied for the simultaneous detection of both types of foodborne pathogens in fresh-cut vegetables. Copyright �

Concentration and Viability of Airborne Bacteria Over the Kuroshio Extension Region in the Northwestern Pacific Ocean: Data From Three Cruises

NASA Astrophysics Data System (ADS)

Hu, Wei; Murata, Kotaro; Fukuyama, Shinichiro; Kawai, Yoshimi; Oka, Eitarou; Uematsu, Mitsuo; Zhang, Daizhou

2017-12-01

Airborne bacteria have been shown to act as condensation and ice nuclei in mixed-phase clouds and are consequently hypothesized to have significant effects on atmospheric processes and even the global climate. However, few data are available regarding their concentration and variation in the air over the open ocean. Aerosol samples were collected during three cruises in the early summers of 2013, 2014, and 2016 over the Kuroshio Extension region of the northwest Pacific Ocean. The concentrations of viable and nonviable bacterial cells in the marine surface air were quantified using epifluorescence enumeration with the LIVE/DEAD BacLight stain. The concentrations of total bacteria varied between 1.0 × 104 and 2.5 × 105 cells m-3 and averaged 5.2 × 104, 1.0 × 105, and 7.5 × 104 cells m-3 in the three respective cruises. The viabilities, i.e., the ratios of the concentration of viable bacterial cells to that of total bacterial cells, ranged from 80% to 100% (average 93%), and the respective means were 93%, 89%, and 96% in the cruises. The total bacterial concentration had a close correlation with the wind speed near the sea surface, and the bacterial viability correlated negatively with the air temperature, sea surface temperature, and concentration of coarse particles (size > 1 μm). The deposition and sea spray fluxes of bacteria were roughly estimated as hundreds of cells m-2 s-1 on average. The limited data on bacterial concentration and viability from the three cruises indicate the rapid air-sea exchange of bacteria over the Kuroshio Extension region of the northwest Pacific Ocean.

Effects of combined sewer overflow and stormwater on indicator bacteria concentrations in the Tama River due to the high population density of Tokyo Metropolitan area.

PubMed

Ham, Young-Sik; Kobori, Hiromi; Takasago, Masahisa

2009-05-01

The indicator bacteria (standard plate count, total coliform, and fecal coliform bacteria) concentrations have been investigated using six ambient habitats (population density, percent sewer penetration, stream flow rate (m(3)/sec), percent residential area, percent forest area and percent agricultural area) in the Tama River basin in Tokyo, Japan during June 2003 to January 2005. The downstream and tributary Tama River showed higher concentrations of TC and FC bacteria than the upstream waters, which exceeded an environmental quality standard for rivers and a bathing water quality criterion. It was estimated that combined sewer overflow (CSO) and stormwater effluents contributed -4-23% to the indicator bacteria concentrations of the Tama River. The results of multiple regression analyses show that the indicator bacteria concentrations of Tama River basin are significantly affected by population density. It is concluded that the Tama River received a significant bacterial contamination load originating from the anthropogenic source.

Analysis of the Relationship Between Physical Environmental Parameters and Beach Water Quality in a Subtropical Setting

NASA Astrophysics Data System (ADS)

Zhu, X.; Wang, J. D.; Elmir, S.; Solo-Gabriele, H. M.; Wright, M. E.; Abdelzaher, A.

2006-12-01

Fecal Indicator Bacteria(FIB) are found in high concentrations in sewage water, and thus are used to indicate whether there is fecal material related pathogen present and to determine whether a beach is safe for recreational use. Studies have shown, however, in subtropical regions, FIB concentrations above EPA standards may be present in the absence of known point sources of human or animal waste, thus reducing the efficacy of FIB beach monitoring programs. An interdisciplinary study is being conducted in Miami, Florida , the goal is to understand the sources and behavior of FIB on a beach without point source loads and also to improve beach health hazard warnings in subtropical regions. This study, examines relationship between enterococci (EPA recommended FIB for use in marine water) and physical environmental parameters such as rain, tide and wind. FIB data employed include Florida Department of Health weekly beach monitoring enterococci (ENT) data during a five year period and a two-day experiment with hourly sampling at Hobie Cat Beach on Virginia Key in the Miami metropolitan area. The environmental data consist of wind from a nearby CMAN tower, and local rain and tide. The analysis also includes data from nearby beaches monitored by the Health Department. Results show the correlation coefficient between ENT and tide at Hobie Cat Beach is positive but not significant(r=0.17). Rain events have a significant influence on ENT at Hobie Cat Beach, with a correlation coefficient of up to 0.7 while at other beaches the correlation is less than 0.2. Reasons for this aberration are being investigated. Although this is the only beach allowing dogs there are other factors of possible importance, such as tidal flats frequented by birds and weaker water circulation and exchange at this beach facing a bay rather than the ocean. Higher ENT levels (> 300CFU/100ml water) are more likely (67% of the time) to be associated with periods of onshore winds, which may affect the

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons.

PubMed

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3-4 and 8-9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

A Genetic Cascade of let-7-ncl-1-fib-1 Modulates Nucleolar Size and rRNA Pool in Caenorhabditis elegans

PubMed Central

Chiou, Pey-Tsyr; Chen, Po-Hsiang; Lee, Ching-Ming; Chu, Yu-De; Yu, Hsiang; Hsiung, Kuei-Ching; Tsai, Yi-Tzang; Lee, Chi-Chang; Chang, Yu-Sun; Chan, Shih-Peng; Tan, Bertrand Chin-Ming; Lo, Szecheng J.

2015-01-01

Ribosome biogenesis takes place in the nucleolus, the size of which is often coordinated with cell growth and development. However, how metazoans control nucleolar size remains largely unknown. Caenorhabditis elegans provides a good model to address this question owing to distinct tissue distribution of nucleolar sizes and a mutant, ncl-1, which exhibits larger nucleoli than wild-type worms. Here, through a series of loss-of-function analyses, we report that the nucleolar size is regulated by a circuitry composed of microRNA let-7, translation repressor NCL-1, and a major nucleolar pre-rRNA processing protein FIB-1/fibrillarin. In cooperation with RNA binding proteins PUF and NOS, NCL-1 suppressed the translation of FIB-1/fibrillarin, while let-7 targeted the 3’UTR of ncl-1 and inhibited its expression. Consequently, the abundance of FIB-1 is tightly controlled and correlated with the nucleolar size. Together, our findings highlight a novel genetic cascade by which post-transcriptional regulators interplay in developmental control of nucleolar size and function. PMID:26492166

Evaluation of APRI and FIB-4 for noninvasive assessment of significant fibrosis and cirrhosis in HBeAg-negative CHB patients with ALT ≤ 2 ULN

PubMed Central

Li, Qiang; Ren, Xiaojing; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-01-01

Abstract To evaluate the performance of aspartate transaminase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4) to predict significant fibrosis and cirrhosis in hepatitis B virus e antigen (HBeAg)-negative chronic hepatitis B (CHB) patients with alanine transaminase (ALT) ≤ twice the upper limit of normal (2 ULN). Histologic and laboratory data of 236 HBeAg-negative CHB patients with ALT ≤ 2 ULN were analyzed. Predicted fibrosis stage, based on established scales and cut-offs for APRI and FIB-4, was compared with METAVIR scores obtained from liver biopsy. In this study, the areas under the receiver operating characteristic curves (AUROCs) of APRI were lower than that of FIB-4 (0.62 vs 0.69; P = 0.019) for diagnosing significant fibrosis; however APRI and FIB-4 were comparable for diagnosing cirrhosis (0.77 vs 0.81; P = 0.374). When the cut-off proposed by WHO HBV guideline for APRI (>2.0) was used, no cirrhotic patients were correctly predicted. For FIB-4, the WHO proposed cut-off of 3.25 correctly identified significant fibrosis 83% of the time; but for APRI, the WHO proposed cut-off of 1.5 identified significant fibrosis 56%. In ruling out significant fibrosis, the WHO proposed APRI cut-off of 0.5 had a predictive value of 39%, and the FIB-4 cut-off of 1.45 correctly identified lack of significant fibrosis in 47% of the patients. In this study, based on ROC analysis, the optimal cut-offs were 0.46 and 0.65 for APRI, and 1.05 and 1.29 for FIB-4, for diagnosing significant fibrosis and cirrhosis, respectively. When the new cut-off of APRI (>0.65) was used, 82% of the cirrhotic patients were correctly predicted. In ruling out significant fibrosis, the new APRI cut-off (<0.46) had a predictive value of 80%, and new FIB-4 cut-off (<1.05) correctly identified lack of significant fibrosis in 84% of the patients. The WHO guidelines proposed cut-offs might be higher for HBeAg-negative CHB patients with ALT ≤2 ULN, and

Making the practically impossible "Merely difficult"--Cryogenic FIB lift-out for "Damage free" soft matter imaging.

PubMed

Parmenter, Christopher D J; Fay, Michael W; Hartfield, Cheryl; Eltaher, Hoda M

2016-04-01

The preparation of thinned lamellae from bulk samples for transmission electron microscopy (TEM) analysis has been possible in the focussed ion beam scanning electron microscope (FIB-SEM) for over 20 years via the in situ lift-out method. Lift-out offers a fast and site specific preparation method for TEM analysis, typically in the field of materials science. More recently it has been applied to a low-water content biological sample (Rubino 2012). This work presents the successful lift-out of high-water content lamellae, under cryogenic conditions (cryo-FIB lift-out) and using a nanomanipulator retaining its full range of motion, which are advances on the work previously done by Rubino (2012). Strategies are explored for maintaining cryogenic conditions, grid attachment using cryo-condensation of water and protection of the lamella when transferring to the TEM. © 2016 Wiley Periodicals, Inc.

Airborne Multidrug-Resistant Bacteria Isolated from a Concentrated Swine Feeding Operation

PubMed Central

Chapin, Amy; Rule, Ana; Gibson, Kristen; Buckley, Timothy; Schwab, Kellogg

2005-01-01

The use of nontherapeutic levels of antibiotics in swine production can select for antibiotic resistance in commensal and pathogenic bacteria in swine. As a result, retail pork products, as well as surface and groundwaters contaminated with swine waste, have been shown to be sources of human exposure to antibiotic-resistant bacteria. However, it is unclear whether the air within swine operations also serves as a source of exposure to antibiotic-resistant bacterial pathogens. To investigate this issue, we sampled the air within a concentrated swine feeding operation with an all-glass impinger. Samples were analyzed using a method for the isolation of Enterococcus. A total of 137 presumptive Enterococcus isolates were identified to species level using standard biochemical tests and analyzed for resistance to erythromycin, clindamycin, virginiamycin, tetracycline, and vancomycin using the agar dilution method. Thirty-four percent of the isolates were confirmed as Enterococcus, 32% were identified as coagulase-negative staphylococci, and 33% were identified as viridans group streptococci. Regardless of bacterial species, 98% of the isolates expressed high-level resistance to at least two antibiotics commonly used in swine production. None of the isolates were resistant to vancomycin, an antibiotic that has never been approved for use in livestock in the United States. In conclusion, high-level multidrug-resistant Enterococcus, coagulase-negative staphylococci, and viridans group streptococci were detected in the air of a concentrated swine feeding operation. These findings suggest that the inhalation of air from these facilities may serve as an exposure pathway for the transfer of multidrug-resistant bacterial pathogens from swine to humans. PMID:15687049

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms.

PubMed

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-06-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH(4)(+)-N per gram of soil) and high (200 μg NH(4)(+)-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

PubMed Central

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-01-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH4+-N per gram of soil) and high (200 μg NH4+-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil. PMID:21228892

Implementation of focused ion beam (FIB) system in characterization of nuclear fuels and materials

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

A. Aitkaliyeva; J. W. Madden; B. D. Miller

2014-10-01

Beginning in 2007, a program was established at the Idaho National Laboratory to update key capabilities enabling microstructural and micro-chemical characterization of highly irradiated and/or radiologically contaminated nuclear fuels and materials at scales that previously had not been achieved for these types of materials. Such materials typically cannot be contact handled and pose unique hazards to instrument operators, facilities, and associated personnel. One of the first instruments to be acquired was a Dual Beam focused ion beam (FIB)-scanning electron microscope (SEM) to support preparation of transmission electron microscopy and atom probe tomography samples. Over the ensuing years, techniques have beenmore » developed and operational experience gained that has enabled significant advancement in the ability to characterize a variety of fuel types including metallic, ceramic, and coated particle fuels, obtaining insights into in-reactor degradation phenomena not obtainable by any other means. The following article describes insights gained, challenges encountered, and provides examples of unique results obtained in adapting Dual Beam FIB technology to nuclear fuels characterization.« less

APRI, the FIB-4 score, and Forn's index have noninvasive diagnostic value for liver fibrosis in patients with chronic hepatitis B.

PubMed

Ucar, Fatma; Sezer, Sevilay; Ginis, Zeynep; Ozturk, Gulfer; Albayrak, Aynur; Basar, Omer; Ekiz, Fuat; Coban, Sahin; Yuksel, Osman; Armutcu, Ferah; Akbal, Erdem

2013-09-01

The aim of this study was to evaluate the potential use of serum transforming growth factor-β1 (TGF-β1), tissue inhibitor of metalloproteinase-1 (TIMP-1), fetuin-A, and fibroblast growth factor 21 (FGF21) in the detection of liver fibrosis in patients with chronic hepatitis B (CHB). The value of the noninvasive fibrosis models - that is, the aspartate aminotransferase to platelet ratio index (APRI), the fibrosis index based on the four factors (FIB-4) score, and Forn's index - was also examined. CHB patients who underwent liver biopsy for the evaluation of fibrosis were included in the study. A total of 73 patients were divided into two groups according to their METAVIR scores (F0-1, no/minimal fibrosis; F2-4, significant fibrosis). Serum levels of TGF-β1, TIMP-1, fetuin-A, and FGF21 were measured besides APRI, FIB-4, and Forn's scores. The area under the receiver operating characteristic curve was measured for each parameter, followed by calculation of sensitivity, specificity, and positive and negative predictive values. APRI, FIB-4, and Forn's index scores were significantly higher in patients with significant fibrosis (P<0.05). There was no difference between no/minimal fibrosis and significant fibrosis groups in terms of serum levels of TGFβ-1, TIMP-1, fetuin-A, and FGF21 (P>0.05). The areas under the receiver operating characteristic curve for TGF-β1, TIMP-1, fetuin-A, FGF21, APRI, FIB-4, and Forn's index were 0.445, 0.483, 0.436, 0.585, 0.662, 0.687, and 0.680, respectively. Our results suggest that serum TGF-β1, TIMP-1, fetuin-A, and FGF21 are not useful for the assessment of the extent of liver fibrosis in CHB in this patient group. However, APRI, FIB-4, and Forn's index have a better diagnostic value in patients with significant fibrosis than in those with no/minimal fibrosis.

Simultaneous concentration of bovine viruses and agricultural zoonotic bacteria from water using sodocalcic glass wool filters

USDA-ARS?s Scientific Manuscript database

Infiltration and runoff from manured agricultural fields can result in livestock pathogens reaching groundwater and surface waters. Here, we measured the effectiveness of glass wool filters to simultaneously concentrate enteric viruses and bacteria of bovine origin from water. The recovery efficienc...

Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging.

PubMed

Schieber, Nicole L; Machado, Pedro; Markert, Sebastian M; Stigloher, Christian; Schwab, Yannick; Steyer, Anna M

2017-01-01

Correlative light and electron microscopy (CLEM) is a powerful tool to perform ultrastructural analysis of targeted tissues or cells. The large field of view of the light microscope (LM) enables quick and efficient surveys of the whole specimen. It is also compatible with live imaging, giving access to functional assays. CLEM protocols take advantage of the features to efficiently retrace the position of targeted sites when switching from one modality to the other. They more often rely on anatomical cues that are visible both by light and electron microscopy. We present here a simple workflow where multicellular specimens are embedded in minimal amounts of resin, exposing their surface topology that can be imaged by scanning electron microscopy (SEM). LM and SEM both benefit from a large field of view that can cover whole model organisms. As a result, targeting specific anatomic locations by focused ion beam-SEM (FIB-SEM) tomography becomes straightforward. We illustrate this application on three different model organisms, used in our laboratory: the zebrafish embryo Danio rerio, the marine worm Platynereis dumerilii, and the dauer larva of the nematode Caenorhabditis elegans. Here we focus on the experimental steps to reduce the amount of resin covering the samples and to image the specimens inside an FIB-SEM. We expect this approach to have widespread applications for volume electron microscopy on multiple model organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

Diagnostic value of FIB-4 for liver fibrosis in patients with hepatitis B: a meta-analysis of diagnostic test.

PubMed

Yin, Zhi; Zou, Jin; Li, Qiongxuan; Chen, Lizhang

2017-04-04

This study is aimed at evaluating the diagnostic value of FIB-4 for liver fibrosis in patients with hepatitis B through a meta-analysis of diagnostic test. We conducted a comprehensive search in the Pubmed, Embase, Web of Science, and Chinese National Knowledge Infrastructure before October 31, 2016. Stata 14.0 software was used for calculation and statistical analyses. We used the sensitivity, specificity, positive and negative likelihood ratio (PLR, NLR), diagnostic odds ratio (DOR) and 95% confidence intervals (CIs) to evaluate the diagnostic value of FIB-4 for liver fibrosis in patients with hepatitis B. Twenty-six studies were included in the final analyses, with a total of 8274 individuals. The pooled parameters are calculated from all studies: sensitivity of 0.69 (95%CI:0.63-0.75), specificity of 0.81 (95%CI: 0.73-0.87), PLR of 3.63 (95%CI:2.66-4.94), NLR of 0.38 (95%CI:0.32-0.44), DOR of 9.57 (95%CI: 6.67-13.74), and area under the curve (AUC) of 0.80 (95%CI: 0.76-0.83). We also conducted subgroup based on the range of cut-off values. Results from subgroup analysis showed that cut-off was the source of heterogeneity in the present study. The sensitivity and specificity of cut-off>2 were 0.69 and 0.95 with the AUC of 0.90 (95%CI: 0.87-0.92). The overall diagnostic value of FIB-4 is not very high for liver fibrosis in patients with hepatitis B. However, the diagnostic value is affected by the cut-off value. FIB-4 has relatively high diagnostic value for detecting liver fibrosis in patients with hepatitis B when the diagnostic threshold value is more than 2.0.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

PubMed Central

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M.; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X.; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner. PMID:26052271

FIB-NanoSIMS-TEM Coordinated Study of a Wark-Lovering Rim in a Vigarano Type A CAI

NASA Technical Reports Server (NTRS)

Cai, A.; Ito, M.; Keller, L. P.; Ross, D. K.; Nakamura-Messenger, K.

2010-01-01

Wark-Lovering (WL) rims are thin multi layered mineral sequences that surround most Ca, Al-rich inclusions (CAIs). Unaltered WL rims are composed of the same primary high temperature minerals as CAIs, such as melilite, spinel, pyroxene, hibonite, perovskite, anorthite and olivine. It is still unclear whether the rim minerals represent a different generation formed by a separate event from their associated CAIs or are a byproduct of CAI formation. Several models have been proposed for the origins of WL rims including condensation, flashheating, reaction of a CAI with a Mg-Si-rich reservoir (nebular gas or solid); on the basis of mineralogy, abundances of trace elements, O and Mg isotopic studies. Detailed mineralogical characterizations of WL rims at micrometer to nanometer scales have been obtained by TEM observations, but so far no coordinated isotopic - mineralogical studies have been performed. Thus, we have applied an O isotopic imaging technique by NanoSIMS 50L to investigate heterogeneous distributions of O isotopic ratios in minerals within a cross section of a WL rim prepared using a focused ion beam (FIB) instrument. After the isotopic measurements, we determine the detailed mineralogy and microstructure of the same WL FIB section to gain insight into its petrogenesis. Here we present preliminary results from O isotopic and elemental maps by NanoSIMS and mineralogical analysis by FE-SEM of a FIB section of a WL rim in the Vigarano reduced CV3 chondrite.

Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation.

PubMed

Belanche, Alejandro; Doreau, Michel; Edwards, Joan E; Moorby, Jon M; Pinloche, Eric; Newbold, Charles J

2012-09-01

Balancing energy and nitrogen in the rumen is a key to both profitability and environmental sustainability. Four dairy cows were used in a Latin square experimental design to investigate the effect of severe nitrogen underfeeding (110 vs. 80% of requirements) and the type of carbohydrate consumed [neutral detergent fiber rich (FIB) vs. starch rich (STA)] on the rumen ecosystem. These dietary treatments modified both rumen fermentation and microbial populations. Compared with STA diets, consumption of FIB diets increased bacterial and fungal diversity in the rumen and also increased the concentrations of cellulolytic microorganisms, including protozoa (+38%), anaerobic fungi (+59%), and methanogens (+27%). This microbial adaptation to fiber utilization led to similar digestibility values for the 2 carbohydrate sources and was accompanied by a shift in the rumen fermentation patterns; when the FIB diets were consumed, the cows had greater ruminal pH, ammonia concentrations, and molar proportions of acetate and propionate compared with when they consumed the STA diets. Certain rumen microorganisms were sensitive to a shortage of nitrogen; rumen concentrations of ammonia were 49% lower when the low-protein (LP) diets were consumed as were total bacteria (-13%), anaerobic fungi (-28%), methanogens (-27%), protozoa (-19%), cellulolytic bacteria, and microbial diversity compared with when the high-protein (HP) diets were consumed. As a result, the digestibility of the LP diets was less than that of the HP diets. These findings demonstrated that the rumen microbial ecosystem is directly linked to the rumen fermentation pattern and, to some extent, to the efficiency of diet utilization by dairy cattle.

Inactivation of Gram-negative and Gram-positive bacteria in red cell concentrates using INACTINE PEN110 chemistry.

PubMed

Zavizion, B; Serebryanik, D; Chapman, J; Alford, B; Purmal, A

2004-10-01

The risk of transfusion-transmitted bacterial infections as a result of the presence of bacteria in blood is one of the major concerns in transfusion medicine. The purpose of this study was to investigate whether bacteria inoculated into red blood cell concentrates can be inactivated by the INACTINE PEN110 pathogen-reduction process. Four bacterial species were chosen for the study: anaerobic Gram-positive Clostridium perfringens and Propionibacterium acnes, known to be transfusion-transmitted; and two Gram-negative species, Acinetobacter johnsonii and Acinetobacter lwoffii, recently reported to be a common cause of transfusion-associated infections in Europe. Identical units of leucoreduced red cell concentrates were inoculated with A. johnsonii, A. lwoffii, C. perfringens, or P. acnes. The 4 degrees C control units were put on storage immediately after receiving the spike. The test units were subjected to PEN110 treatment and then stored. The bacterial titre in all units was monitored during a 6-week storage period. The PEN110 inactivation of all tested bacterial strains was time- and titre-dependent. For A. johnsonii and A. lwoffii, no viable bacteria were detected in the units spiked with up to 10(4) colony-forming units (CFU)/ml and treated with PEN110. For red cell units spiked with 10(4)-10(5) CFU/ml of C. perfringens and P. acnes, no viable bacteria were detected in the units treated with PEN110. In control units, there was a gradual decrease in A. johnsonii, A. lwoffii and C. perfringens titres during cold storage, while P. acnes titres remained stable. The PEN110 pathogen-reduction process was demonstrated to inactivate high titres of A. johnsonii, A. lwoffii, C. perfringens and P. acnes in red cell concentrates.

Image contrast enhancement of Ni/YSZ anode during the slice-and-view process in FIB-SEM.

PubMed

Liu, Shu-Sheng; Takayama, Akiko; Matsumura, Syo; Koyama, Michihisa

2016-03-01

Focused ion beam-scanning electron microscopy (FIB-SEM) is a widely used and easily operational equipment for three-dimensional reconstruction with flexible analysis volume. It has been using successfully and increasingly in the field of solid oxide fuel cell. However, the phase contrast of the SEM images is indistinct in many cases, which will bring difficulties to the image processing. Herein, the phase contrast of a conventional Ni/yttria stabilized zirconia anode is tuned in an FIB-SEM with In-Lens secondary electron (SE) and backscattered electron detectors. Two accessories, tungsten probe and carbon nozzle, are inserted during the observation. The former has no influence on the contrast. When the carbon nozzle is inserted, best and distinct contrast can be obtained by In-Lens SE detector. This method is novel for contrast enhancement. Phase segmentation of the image can be automatically performed. The related mechanism for different images is discussed. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

FE-SEM, FIB and TEM Study of Surface Deposits of Apollo 15 Green Glass Volcanic Spherules

NASA Technical Reports Server (NTRS)

Ross, Daniel K.; Thomas-Keprta, K. L.; Rahman, Z.; Wentworth, S. J.; McKay, D. S.

2011-01-01

Surface deposits on lunar pyroclastic green (Apollo 15) and orange (Apollo 17) glass spherules have been attributed to condensation from the gas clouds that accompanied fire-fountain eruptions. The fire fountains cast molten lava high above the lunar surface and the silicate melt droplets quenched before landing producing the glass beads. Early investigations showed that these deposits are rich in sulfur and zinc. The deposits are extremely fine-grained and thin, so that it was never possible to determine their chemical compositions cleanly by SEM/EDX or electron probe x-ray analysis because most of the excited volume was in the under-lying silicate glass. We are investigating the surface deposits by TEM, using focused ion beam (FIB) microscopy to extract and thin the surface deposits. Here we report on chemical mapping of a FIB section of surface deposits of an Apollo green glass bead 15401using the ultra-high resolution JEOL 2500 STEM located at NASA Johnson Space Center.

Compositional and Microstructural Evolution of Olivine During Pulsed Laser Irradiation: Insights Based on a FIB/Field-Emission TEM Study

NASA Technical Reports Server (NTRS)

Christoffersen, R.; Loeffler, M. J.; Dukes, C. A.; Baragiola, R. A.

2015-01-01

Introduction: The use of pulsed laser irradiation to simulate the short duration, high-energy conditions characteristic of micrometeorite impacts is now an established approach in experimental space weathering studies. The laser generates both melt and vapor deposits that contain nanophase metallic Fe (npFe(sup 0)) grains with size distributions and optical properties similar to those in natural impact-generated melt and vapor deposits. There remains uncertainty, however, about how well lasers simulate the mechanical work and internal (thermal) energy partitioning that occurs in actual impacts. We are currently engaged in making a direct comparison between the products of laser irradiation and experimental/natural hypervelocity impacts. An initial step reported here is to use analytical TEM is to attain a better understanding of how the microstructure and composition of laser deposits evolve over multiple cycles of pulsed laser irradiation. Experimental Methods: We irradiated pressed-powder pellets of San Carlos olivine (Fo(sub 90)) with up to 99 rastered pulses of a GAM ArF excimer laser. The irradiated surface of the sample were characterized by SEM imaging and areas were selected for FIB cross sectioning for TEM study using an FEI Quanta dual-beam electron/focused ion beam instrument. FIB sections were characterized using a JEOL2500SE analytical field-emission scanning transmission electron microscope (FE-STEM) optimized for quantitative element mapping at less than 10 nm spatial resolutions. Results: In the SEM the 99 pulse pressed pellet sample shows a complex, inhomogeneous, distribution of laser-generated material, largely concentrated in narrow gaps and larger depressions between grains. Local concentrations of npFe0 spherules 0.1 to 1 micrometers in size are visible within these deposits in SEM back-scatter images. Fig. 1 shows bright-field STEM images of a FIB cross-section of a one of these deposits that continuously covers the top and sloping side of an

A flexible method for the preparation of thin film samples for in situ TEM characterization combining shadow-FIB milling and electron-beam-assisted etching.

PubMed

Liebig, J P; Göken, M; Richter, G; Mačković, M; Przybilla, T; Spiecker, E; Pierron, O N; Merle, B

2016-12-01

A new method for the preparation of freestanding thin film samples for mechanical testing in transmission electron microscopes is presented. It is based on a combination of focused ion beam (FIB) milling and electron-beam-assisted etching with xenon difluoride (XeF 2 ) precursor gas. The use of the FIB allows for the target preparation of microstructural defects and enables well-defined sample geometries which can be easily adapted in order to meet the requirements of various testing setups. In contrast to existing FIB-based preparation approaches, the area of interest is never exposed to ion beam irradiation which preserves a pristine microstructure. The method can be applied to a wide range of thin film material systems compatible with XeF 2 etching. Its feasibility is demonstrated for gold and alloyed copper thin films and its practical application is discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous effect of temperature, cyanide and ammonia-oxidizing bacteria concentrations on ammonia oxidation.

PubMed

Do, Hyojin; Lim, Juntaek; Shin, Seung Gu; Wu, Yi-Ju; Ahn, Johng-Hwa; Hwang, Seokhwan

2008-11-01

For biological nitrification, a set of experiments were carried out to approximate the response of lag period along with ammonia oxidation rate with respect to different concentrations of cyanide (CN-) and ammonia-oxidizing bacteria (AOB), and temperature variation in laboratory-scale batch reactors. The effects of simultaneous changes in these three factors on ammonia oxidation were quantitatively estimated and modeled using response surface analysis. The lag period and the ammonia oxidation rate responded differently to changes in the three factors. The lag period and the ammonia oxidation rate were significantly affected by the CN- and AOB concentrations, while temperature changes only affected the ammonia oxidation rate. The increase of AOB concentration and temperature alleviated the inhibition effect of cyanide on ammonia oxidation. The statistical method used in this study can be extended to estimate the quantitative effects of other environmental factors that can change simultaneously.

Ability of Cytokeratin-18 Fragments and FIB-4 Index to Diagnose Overall and Mild Fibrosis Nonalcoholic Steatohepatitis in Japanese Nonalcoholic Fatty Liver Disease Patients.

PubMed

Kobayashi, Natsuko; Kumada, Takashi; Toyoda, Hidenori; Tada, Toshifumi; Ito, Takanori; Kage, Masayoshi; Okanoue, Takeshi; Kudo, Masatoshi

2017-01-01

Several laboratory markers used in lieu of liver biopsy are reportedly useful in the diagnosis of nonalcoholic steatohepatitis (NASH). In the present study, we investigated the diagnostic impact of various non-invasive markers for predicting NASH. A total of 229 nonalcoholic fatty liver disease (NAFLD) patients who underwent liver biopsy were enrolled for the study. The diagnostic ability of various markers to diagnose NASH from NAFLD was investigated. A total of 140 patients were histologically diagnosed with NASH. Of these, 104 had degree 0-2 fibrosis (F0-2), and 36 had degree 3-4 fibrosis (F3-4). Multiple logistic regression analysis identified hyaluronic acid (HA) (OR 1.014; 95% CI 1.002-1.026; p = 0.024), FIB-4 index (OR 2.097; 95% CI 1.177-3.735; p = 0.012), and cytokeratin-18 fragments (CK-18F) (OR 1.002; 95% CI 1.001-1.002; p < 0.001) as factors independently associated with the diagnosis of NASH. The areas under the receiver operating characteristic curves (AUROCs) of HA, FIB-4 index, and CK-18F for the diagnosis of NASH were 0.77, 0.76, and 0.72, respectively. In addition, FIB-4 index (OR 1.907; 95% CI 1.063-3.419; p = 0.03) and CK-18F (OR 1.002; 95% CI 1.001-1.002; p < 0.001) could differentiate between NASH and NAFL, even when NASH patients with advanced fibrosis (F3-4) were excluded. AUROCs of FIB-4 index and CK-18F for the diagnosis of NASH with mild fibrosis (F0-2) from NAFLD were 0.70 and 0.70, respectively. FIB-4 index and CK-18F have good diagnostic abilities not only for NASH overall, but also for NASH with mild fibrosis. © 2017 S. Karger AG, Basel.

Value of Egy-Score in diagnosis of significant, advanced hepatic fibrosis and cirrhosis compared to aspartate aminotransferase-to-platelet ratio index, FIB-4 and Forns' index in chronic hepatitis C virus.

PubMed

Alboraie, Mohamed; Khairy, Marwa; Elsharkawy, Marwa; Asem, Noha; Elsharkawy, Aisha; Esmat, Gamal

2015-05-01

Serum markers and developed scores are of rising importance in non-invasive diagnosis of hepatic fibrosis. Aspartate aminotransferase-to-platelet ratio index (APRI), FIB-4 and Forns' index are validated scores used for diagnosis of liver fibrosis. The Egy-Score is a newly developed score for detection of hepatic fibrosis with promising results. We aimed to assess the accuracy of the Egy-Score in the diagnosis of significant fibrosis, advanced fibrosis and cirrhosis compared to APRI, FIB-4 and Forns' in chronic hepatitis C virus (HCV) patients. A retrospective study including 100 chronic hepatitis C naïve Egyptian patients was performed. Patients were classified according to stages of fibrosis into three groups: significant fibrosis (≥ F2), advanced fibrosis (≥ F3) and cirrhosis (F4). Egy-Score, APRI, FIB-4 and Forns' index were calculated. Regression analysis and receiver-operator curves were plotted to assess the sensitivity, specificity and predictive values for the significant scores with the best cut-off for diagnosis. An Egy-Score of 3.28 or more was superior to APRI, FIB-4 and Forns' index for detecting advanced fibrosis with a sensitivity of 91% and specificity of 78%. An Egy-Score of 3.67 or more was superior to APRI, FIB-4 and Forns' index for detecting cirrhosis with a sensitivity of 82% and specificity of 87%. Forns' index was superior to Egy-Score, FIB-4 and APRI for detecting significant fibrosis. The Egy-Score is a promising, accurate, easily calculated, cost-effective score in the prediction of hepatic fibrosis in chronic HCV patients with superiority over APRI, FIB-4 and Forns' index in advanced hepatic fibrosis and cirrhosis. © 2014 The Japan Society of Hepatology.

The Diagnostic Value of the FIB-4 Index for Staging Hepatitis B-Related Fibrosis: A Meta-Analysis

PubMed Central

Li, Yuanyuan; Chen, Yu; Zhao, Ying

2014-01-01

Background Liver fibrosis stage is an important factor in determining prognosis and need for treatment in patients infected with hepatitis B virus (HBV). Liver biopsies are typically used to assess liver fibrosis; however, noninvasive alternatives such as the FIB-4 index have also been developed. Aims To quantify the accuracy of the FIB-4 index in the diagnosis of HBV related fibrosis and cirrhosis. Methods A meta-analysis of studies comparing the diagnostic accuracy of the FIB-4 index vs. liver biopsy in HBV-infected patients was performed using studies retrieved from the following databases: PubMed, Ovid, EMBASE, the Cochrane Library, the Chinese National Knowledge Infrastructure and the Chinese Biology Medicine disc. A hierarchical summary receiver operating curves model and bivariate model were used to produce summary receiver operating characteristic curves and pooled estimates of sensitivity and specificity. The heterogeneity was explored with meta-regression analysis. Publication bias was detected using Egger’s test and the trim and fill method. Results 12 studies (N = 1,908) and 10 studies (N = 2,105) were included in the meta-analysis for significant fibrosis and cirrhosis, respectively. For significant fibrosis, the area under the hierarchical summary receiver operating curve (AUHSROC) was 0.78 (95% CI = 0.74–0.81). The recommended cutoff value was between 1.45 and 1.62, and the AUHSROC, summary sensitivity and specificity were 0.78 (95% CI = 0.74–0.81), 0.65 (95% CI = 0.56–0.73) and 0.77 (95% CI = 0.7–0.83), respectively. For cirrhosis, the AUHSROC was 0.89 (95% CI = 0.85–0.91). The recommended cutoff value was between 2.9 and 3.6, and the AUHSROC, summary sensitivity and specificity were 0.96 (95% CI = 0.92–1.00), 0.42 (95% CI = 0.36–0.48) and 0.96 (95% CI = 0.95–0.97), respectively. No publication bias was detected. Conclusions The FIB-4 index is valuable for detecting significant fibrosis and

Impact of FIB-4 index on hepatocellular carcinoma incidence during nucleos(t)ide analogue therapy in patients with chronic hepatitis B: An analysis using time-dependent receiver operating characteristic.

PubMed

Tada, Toshifumi; Kumada, Takashi; Toyoda, Hidenori; Tsuji, Kunihiko; Hiraoka, Atsushi; Tanaka, Junko

2017-02-01

Nucleos(t)ide analogue (NA) therapy has been reported to reduce the risk of hepatocellular carcinoma (HCC) development in patients with chronic hepatitis B (CHB). However, even during NA therapy, development of HCC has been observed in patients with CHB. Therefore, we clarified the predictive power of clinical factors for HCC incidence using receiver operating characteristic (ROC) analysis that takes time dependence into account. A total of 539 patients with CHB treated with NAs were enrolled. Univariate, multivariate, and time-dependent ROC curves for clinical factors associated with the development of HCC were analyzed. Eighty-one patients developed HCC during the follow-up period (median duration, 5.9 years). α-fetoprotein (AFP) and FIB-4 index at 24 weeks from the initiation of treatment and sex were significantly associated with HCC incidence according to the log-rank test. Cox proportional hazards models including the covariates of sex, hepatitis B genotype, basal core promoter mutations, AFP at 24 weeks, and FIB-4 index at 24 weeks showed that FIB-4 index >2.65 (HR, 5.03; 95% CI, 3.06-8.26; P < 0.001) and male sex were independently associated with HCC incidence. In addition, time-dependent ROC analysis showed that compared with AFP at 24 weeks, FIB-4 index at 24 weeks had higher predictive power for HCC incidence throughout the follow-up period. Elevated FIB-4 index at 24 weeks in patients with CHB receiving NA therapy is a risk factor for developing HCC. The FIB-4 index is an excellent predictor of HCC development. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Quantitative HAADF STEM of SiGe in presence of amorphous surface layers from FIB preparation.

PubMed

Grieb, Tim; Tewes, Moritz; Schowalter, Marco; Müller-Caspary, Knut; Krause, Florian F; Mehrtens, Thorsten; Hartmann, Jean-Michel; Rosenauer, Andreas

2018-01-01

The chemical composition of four Si 1-x Ge x layers grown on silicon was determined from quantitative scanning transmission electron microscopy (STEM). The chemical analysis was performed by a comparison of the high-angle annular dark field (HAADF) intensity with multislice simulations. It could be shown that amorphous surface layers originating from the preparation process by focused-ion beam (FIB) at 30 kV have a strong influence on the quantification: the local specimen thickness is overestimated by approximately a factor of two, and the germanium concentration is substantially underestimated. By means of simulations, the effect of amorphous surface layers on the HAADF intensity of crystalline silicon and germanium is investigated. Based on these simulations, a method is developed to analyze the experimental HAADF-STEM images by taking the influence of the amorphous layers into account which is done by a reduction of the intensities by multiplication with a constant factor. This suggested modified HAADF analysis gives germanium concentrations which are in agreement with the nominal values. The same TEM lamella was treated with low-voltage ion milling which removed the amorphous surface layers completely. The results from subsequent quantitative HAADF analyses are in agreement with the nominal concentrations which validates the applicability of the used frozen-lattice based multislice simulations to describe the HAADF scattering of Si 1-x Ge x in STEM. Copyright © 2017 Elsevier B.V. All rights reserved.

Staging liver fibrosis in chronic hepatitis B with T1 relaxation time index on gadoxetic acid-enhanced MRI: Comparison with aspartate aminotransferase-to-platelet ratio index and FIB-4.

PubMed

Yang, Li; Ding, Ying; Rao, Shengxiang; Chen, Caizhong; Wu, Lifang; Sheng, Ruofan; Fu, Caixia; Zeng, Mengsu

2017-04-01

To assess the accuracy of the T 1 relaxation time index on gadoxetic acid-enhanced magnetic resonance imaging (MRI) for staging liver fibrosis in chronic hepatitis B (CHB), in comparison and combination with the aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis-4 (FIB-4). A retrospective study of gadoxetic acid-enhanced T 1 mapping and serum biochemical tests was performed on 126 CHB patients who underwent gadoxetic acid-enhanced 1.5T MRI, and the histological score used as the gold standard. The reduction rate of T 1 relaxation time before and 20 minutes after gadoxetic acid injection (ΔT 1 , ΔR1%), the contrast uptake rate (K Hep ), APRI, and FIB-4 were calculated. The diagnostic efficacy of ΔT 1 , ΔR1%, K Hep , APRI, and FIB-4 for predicting stage 2 or greater (≥S2), stage 3 or greater (≥S3), and stage 4 (S4) was compared. ΔT 1 (r = -0.513, P < 0.001), ΔR1% (r = -0.626, P < 0.001), K Hep (r = -0.527, P < 0.001), APRI (r = 0.519, P < 0.001), and FIB-4 (r = 0.476, P < 0.001) correlated significantly with fibrosis stages. Areas under the curves (AUCs) of ΔR1% for detecting ≥S2, ≥S3, and S4 were 0.849, 0.827, and 0.809, which were greater than that of APRI (0.763, 0.745, 0.787) and FIB-4 (0.727, 0.738, 0.772), but significant difference was found only in discriminating ≥S2 between ΔR1% and FIB-4 (P = 0.027). The combination of all five indices performed best, with AUC, sensitivity, and specificity of 0.860, 87.21%, and 72.50% for diagnosing ≥S2, 0.878, 82.81%, and 85.48% for ≥S3, and 0.867, 80.00%, and 83.95% for S4. The gadoxetic acid-enhanced T 1 relaxation time index appears to be superior to APRI and FIB-4 for predicting hepatic fibrosis. The combined use of gadoxetic acid-enhanced T 1 mapping, APRI, and FIB-4 may be more reliable for staging liver fibrosis in CHB. 4 J. Magn. Reson. Imaging 2017;45:1186-1194. © 2016 International Society for Magnetic Resonance in Medicine.

Methylotrophic bacteria symbiosis with the higher plants as means of minimization of the lower hydrocarbons concentration during artificial ecosystem gas exchange

NASA Astrophysics Data System (ADS)

Berkovich, Yuliy; Smolyanina, Svetlana; Moukhamedieva, Lana; Mardanov, Robert; Doronina, Nina; Ivanova, Ekaterina

Plant growth unit should be included in the LSS for the space vehicles for vitamin greens supply and psychological support of cosmonauts during long-term missions. The lower hydrocarbons such as methane, methanol, methylated sulfuric compounds and methylated amines, ethylene and so on, are the natural products of human and plant metabolism and usually considered as the air pollutions. It is shown, that one way to decrease the lower hydrocarbons concentration in the artificial ecosystems could be colonization of the plants by methylotrophic bacteria. The aerobic methylotrophic bacteria possess unique ability to use methane and its oxidized or replaced derivatives without food damage and human, animals or plants infection. We have found that methylotrophic bacteria are the phyto-symbiotic bacteria: they stimulate growth and development of the colonized plants because of synthesizing cytokinins and auxins, and vitamin B12.Two collection strains of the obligate methylotrophic bacteria - Methylovorus mays C and Methylomonas metanica S - were chosen because of their high activity to assimilate the lower hydrocarbons due to functioning of methanoldehydrogenase, methanmonooxigenase and ribulose monophosphate cycle enzymes system.Colonization of the leaf cabbage Brassica chinensis L. by these strains led to approximately 30 % reduce of methanol and methane concentration in the air inside phytotron. Experimental estimations of the influence of methylotrophic bacteria on leafy greens growth and development are obtained.

A novel PFIB sample preparation protocol for correlative 3D X-ray CNT and FIB-TOF-SIMS tomography.

PubMed

Priebe, Agnieszka; Audoit, Guillaume; Barnes, Jean-Paul

2017-02-01

We present a novel sample preparation method that allows correlative 3D X-ray Computed Nano-Tomography (CNT) and Focused Ion Beam Time-Of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS) tomography to be performed on the same sample. In addition, our invention ensures that samples stay unmodified structurally and chemically between the subsequent experiments. The main principle is based on modifying the topography of the X-ray CNT experimental setup before FIB-TOF-SIMS measurements by incorporating a square washer around the sample. This affects the distribution of extraction field lines and therefore influences the trajectories of secondary ions that are now guided more efficiently towards the detector. As the result, secondary ion detection is significantly improved and higher, i.e. statistically better, signals are obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

Diagnostic Accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex Scores in Predicting the Presence of Esophageal Varices in Liver Cirrhosis

PubMed Central

Deng, Han; Qi, Xingshun; Guo, Xiaozhong

2015-01-01

Abstract Aspartate aminotransferase-to-platelet ratio (APRI), aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), FIB-4, FI, King, Lok, Forns, and FibroIndex scores may be simple and convenient noninvasive diagnostic tests, because they are based on the regular laboratory tests and demographic data. This study aimed to systematically evaluate their diagnostic accuracy for the prediction of varices in liver cirrhosis. All relevant papers were searched via PubMed, EMBASE, CNKI, and Wanfang databases. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated. Overall, 12, 4, 5, 0, 0, 4, 3, and 1 paper was identified to explore the diagnostic accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex scores, respectively. The AUSROCs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of varices were 0.6774, 0.7275, 0.7755, 0.7885, and 0.7517, respectively; and those for the prediction of large varices were 0.7278, 0.7448, 0.7095, 0.7264, and 0.6530, respectively. The diagnostic threshold effects of FIB-4 and Forns scores for the prediction of varices were statistically significant. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, and Lok scores for the prediction of varices were 0.60/0.67/1.77/0.58/3.13, 0.64/0.63/1.97/0.54/4.18, and 0.74/0.68/2.34/0.40/5.76, respectively. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of large varices were 0.65/0.66/2.15/0.47/4.97, 0.68/0.58/2.07/0.54/3.93, 0.62/0.64/2.02/0.56/3.57, 0.78/0.63/2.09/0.37/5.55, and 0.65/0.61/1.62/0.59/2.75, respectively. APRI, AAR, FIB-4, Lok, and Forns scores had low to moderate diagnostic accuracy in predicting the presence of varices in liver cirrhosis. PMID:26496312

Characterizing Virus Decay in Environmental Freshwater Habitats

EPA Science Inventory

Recreational water quality is typically assessed using fecal indicator bacteria (FIB), however, FIB are inadequate surrogates for the viral pathogens. Bacteriophage share similar morphologies to viral pathogens allowing closer representation of viral behavior, making their inclu...

Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations.

PubMed

van der Ha, David; Vanwonterghem, Inka; Hoefman, Sven; De Vos, Paul; Boon, Nico

2013-03-01

Due to the increasing atmospheric concentration of the greenhouse gas methane, more knowledge is needed on the management of methanotrophic communities. While most studies have focused on the characteristics of the methane-oxidizing bacteria (MOB), less is known about their interactions with the associated heterotrophs. Interpretative tools based on denaturing gradient gel electrophoresis allowed to evaluate the influence of copper-an important enzymatic regulator for MOB-on the activity and composition of the bacterial community. Over 30 days, enrichments with 0.1, 1.0 and 10 μM Cu(2+) respectively, showed comparable methane oxidation activities. The different copper concentrations did not create major shifts in the methanotrophic communities, as a Methylomonas sp. was able to establish dominance at all different copper concentrations by switching between both known methane monooxygenases. The associated heterotrophic communities showed continuous shifts, but over time all cultures evolved to a comparable composition, independent of the copper concentration. This indicates that the MOB selected for certain heterotrophs, possibly fulfilling vital processes such as removal of toxic compounds. The presence of a large heterotrophic food web indirectly depending on methane as sole carbon and energy source was confirmed by a clone library wherein MOB only formed a minority of the identified species.

Run-off studies demonstrate parallel transport behaviour for a marker of poultry fecal contamination and Staphylococcus aureus.

PubMed

Weidhaas, J; Garner, E; Basden, T; Harwood, V J

2014-08-01

To determine whether poultry litter marker gene LA35 is correlated with pathogens and fecal indicator bacteria (FIB) in run-off from poultry litter-amended plots. A rainfall simulator with various vegetative filter strip lengths was employed to evaluate the correlation of a microbial source tracking (MST) marker for poultry feces/litter (the 16S rRNA gene of Brevibacterium sp. LA35 [LA35] measured by quantitative PCR) with pathogens and FIB in run-off. LA35 was correlated with Staphylococcus aureus, Escherichia coli, Enterococcus spp. and Bacteroidales levels. Salmonella was present at low concentration in litter, but became undetectable by qPCR in run-off. Escherichia coli, LA35 and Staph. aureus exhibited mass-based first flush behaviour in the run-off. Correlation of LA35 with FIB and pathogens in run-off from poultry litter-amended fields suggest comparable transport mechanisms and that LA35 is a useful tracer for harmful bacteria in the environment released from poultry litter. To protect human health, an effective marker for poultry fecal contamination should exhibit similar fate and transport characteristics compared to pathogens. This study is among the first to demonstrate such a relationship in run-off for a MST marker. © 2014 The Society for Applied Microbiology.

Evaluation of APRI and FIB-4 for noninvasive assessment of significant fibrosis and cirrhosis in HBeAg-negative CHB patients with ALT ≤ 2 ULN: A retrospective cohort study.

PubMed

Li, Qiang; Ren, Xiaojing; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-03-01

To evaluate the performance of aspartate transaminase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4) to predict significant fibrosis and cirrhosis in hepatitis B virus e antigen (HBeAg)-negative chronic hepatitis B (CHB) patients with alanine transaminase (ALT) ≤ twice the upper limit of normal (2 ULN).Histologic and laboratory data of 236 HBeAg-negative CHB patients with ALT ≤ 2 ULN were analyzed. Predicted fibrosis stage, based on established scales and cut-offs for APRI and FIB-4, was compared with METAVIR scores obtained from liver biopsy.In this study, the areas under the receiver operating characteristic curves (AUROCs) of APRI were lower than that of FIB-4 (0.62 vs 0.69; P = 0.019) for diagnosing significant fibrosis; however APRI and FIB-4 were comparable for diagnosing cirrhosis (0.77 vs 0.81; P = 0.374). When the cut-off proposed by WHO HBV guideline for APRI (>2.0) was used, no cirrhotic patients were correctly predicted. For FIB-4, the WHO proposed cut-off of 3.25 correctly identified significant fibrosis 83% of the time; but for APRI, the WHO proposed cut-off of 1.5 identified significant fibrosis 56%. In ruling out significant fibrosis, the WHO proposed APRI cut-off of 0.5 had a predictive value of 39%, and the FIB-4 cut-off of 1.45 correctly identified lack of significant fibrosis in 47% of the patients. In this study, based on ROC analysis, the optimal cut-offs were 0.46 and 0.65 for APRI, and 1.05 and 1.29 for FIB-4, for diagnosing significant fibrosis and cirrhosis, respectively. When the new cut-off of APRI (>0.65) was used, 82% of the cirrhotic patients were correctly predicted. In ruling out significant fibrosis, the new APRI cut-off (<0.46) had a predictive value of 80%, and new FIB-4 cut-off (<1.05) correctly identified lack of significant fibrosis in 84% of the patients.The WHO guidelines proposed cut-offs might be higher for HBeAg-negative CHB patients with ALT ≤2 ULN, and might

Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

PubMed Central

Jensen, Mikkel R. B.; Łopacińska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian

2013-01-01

Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

FIB-4 stage of liver fibrosis predicts incident heart failure among HIV-infected and uninfected patients.

PubMed

So-Armah, Kaku A; Lim, Joseph K; Lo Re, Vincent; Tate, Janet P; Chang, Chung-Chou H; Butt, Adeel A; Gibert, Cynthia L; Rimland, David; Marconi, Vincent C; Goetz, Matthew B; Rodriguez-Barradas, Maria C; Budoff, Matthew J; Tindle, Hilary A; Samet, Jeffrey H; Justice, Amy C; Freiberg, Matthew S

2017-10-01

Liver fibrosis is common, particularly in individuals who are infected with human immunodeficiency virus (HIV). HIV-infected individuals have excess congestive heart failure (CHF) risk compared with uninfected people. It remains unknown whether liver fibrosis stage influences the CHF risk or if HIV or hepatitis C virus (HCV) infection modifies this association. Our objectives were to assess whether 1) stage of liver fibrosis is independently associated with incident CHF and 2) the association between stage of liver fibrosis and incident CHF is modified by HIV/HCV status. Participants alive on or after April 1, 2003, in the Veterans Aging Cohort Study were included. Those without prevalent cardiovascular disease were followed until their first CHF event, death, last follow-up date, or December 31, 2011. Liver fibrosis was measured using the fibrosis 4 index (FIB-4), which is calculated using age, aminotransferases, and platelets. Cox proportional hazards regression models were adjusted for cardiovascular disease risk factors. Among 96,373 participants over 6.9 years, 3844 incident CHF events occurred. FIB-4 between 1.45 and 3.25 (moderate fibrosis) and FIB-4 > 3.25 (advanced fibrosis/cirrhosis) were associated with CHF (hazard ratio [95% confidence interval], 1.17 [1.07-1.27] and 1.65 [1.43-1.92], respectively). The association of advanced fibrosis/cirrhosis and incident CHF persisted regardless of HIV/HCV status. Moderate and advanced liver fibrosis/cirrhosis are associated with an increased risk of CHF. The association for advanced fibrosis/cirrhosis persists even among participants without hepatitis C and/or HIV infection. Assessing liver health may be important for reducing the risk of future CHF events, particularly among HIV and hepatitis C infected people among whom cardiovascular disease risk is elevated and liver disease is common. (Hepatology 2017;66:1286-1295). © 2017 by the American Association for the Study of Liver Diseases.

Modeling coliform-bacteria concentrations and pH in the salt-wedge reach of the Duwamish River Estuary, King County, Washington

USGS Publications Warehouse

Haushild, W.L.; Prych, Edmund A.

1976-01-01

Total- and fecal-coliform bacteria, plus pH, alkalinity, and dissolved inorganic carbon are water-quality parameters that have been added to an existing numerical model of water quality in the salt-wedge reach of the Duwamish River estuary in Washington. The coliform bacteria are modeled using a first-order decay (death) rate, which is a function of the local salinity, temperature, and daily solar radiation. The pH is computed by solving a set of chemical-equilibrium equations for carbonate-bicarbonate buffered aqueous solutions. Concentrations of total- and fecal-coliform bacteria computed by the model for the Duwamish River estuary during June-September 1971 generally agreed with observed concentrations within about 40 and 60 percent, respectively. The computed pH generally agreed with observed pH within about a 0.2 pH unit; however, for one 3-week period the computed pH was about a 0.4 unit lower than the observed pH. (Woodard-USGS)

Three-Phase 3D Reconstruction of a LiCoO 2 Cathode via FIB-SEM Tomography

DOE PAGES

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun; ...

2016-01-14

Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area,more » feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. In conclusion, the electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

Two planar polishing methods by using FIB technique: Toward ultimate top-down delayering for failure analysis

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

Wang, D. D., E-mail: dandan.wang@globalfoundries.com; Huang, Y. M.; Tan, P. K.

2015-12-15

Presently two major limiting factors are hindering the failure analysis (FA) development during the semiconductor manufacturing process and technology improvement: (1) Impossibility of manual polishing on the edge dies due to the amenability of layer peeling off; (2) Abundant demand of multi-locations FA, especially focusing different levels of layers simultaneously. Aiming at resolving these limitations, here we demonstrate two unique high precision polishing methods by using focused ion beam (FIB) technique. One is the vertical top down chemical etching at the aimed location; the other one is the planar top down slicing. Using the FIB for delayering not only solvesmore » these problems mentioned above, but also offers significant advantages over physical planar polishing methods such as: (1) having a better control of the delayering progress, (2) enabling precisely milling at a region of interest, (3) providing the prevention of over-delayering and (4) possessing capability to capture images at the region of interest simultaneously and cut into the die directly to expose the exact failure without damaging other sections of the specimen.« less

Diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index and liver stiffness measurement in hepatitis B virus-infected patients with persistently normal alanine aminotransferase.

PubMed

Tan, You-Wen; Zhou, Xing-Bei; Ye, Yun; He, Cong; Ge, Guo-Hong

2017-08-21

To assess the diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index (APRI), and liver stiffness measurement (LSM) in patients with hepatitis B virus infection who have persistently normal alanine transaminase (PNALT). We enrolled 245 patients with chronic hepatitis B: 95 in PNALT group, 86 in intermittently elevated alanine transaminase (PIALT1) group [alanine transaminase (ALT) within 1-2 × upper limit of normal value (ULN)], and 64 in PIALT2 group (ALT > 2 × ULN). All the patients received a percutaneous liver biopsy guided by ultrasonography. LSM, biochemical tests, and complete blood cell counts were performed. The pathological examination revealed moderate inflammatory necrosis ratios of 16.81% (16/95), 32.56% (28/86), and 45.31% (28/64), and moderate liver fibrosis of 24.2% (23/95), 33.72% (29/86), and 43.75% (28/64) in the PNALT, PIALT1, and PIALT2 groups, respectively. The degrees of inflammation and liver fibrosis were significantly higher in the PIALT groups than in the PNALT group ( P < 0.05). No significant difference was found in the areas under the curve (AUCs) between APRI and FIB-4 in the PNALT group; however, significant differences were found between APRI and LSM, and between FIB-4 and LSM in the PNALT group ( P < 0.05 for both). In the PIALT1 and PIALT2 groups, no significant difference ( P > 0.05) was found in AUCs for all comparisons ( P > 0.05 for all). In the overall patients, a significant difference in the AUCs was found only between LSM and APRI ( P < 0.05). APRI and FIB-4 are not the ideal noninvasive hepatic fibrosis markers for PNALT patients. LSM is superior to APRI and FIB-4 in PNALT patients because of the influence of liver inflammation and necrosis.

Diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index and liver stiffness measurement in hepatitis B virus-infected patients with persistently normal alanine aminotransferase

PubMed Central

Tan, You-Wen; Zhou, Xing-Bei; Ye, Yun; He, Cong; Ge, Guo-Hong

2017-01-01

AIM To assess the diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index (APRI), and liver stiffness measurement (LSM) in patients with hepatitis B virus infection who have persistently normal alanine transaminase (PNALT). METHODS We enrolled 245 patients with chronic hepatitis B: 95 in PNALT group, 86 in intermittently elevated alanine transaminase (PIALT1) group [alanine transaminase (ALT) within 1-2 × upper limit of normal value (ULN)], and 64 in PIALT2 group (ALT > 2 × ULN). All the patients received a percutaneous liver biopsy guided by ultrasonography. LSM, biochemical tests, and complete blood cell counts were performed. RESULTS The pathological examination revealed moderate inflammatory necrosis ratios of 16.81% (16/95), 32.56% (28/86), and 45.31% (28/64), and moderate liver fibrosis of 24.2% (23/95), 33.72% (29/86), and 43.75% (28/64) in the PNALT, PIALT1, and PIALT2 groups, respectively. The degrees of inflammation and liver fibrosis were significantly higher in the PIALT groups than in the PNALT group (P < 0.05). No significant difference was found in the areas under the curve (AUCs) between APRI and FIB-4 in the PNALT group; however, significant differences were found between APRI and LSM, and between FIB-4 and LSM in the PNALT group (P < 0.05 for both). In the PIALT1 and PIALT2 groups, no significant difference (P > 0.05) was found in AUCs for all comparisons (P > 0.05 for all). In the overall patients, a significant difference in the AUCs was found only between LSM and APRI (P < 0.05). CONCLUSION APRI and FIB-4 are not the ideal noninvasive hepatic fibrosis markers for PNALT patients. LSM is superior to APRI and FIB-4 in PNALT patients because of the influence of liver inflammation and necrosis. PMID:28883700

Bacteriophages as indicators of faecal pollution and enteric virus removal

EPA Science Inventory

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize con...

Zn nanoparticle formation in FIB irradiated single crystal ZnO

NASA Astrophysics Data System (ADS)

Pea, M.; Barucca, G.; Notargiacomo, A.; Di Gaspare, L.; Mussi, V.

2018-03-01

We report on the formation of Zn nanoparticles induced by Ga+ focused ion beam on single crystal ZnO. The irradiated materials have been studied as a function of the ion dose by means of atomic force microscopy, scanning electron microscopy, Raman spectroscopy and transmission electron microscopy, evidencing the presence of Zn nanoparticles with size of the order of 5-30 nm. The nanoparticles are found to be embedded in a shallow amorphous ZnO matrix few tens of nanometers thick. Results reveal that ion beam induced Zn clustering occurs producing crystalline particles with the same hexagonal lattice and orientation of the substrate, and could explain the alteration of optical and electrical properties found for FIB fabricated and processed ZnO based devices.

Comparative evaluation of GPR versus APRI and FIB-4 in predicting different levels of liver fibrosis of chronic hepatitis B.

PubMed

Liu, D-P; Lu, W; Zhang, Z-Q; Wang, Y-B; Ding, R-R; Zhou, X-L; Huang, D; Li, X-F

2018-05-01

It is of great significance to develop and evaluate noninvasive indexes predicting the level of liver fibrosis. The aim of this study was to comparatively evaluate gamma-glutamyl transpeptidase-to-platelet ratio (GPR) versus aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis index based on 4 factors (FIB-4) in predicting different levels of liver fibrosis of chronic hepatitis B (CHB) within the framework of HBeAg-positive and HBeAg-negative patients. A total of 1157 HBeAg-positive and 859 HBeAg-negative CHB patients were enrolled, among whom the pathological stage ≥S2, ≥S3, ≥S4 were defined as significant fibrosis, extensive fibrosis and cirrhosis, respectively. Receiver operating characteristic (ROC) curves were used to evaluate the performance of GPR, APRI and FIB-4 in predicting different levels of liver fibrosis. In HBeAg-positive patients, the area under ROC curves (AUROCs) of GPR in predicting extensive fibrosis and cirrhosis were both significantly larger than those of APRI (P = .0001 and P < .0001). In HBeAg-negative patients, the AUROCs of GPR in predicting significant fibrosis and cirrhosis were significantly larger than those of FIB-4 (P = .0006 and P = .0041). The AUROC of GPR in predicting extensive fibrosis was significantly larger than that of APRI and FIB-4 (P = .0320 and P = .0018). Using a cut-off of GPR > 0.500 as standard, the sensitivities and specificities of GPR in predicting significant fibrosis in HBeAg-positive patients were 59.6% and 81.2%, and for cirrhosis 80.9% and 63.8%, respectively; and those of HBeAg-negative patients were 60.3% and 78.3%, 84.5% and 66.1%, respectively. Regardless of HBeAg-positive or HBeAg-negative status, GPR had the best performance in predicting different levels of liver fibrosis. © 2017 John Wiley & Sons Ltd.

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

RAPIDLY-MEASURED INDICATORS OF RECREATIONAL WATER QUALITY ARE PREDICTIVE OF SWIMMING-ASSOCIATED GASTROINTESTINAL ILLNESS

EPA Science Inventory

Fecal indicator bacteria (FIB) are used to monitor recreational water quality worldwide. Current methods of measuring FIB require at least 24-hours for growth of bacterial colonies. We conducted studies at four Great Lake beaches to examine the relationship between novel and fas...

A FASTER METHOD OF MEASURING RECREATIONAL WATER QUALITY FOR BETTER PROTECTION OF SWIMMER'S HEALTH

EPA Science Inventory

Introduction

Fecal indicator bacteria (FIB) are used to monitor recreational water quality worldwide. Current methods of measuring FIB require at least 24-hours for visible bacterial colonies to grow. We previously reported that a faster method (< 2 hours) of measuring FI...

Efficacy of monitoring and empirical predictive modeling at improving public health protection at Chicago beaches

USGS Publications Warehouse

Nevers, Meredith B.; Whitman, Richard L.

2011-01-01

Efforts to improve public health protection in recreational swimming waters have focused on obtaining real-time estimates of water quality. Current monitoring techniques rely on the time-intensive culturing of fecal indicator bacteria (FIB) from water samples, but rapidly changing FIB concentrations result in management errors that lead to the public being exposed to high FIB concentrations (type II error) or beaches being closed despite acceptable water quality (type I error). Empirical predictive models may provide a rapid solution, but their effectiveness at improving health protection has not been adequately assessed. We sought to determine if emerging monitoring approaches could effectively reduce risk of illness exposure by minimizing management errors. We examined four monitoring approaches (inactive, current protocol, a single predictive model for all beaches, and individual models for each beach) with increasing refinement at 14 Chicago beaches using historical monitoring and hydrometeorological data and compared management outcomes using different standards for decision-making. Predictability (R2) of FIB concentration improved with model refinement at all beaches but one. Predictive models did not always reduce the number of management errors and therefore the overall illness burden. Use of a Chicago-specific single-sample standard-rather than the default 235 E. coli CFU/100 ml widely used-together with predictive modeling resulted in the greatest number of open beach days without any increase in public health risk. These results emphasize that emerging monitoring approaches such as empirical models are not equally applicable at all beaches, and combining monitoring approaches may expand beach access.

A relatively small change in sodium chloride concentration has a strong effect on adhesion of ocular bacteria to contact lenses.

PubMed

Cowell, B A; Willcox, M D; Schneider, R P

1998-06-01

Adhesion of bacteria to hydrogel lenses is thought to be an initial step of ocular colonization allowing evasion of normal host defences. The salt concentration of media is an important parameter controlling microbial adhesion. Salinity varies from 0.97% NaCl equivalents in the open eye to 0.89% in the closed eye state. In this study, the effect of sodium chloride in the concentration range of 0.8-1.0% (w/v) NaCl on adhesion of ocular bacteria to soft contact lenses was investigated using a static adhesion assay. Pseudomonas aeruginosa was found to adhere to lenses in significantly greater amounts than Serratia marcescens, Flavobacterium meningosepticum, Stenotrophomonas maltophilia and Staphylococcus intermedius. Increasing NaCl from 0.8% to 1.0% (w/v) increased adhesion of all bacteria tested. This adhesion was strong since the organisms could not be removed by washing in low ionic buffer. Adhesion of these organisms did not correlate with their cell surface properties as determined by bacterial adhesion to hydrocarbons (BATH) and retention on sepharose columns.

Evolution of Regions Containing Antibiotic Resistance Genes in FII-2-FIB-1 ColV-Colla Virulence Plasmids.

PubMed

Moran, Robert A; Hall, Ruth M

2018-05-01

Three ColV virulence plasmids carrying antibiotic resistance genes were assembled from draft genome sequences of commensal ST95, ST131, and ST2705 Escherichia coli isolates from healthy Australians. Plasmids pCERC4, pCERC5, and pCERC9 include almost identical backbones containing FII-2 and FIB-1 replicons and the conserved ColV virulence region with an additional ColIa determinant. Only pCERC5 includes a complete, uninterrupted F-like transfer region and was able to conjugate. pCERC5 and pCERC9 contain Tn1721, carrying the tet(A) tetracycline resistance determinant in the same location, with Tn2 (bla TEM ; ampicillin resistance) interrupting the Tn1721 in pCERC5. pCERC4 has a Tn1721/Tn21 hybrid transposon carrying dfrA5 (trimethoprim resistance) and sul1 (sulfamethoxazole resistance) in a class 1 integron. Four FII-2:FIB-1 ColV-ColIa plasmids in the GenBank nucleotide database have a related transposon in the same position, but an IS26 has reshaped the resistance gene region, deleting 2,069 bp of the integron 3'-CS, including sul1, and serving as a target for IS26 translocatable units containing bla TEM , sul2 and strAB (streptomycin resistance), or aphA1 (kanamycin/neomycin resistance). Another ColV-ColIa plasmid containing a related resistance gene region has lost the FII replicon and acquired a unique transfer region via recombination within the resistance region and at oriT. Eighteen further complete ColV plasmid sequences in GenBank contained FIB-1, but the FII replicons were of three types, FII-24, FII-18, and a variant of FII-36.

Three-dimensional micro/nano-scale structure fabricated by combination of non-volatile polymerizable RTIL and FIB irradiation

PubMed Central

Kuwabata, Susumu; Minamimoto, Hiro; Inoue, Kosuke; Imanishi, Akihito; Hosoya, Ken; Uyama, Hiroshi; Torimoto, Tsukasa; Tsuda, Tetsuya; Seki, Shu

2014-01-01

Room-temperature ionic liquid (RTIL) has been widely investigated as a nonvolatile solvent as well as a unique liquid material because of its interesting features, e.g., negligible vapor pressure and high thermal stability. Here we report that a non-volatile polymerizable RTIL is a useful starting material for the fabrication of micro/nano-scale polymer structures with a focused-ion-beam (FIB) system operated under high-vacuum condition. Gallium-ion beam irradiation to the polymerizable 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide RTIL layer spread on a Si wafer induced a polymerization reaction without difficulty. What is interesting to note is that we have succeeded in provoking the polymerization reaction anywhere on the Si wafer substrate by using FIB irradiation with a raster scanning mode. By this finding, two- and three-dimensional micro/nano-scale polymer structure fabrications were possible at the resolution of 500,000 dpi. Even intricate three-dimensional micro/nano-figures with overhang and hollow moieties could be constructed at the resolution of approximately 100 nm. PMID:24430465

QPCR Determined Fecal Indicator Bacterial Densities in Marine Waters from Two Recreational Beaches

EPA Science Inventory

The use of real-time qPCR to determine fecal indicator bacteria (FIB) densities is currently being investigated by the U.S. EPA. The present recreational water quality guidelines, based on culturable FIB, prevent same day determinations of water quality whereas results from the ...

3D-characterization of the veneer-zirconia interface using FIB nano-tomography.

PubMed

Mainjot, Amélie K; Douillard, Thierry; Gremillard, Laurent; Sadoun, Michaël J; Chevalier, Jérôme

2013-02-01

The phenomena occurring during zirconia frameworks veneering process are not yet fully understood. In particular the study of zirconia behavior at the interface with the veneer remains a challenge. However this interface has been reported to act on residual stress in the veneering ceramic, which plays a significant role in clinical failures such as chipping. The objective of this study was thus to investigate the veneer-zirconia interface using a recent 3D-analysis tool and to confront these observations to residual stress measurements in the veneering ceramic. Two cross-sectioned bilayered disc samples (veneer on zirconia), exhibiting different residual stress profiles in the veneering ceramic, were investigated using 2D and 3D imaging (respectively Scanning Electron Microscopy (SEM) and Focused Ion Beam nanotomography (FIB-nt), associated with chemical analysis by Energy Dispersive X-ray Spectroscopy (EDS). The observations did not reveal any structural change in the bulk of zirconia layer of both samples. However the presence of structural alterations and sub-surface microcracks were highlighted in the first micrometer of zirconia surface, exclusively for the sample exhibiting interior tensile stress in the veneering ceramic. No interdiffusion phenomena were observed. FIB nanotomography was proven to be a powerful technique to study the veneer-zirconia interface. The determination of the origin and the nature of zirconia alterations need to be further studied. The results of the present study support the hypothesis that zirconia surface property changes could be involved in the development of tensile stress in the veneering ceramic, increasing the risk of chipping. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

The Myxococcus xanthus Spore Cuticula Protein C Is a Fragment of FibA, an Extracellular Metalloprotease Produced Exclusively in Aggregated Cells

PubMed Central

Lee, Bongsoo; Mann, Petra; Grover, Vidhi; Treuner-Lange, Anke; Kahnt, Jörg; Higgs, Penelope I.

2011-01-01

Myxococcus xanthus is a soil bacterium with a complex life cycle involving distinct cell fates, including production of environmentally resistant spores to withstand periods of nutrient limitation. Spores are surrounded by an apparently self-assembling cuticula containing at least Proteins S and C; the gene encoding Protein C is unknown. During analyses of cell heterogeneity in M. xanthus, we observed that Protein C accumulated exclusively in cells found in aggregates. Using mass spectrometry analysis of Protein C either isolated from spore cuticula or immunoprecipitated from aggregated cells, we demonstrate that Protein C is actually a proteolytic fragment of the previously identified but functionally elusive zinc metalloprotease, FibA. Subpopulation specific FibA accumulation is not due to transcriptional regulation suggesting post-transcriptional regulation mechanisms mediate its heterogeneous accumulation patterns. PMID:22174937

Changes of FibroScan, APRI, and FIB-4 in chronic hepatitis B patients with significant liver histological changes receiving 3-year entecavir therapy.

PubMed

Li, Qiang; Chen, Liang; Zhou, Yu

2018-05-01

Noninvasive fibrosis tests have been used widely for evaluation of liver fibrosis in patients with chronic hepatitis B (CHB). We aimed to investigate the influence of antiviral treatment on FibroScan, APRI, and FIB-4 in CHB patients with significant liver histological changes (SLHC) defined as inflammatory grade ≥ A2 and/or fibrosis stage ≥ F2. A total of 104 CHB patients with SLHC at the baseline were included. FibroScan, APRI, and FIB-4 values were compared before and after 3-year entecavir (ETV) treatment. Liver stiffness measurement values decreased significantly after 3-year ETV treatment in cirrhosis group (from 13.6 to 9.6 kPa, p = 0.018), significant fibrosis group (from 8.4 to 5.8 kPa, p = 0.001), and mild fibrosis group (from 5.5 to 4 kPa, p < 0.001). APRI decreased significantly after 3-year ETV treatment in patients with cirrhosis (from 0.80 to 0.25, p < 0.001), patients with significant fibrosis (from 0.54 to 0.24, p < 0.001), and those with mild fibrosis (from 0.35 to 0.23, p < 0.001). FIB-4 decreased significantly after 3-year ETV treatment in patients with cirrhosis (from 1.27 to 0.81, p = 0.007) and significant fibrosis (from 1.12 to 0.78, p < 0.001), while did not decrease significantly in patients with mild fibrosis (from 0.90 to 0.80, p = 0.389). FibroScan, APRI, and FIB-4 values decreased significantly after 3-year ETV treatment in CHB patients, which indicates that these noninvasive fibrosis tests might be useful for monitoring regression of liver fibrosis and assessing treatment efficacy during long-term ETV treatment.

High-Flow-Rate Impinger for the Study of Concentration, Viability, Metabolic Activity, and Ice-Nucleation Activity of Airborne Bacteria.

PubMed

Šantl-Temkiv, Tina; Amato, Pierre; Gosewinkel, Ulrich; Thyrhaug, Runar; Charton, Anaïs; Chicot, Benjamin; Finster, Kai; Bratbak, Gunnar; Löndahl, Jakob

2017-10-03

The study of airborne bacteria relies on a sampling strategy that preserves their integrity and in situ physiological state, e.g. viability, cultivability, metabolic activity, and ice-nucleation activity. Because ambient air harbors low concentrations of bacteria, an effective bioaerosol sampler should have a high sampling efficiency and a high airflow. We characterize a high-flow-rate impinger with respect to particle collection and retention efficiencies in the range 0.5-3.0 μm, and we investigated its ability to preserve the physiological state of selected bacterial species and seawater bacterial community in comparison with four commercial bioaerosol samplers. The collection efficiency increased with particle size and the cutoff diameter was between 0.5 and 1 μm. During sampling periods of 120-300 min, the impinger retained the cultivability, metabolic activity, viability, and ice-nucleation activity of investigated bacteria. Field studies in semiurban, high-altitude, and polar environments included periods of low bacterial air concentrations, thus demonstrating the benefits of the impinger's high flow rate. In conclusion, the impinger described here has many advantages compared with other bioaerosol samplers currently on the market: a potential for long sampling time, a high flow rate, a high sampling and retention efficiency, low costs, and applicability for diverse downstream microbiological and molecular analyses.

Fecal-coliform bacteria concentrations in streams of the Chattahoochee River National Recreation Area, Metropolitan Atlanta, Georgia, May-October 1994 and 1995

USGS Publications Warehouse

Gregory, M. Brian; Frick, Elizabeth A.

2000-01-01

Introduction: The Metropolitan Atlanta area has been undergoing a period of rapid growth and development. The population in the 10-county metropolitan area almost doubled from about 1.5 million people in 1970 to 2.9 million people in 1995 (Atlanta Regional Commission, written commun., 2000). Residential, commercial, and other urban land uses more than tripled during the same period (Frick and others, 1998). The Chattahoochee River is the most utilized water resource in Georgia. The rapid growth of Metropolitan Atlanta and its location downstream of the headwaters of the drainage basin make the Chattahoochee River a vital resource for drinking-water supplies, recreational opportunities, and wastewater assimilation. In 1978, the U.S. Congress declared the natural, scenic, recreation, and other values of 48 miles of the Chattahoochee River from Buford Dam to Peachtree Creek to be of special national significance. To preserve this reach of the Chattahoochee River, the U.S. Congress created the Chattahoochee River National Recreational Area (CRNRA), which includes the Chattahoochee River downstream from Buford Dam to the mouth of Peachtree Creek and a series of park areas adjacent to the river in northern Metropolitan Atlanta Even with this protection, waters of the Chattahoochee River and many of its tributaries in Metropolitan Atlanta did not meet water-quality standards set for designated uses during 1994 and 1995 (fig. 1 and table 1). Much of the degradation of water quality has been associated with areas undergoing rapid urban growth and sprawling suburban development. The resulting conversion of mostly forested land to urban land has multiple adverse effects on water quality. Degradation of water quality may be caused by a number of factors including an increase in nutrient concentrations, sediment and sedimentbound contaminant concentrations (e.g., metals and pesticides) (Frick and others, 1998), and fecal-coliform bacteria concentrations (Center for Watershed

Estimated fecal coliform bacteria concentrations using near real-time continuous water-quality and streamflow data from five stream sites in Chester County, Pennsylvania, 2007–16

USGS Publications Warehouse

Senior, Lisa A.

2017-09-15

Several streams used for recreational activities, such as fishing, swimming, and boating, in Chester County, Pennsylvania, are known to have periodic elevated concentrations of fecal coliform bacteria, a type of bacteria used to indicate the potential presence of fecally related pathogens that may pose health risks to humans exposed through water contact. The availability of near real-time continuous stream discharge, turbidity, and other water-quality data for some streams in the county presents an opportunity to use surrogates to estimate near real-time concentrations of fecal coliform (FC) bacteria and thus provide some information about associated potential health risks during recreational use of streams.The U.S. Geological Survey (USGS), in cooperation with the Chester County Health Department (CCHD) and the Chester County Water Resources Authority (CCWRA), has collected discrete stream samples for analysis of FC concentrations during March–October annually at or near five gaging stations where near real-time continuous data on stream discharge, turbidity, and water temperature have been collected since 2007 (or since 2012 at 2 of the 5 stations). In 2014, the USGS, in cooperation with the CCWRA and CCHD, began to develop regression equations to estimate FC concentrations using available near real-time continuous data. Regression equations included possible explanatory variables of stream discharge, turbidity, water temperature, and seasonal factors calculated using Julian Day with base-10 logarithmic (log) transformations of selected variables.The regression equations were developed using the data from 2007 to 2015 (101–106 discrete bacteria samples per site) for three gaging stations on Brandywine Creek (West Branch Brandywine Creek at Modena, East Branch Brandywine Creek below Downingtown, and Brandywine Creek at Chadds Ford) and from 2012 to 2015 (37–38 discrete bacteria samples per site) for one station each on French Creek near Phoenixville and

Concentrations of Staphylococcus species in indoor air as associated with other bacteria, season, relative humidity, air change rate, and S. aureus-positive occupants.

PubMed

Madsen, Anne Mette; Moslehi-Jenabian, Saloomeh; Islam, Md Zohorul; Frankel, Mika; Spilak, Michal; Frederiksen, Margit W

2018-01-01

The aim of this study was to obtain knowledge about concentrations of Staphylococcus aureus, MRSA (methicillin-resistant S. aureus), and other Staphylococcus species in indoor air in Greater Copenhagen and about factors affecting the concentrations. The effects of season, temperature, relative humidity, air change rate (ACR), other bacterial genera, area per occupant, and presence of S. aureus-positive occupants were studied. In samples from 67 living rooms, S. hominis, S. warneri, S. epidermidis, and S. capitis were found in 13-25%; S. saprophyticus, S. cohnii, and S. pasteuri in 5-10%; and S. lugdunensis, S. haemolyticus, S. caprae, S. equorum, S. kloosii, S. pettenkoferi, S. simulans, and S. xylosus in less than 3%. Staphylococcus aureus were found in two of 67 living rooms: spa type t034 (an MRSA) was recovered from a farmhouse, while spa type t509 was found in an urban home. Two species, S. equorum and S. kloosii, were found only in the farmhouse. Staphylococcus was significantly associated with season with lowest concentration and richness in winter. Genera composition was associated with ACR with smaller fractions of Staphylococcus at higher ACR, while richness was significantly and negatively associated with area per occupant. Concentration of Staphylococcus correlated positively with the total concentration of bacteria, but negatively with the total concentration of other bacteria. The concentration of Staphylococcus was not significantly associated with concentrations of the other abundant genera Bacillus, Kocuria, and Micrococcus. In offices with S. aureus-positive occupants, airborne S. aureus was not found. In conclusion, Staphylococcus species constitute a considerable proportion of the airborne bacteria in the studied homes and offices. However, both S. aureus and MRSA had very low prevalence during all seasons. Thus, transmission of S. aureus and MRSA through the air in living rooms in Copenhagen is expected to be limited. The negative associations

Characterization Of Nutrients And Fecal Indicator Bacteria At A Concentrated Swine Feeding Operation In Wake County, North Carolina, 2009-2011

EPA Science Inventory

Hydrologic and water-quality data were collected during October 2009 - January 2011 to characterize nutrient and bacteria concentrations in stormwater runoff from agricultural fields that receive wastewater originating at a swine facility at North CarolinaState University's Lake ...

The organized melee: Emergence of collective behavior in concentrated suspensions of swimming bacteria and associated phenomena

NASA Astrophysics Data System (ADS)

Cisneros Salerno, Luis

Suspensions of the aerobic bacteria Bacilus subtilis develop patterns and flows from the interplay of motility, chemotaxis and buoyancy. In sessile drops, such bioconvectively driven flows carry plumes down the slanted meniscus and concentrate cells at the drop edge, while in pendant drops such self-concentration occurs at the bottom. These dynamics are explained quantitatively by a mathematical model consisting of oxygen diffusion and consumption, chemotaxis, and viscous fluid dynamics. Concentrated regions in both geometries comprise nearly close-packed populations, forming the collective "Zooming BioNematic" (ZBN) phase. This state exhibits large-scale orientational coherence, analogous to the molecular alignment of nematic liquid crystals, coupled with remarkable spatial and temporal correlations of velocity and vorticity, as measured by both novel and standard applications of particle imaging velocimetry. To probe mechanisms leading to this phase, response of individual cells to steric stress was explored, finding that they can reverse swimming direction at spatial constrictions without turning the cell body. The consequences of this propensity to flip the flagella are quantified, showing that "forwards" and "backwards" motion are dynamically and morphologically indistinguishable. Finally, experiments and mathematical modeling show that complex flows driven by previously unknown bipolar flagellar arrangements are induced when B. subtilis are confined in a thin layer of fluid, between asymmetric boundaries. The resulting driven flow circulates around the cell body ranging over several cell diameters, in contrast to the more localized flows surrounding free swimmers. This discovery extends our knowledge of the dynamic geometry of bacteria and their flagella, and reveals new mechanisms for motility-associated molecular transport and intercellular communication.

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food.

PubMed

Irwin, Sally V; Fisher, Peter; Graham, Emily; Malek, Ashley; Robidoux, Adriel

2017-01-01

Sulfites and other preservatives are considered food additives to limit bacterial contamination, and are generally regarded as safe for consumption by governmental regulatory agencies at concentrations up to 5000 parts per million (ppm). Consumption of bactericidal and bacteriostatic drugs have been shown to damage beneficial bacteria in the human gut and this damage has been associated with several diseases. In the present study, bactericidal and bacteriostatic effects of two common food preservatives, sodium bisulfite and sodium sulfite, were tested on four known beneficial bacterial species common as probiotics and members of the human gut microbiota. Lactobacillus species casei, plantarum and rhamnosus, and Streptococcus thermophilus were grown under optimal environmental conditions to achieve early log phase at start of experiments. Bacterial cultures were challenged with sulfite concentrations ranging between 10 and 3780 ppm for six hours. To establish a control, a culture of each species was inoculated into media containing no sulfite preservative. By two hours of exposure, a substantial decrease (or no increase) of cell numbers (based on OD600 readings) were observed for all bacteria types, in concentrations of sulfites between 250-500 ppm, compared to cells in sulfite free media. Further testing using serial dilution and drop plates identified bactericidal effects in concentrations ranging between 1000-3780 ppm on all the Lactobacillus species by 4 hours of exposure and bactericidal effects on S. thermophilus in 2000ppm NaHSO3 after 6 hours of exposure.

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food

PubMed Central

2017-01-01

Sulfites and other preservatives are considered food additives to limit bacterial contamination, and are generally regarded as safe for consumption by governmental regulatory agencies at concentrations up to 5000 parts per million (ppm). Consumption of bactericidal and bacteriostatic drugs have been shown to damage beneficial bacteria in the human gut and this damage has been associated with several diseases. In the present study, bactericidal and bacteriostatic effects of two common food preservatives, sodium bisulfite and sodium sulfite, were tested on four known beneficial bacterial species common as probiotics and members of the human gut microbiota. Lactobacillus species casei, plantarum and rhamnosus, and Streptococcus thermophilus were grown under optimal environmental conditions to achieve early log phase at start of experiments. Bacterial cultures were challenged with sulfite concentrations ranging between 10 and 3780 ppm for six hours. To establish a control, a culture of each species was inoculated into media containing no sulfite preservative. By two hours of exposure, a substantial decrease (or no increase) of cell numbers (based on OD600 readings) were observed for all bacteria types, in concentrations of sulfites between 250–500 ppm, compared to cells in sulfite free media. Further testing using serial dilution and drop plates identified bactericidal effects in concentrations ranging between 1000–3780 ppm on all the Lactobacillus species by 4 hours of exposure and bactericidal effects on S. thermophilus in 2000ppm NaHSO3 after 6 hours of exposure. PMID:29045472

[Bioaerosol concentrations and the identification of aerosolized bacteria by 16S rDNA analysis in work environments].

PubMed

Ishimatsu, Sumiyo; Abe, Hiroki; Fukuda, Kazumasa; Ishidao, Toru; Taniguchi, Hatsumi; Hori, Hajime

2007-03-01

Bioaerosols cause sick building syndrome (SBS) and allergy. Many kinds of bioaerosol impactors are used for measurement of airborne microorganism concentrations in Japan. However, because the impactors are set on agar plates, some microorganisms cannot make colonies on the plates because of their lower viability or demands of nutrition. On the other hand, by double staining using ethidium bromide (EtBr) and carboxyfluorescein diacetate (CFDA), both total cells and cells with esterase activities can be detected without incubation. In this study, we calculated total cell concentrations and percentages of cells with esterase activities by the combination of filter sampling and double staining (EtBr and CFDA) from air of a laboratory, a conference room and outdoors. Temperature and humidity in the laboratory were constantly kept by an air conditioner, but in the conference room, an air conditioner was only operated sometimes because of its low frequency of use. There were no significant differences between total cell concentrations and humidity in both rooms, but increase of the percentages of cells with esterase activities depended on rainfall before the samplings (n=15, p<0.05 by Mann-Whitney test). The increase of active microorganisms by rainfall should be considered when we evaluate the risk of bioaerosols in the workplace. There were few differences in classifications of aerosolized bacteria by 16S rDNA sequence-based homology between the laboratory and the conference room. In both rooms, few pathogenic bacteria were observed.

Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.

PubMed

Bengtsson-Palme, Johan; Larsson, D G Joakim

2016-01-01

There are concerns that selection pressure from antibiotics in the environment may accelerate the evolution and dissemination of antibiotic-resistant pathogens. Nevertheless, there is currently no regulatory system that takes such risks into account. In part, this is due to limited knowledge of environmental concentrations that might exert selection for resistant bacteria. To experimentally determine minimal selective concentrations in complex microbial ecosystems for all antibiotics would involve considerable effort. In this work, our aim was to estimate upper boundaries for selective concentrations for all common antibiotics, based on the assumption that selective concentrations a priori need to be lower than those completely inhibiting growth. Data on Minimal Inhibitory Concentrations (MICs) were obtained for 111 antibiotics from the public EUCAST database. The 1% lowest observed MICs were identified, and to compensate for limited species coverage, predicted lowest MICs adjusted for the number of tested species were extrapolated through modeling. Predicted No Effect Concentrations (PNECs) for resistance selection were then assessed using an assessment factor of 10 to account for differences between MICs and minimal selective concentrations. The resulting PNECs ranged from 8 ng/L to 64 μg/L. Furthermore, the link between taxonomic similarity between species and lowest MIC was weak. This work provides estimated upper boundaries for selective concentrations (lowest MICs) and PNECs for resistance selection for all common antibiotics. In most cases, PNECs for selection of resistance were below available PNECs for ecotoxicological effects. The generated PNECs can guide implementation of compound-specific emission limits that take into account risks for resistance promotion. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

The relationship between land management, fecal indicator bacteria, and the occurrence of Campylobacter and Listeria spp. in water and sediments during synoptic sampling in the S. Fork Broad River Watershed, N.E. Georgia, U.S.A

NASA Astrophysics Data System (ADS)

Bradshaw, J. K.; Molina, M.; Sidle, R. C.; Sullivan, K.; Oakley, B.; Berrang, M.; Meinersmann, R.

2013-12-01

Fecal indicator bacteria (FIB) and pathogens stored in the bed sediments of streams and rivers may be mobilized into the water column affecting overall water quality. Furthermore, land management may play an important role in the concentrations of FIB and the occurrence of pathogens in stream water and sediments. The purpose of this study was to determine the relationship between FIB and pathogens in stream water and sediment based on three land management-affected categories: agricultural, forest, and waters receiving treated municipal wastewater. Two synoptic sampling events were conducted under baseflow conditions (<0.64 cm of rain within 24h) between October-November, 2012 and May-June, 2013. Counts of the E. coli and E. faecalis and occurrences of the enteric pathogens Campylobacter and Listeria spp. were measured in stream water and sediment samples collected at 15 locations (six agricultural (AG); six forested (FORS); and three receiving discharge from water pollution control plants (WPCP)) in the S. Fork Broad River watershed located in northeast Georgia, USA. Mean E. coli and E. faecalis concentrations were highest in the AG stream water samples (3.08 log MPN 100 mL -1 for E. coli and 3.07 log CFU 100 mL -1 for E. faecalis ) and lowest in the FORS water samples for E. coli (2.37 log MPN 100 mL -1 ) and WPCP water samples for E. faecalis (2.53 log CFU 100 mL -1 ). E. coli concentrations (2.74 log MPN 100 mL -1 ) in the WPCP streams were intermediate. Similar to water samples, E. coli concentrations were highest in the AG sediments (4.31 log MPN g -1 ), intermediate in the WPCP sediments (4.06 log MPN g -1 ), and lowest in the FORS sediments (3.46 log MPN g -1 ). In contrast to E. coli, E. faecalis concentrations were lower (1.10 to 1.31 log CFU g -1 ) and relatively more constant than E. coli in sediments over the three land management categories. Campylobacter was detected in 27% of the water samples and 8% of the sediment samples. The highest occurrence

Fecal-indicator bacteria concentrations in the Illinois River between Hennepin and Peoria, Illinois: 2007-08

USGS Publications Warehouse

Dupre, David H.; Hortness, Jon E.; Terrio, Paul J.; Sharpe, Jennifer B.

2012-01-01

The Illinois Environmental Protection Agency has designated portions of the Illinois River in Peoria, Woodford, and Tazewell Counties, Illinois, as impaired owing to the presence of fecal coliform bacteria. The U.S. Geological Survey, in cooperation with the Tri-County Regional Planning Commission, examined the water quality in the Illinois River and major tributaries within a 47-mile reach between Peoria and Hennepin, Ill., during water year 2008 (October 2007–September 2008). Investigations included synoptic (snapshot) sampling at multiple locations in a 1-day period: once in October 2007 during lower streamflow conditions, and again in June 2008 during higher streamflow conditions. Five locations in the study area were monitored for the entire year at monthly or more frequent intervals. Two indicator bacteria were analyzed in each water sample: fecal coliform and Escherichia coli (E. coli). Streamflow information from previously established monitoring locations in the study area was used in the analysis. Correlation analyses were used to characterize the relation between the two fecal-indicator bacteria and the relation of either indicator to streamflow. Concentrations of the two measured fecal-indicator bacteria correlated well for all samples analyzed (r = 0.94, p E. coli: rho = -0.43, p = 0.0157). The correlation between fecal indicators and streamflow in tributaries or in the Illinois River at Hennepin was found to be statistically significant, yet moderate in strength with coefficient values ranging from r = 0.4 to 0.6. Indirect observations from the June 2008 higher flow synoptic event may indicate continued effects from combined storm and sanitary sewers in the vicinity of the Illinois River near Peoria, Ill., contributing to observed single-sample exceedance of the State criterion for fecal coliform.

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.

Chemotactic selection of pollutant degrading soil bacteria

DOEpatents

Hazen, Terry C.

1994-01-01

A method for identifying soil microbial strains which may be bacterial degraders of pollutants comprising the steps of placing a concentration of a pollutant in a substantially closed container, placing the container in a sample of soil for a period of time ranging from one minute to several hours, retrieving the container, collecting the contents of the container, and microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to inoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

Chemotactic selection of pollutant degrading soil bacteria

DOEpatents

Hazen, T.C.

1991-03-04

A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state.

PubMed

Vidavsky, Netta; Akiva, Anat; Kaplan-Ashiri, Ifat; Rechav, Katya; Addadi, Lia; Weiner, Steve; Schertel, Andreas

2016-12-01

Many important biological questions can be addressed by studying in 3D large volumes of intact, cryo fixed hydrated tissues (⩾10,000μm 3 ) at high resolution (5-20nm). This can be achieved using serial FIB milling and block face surface imaging under cryo conditions. Here we demonstrate the unique potential of the cryo-FIB-SEM approach using two extensively studied model systems; sea urchin embryos and the tail fin of zebrafish larvae. We focus in particular on the environment of mineral deposition sites. The cellular organelles, including mitochondria, Golgi, ER, nuclei and nuclear pores are made visible by the image contrast created by differences in surface potential of different biochemical components. Auto segmentation and/or volume rendering of the image stacks and 3D reconstruction of the skeleton and the cellular environment, provides a detailed view of the relative distribution in space of the tissue/cellular components, and thus of their interactions. Simultaneous acquisition of secondary and back-scattered electron images adds additional information. For example, a serial view of the zebrafish tail reveals the presence of electron dense mineral particles inside mitochondrial networks extending more than 20μm in depth in the block. Large volume imaging using cryo FIB SEM, as demonstrated here, can contribute significantly to the understanding of the structures and functions of diverse biological tissues. Copyright © 2016 Elsevier Inc. All rights reserved.

Diagnostic Accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex Scores in Predicting the Presence of Esophageal Varices in Liver Cirrhosis: A Systematic Review and Meta-Analysis.

PubMed

Deng, Han; Qi, Xingshun; Guo, Xiaozhong

2015-10-01

Aspartate aminotransferase-to-platelet ratio (APRI), aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), FIB-4, FI, King, Lok, Forns, and FibroIndex scores may be simple and convenient noninvasive diagnostic tests, because they are based on the regular laboratory tests and demographic data. This study aimed to systematically evaluate their diagnostic accuracy for the prediction of varices in liver cirrhosis.All relevant papers were searched via PubMed, EMBASE, CNKI, and Wanfang databases. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated.Overall, 12, 4, 5, 0, 0, 4, 3, and 1 paper was identified to explore the diagnostic accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex scores, respectively. The AUSROCs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of varices were 0.6774, 0.7275, 0.7755, 0.7885, and 0.7517, respectively; and those for the prediction of large varices were 0.7278, 0.7448, 0.7095, 0.7264, and 0.6530, respectively. The diagnostic threshold effects of FIB-4 and Forns scores for the prediction of varices were statistically significant. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, and Lok scores for the prediction of varices were 0.60/0.67/1.77/0.58/3.13, 0.64/0.63/1.97/0.54/4.18, and 0.74/0.68/2.34/0.40/5.76, respectively. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of large varices were 0.65/0.66/2.15/0.47/4.97, 0.68/0.58/2.07/0.54/3.93, 0.62/0.64/2.02/0.56/3.57, 0.78/0.63/2.09/0.37/5.55, and 0.65/0.61/1.62/0.59/2.75, respectively.APRI, AAR, FIB-4, Lok, and Forns scores had low to moderate diagnostic accuracy in predicting the presence of varices in liver cirrhosis.

Application of empirical predictive modeling using conventional and alternative fecal indicator bacteria in eastern North Carolina waters

USGS Publications Warehouse

Gonzalez, Raul; Conn, Kathleen E.; Crosswell, Joey; Noble, Rachel

2012-01-01

Coastal and estuarine waters are the site of intense anthropogenic influence with concomitant use for recreation and seafood harvesting. Therefore, coastal and estuarine water quality has a direct impact on human health. In eastern North Carolina (NC) there are over 240 recreational and 1025 shellfish harvesting water quality monitoring sites that are regularly assessed. Because of the large number of sites, sampling frequency is often only on a weekly basis. This frequency, along with an 18–24 h incubation time for fecal indicator bacteria (FIB) enumeration via culture-based methods, reduces the efficiency of the public notification process. In states like NC where beach monitoring resources are limited but historical data are plentiful, predictive models may offer an improvement for monitoring and notification by providing real-time FIB estimates. In this study, water samples were collected during 12 dry (n = 88) and 13 wet (n = 66) weather events at up to 10 sites. Statistical predictive models for Escherichiacoli (EC), enterococci (ENT), and members of the Bacteroidales group were created and subsequently validated. Our results showed that models for EC and ENT (adjusted R2 were 0.61 and 0.64, respectively) incorporated a range of antecedent rainfall, climate, and environmental variables. The most important variables for EC and ENT models were 5-day antecedent rainfall, dissolved oxygen, and salinity. These models successfully predicted FIB levels over a wide range of conditions with a 3% (EC model) and 9% (ENT model) overall error rate for recreational threshold values and a 0% (EC model) overall error rate for shellfish threshold values. Though modeling of members of the Bacteroidales group had less predictive ability (adjusted R2 were 0.56 and 0.53 for fecal Bacteroides spp. and human Bacteroides spp., respectively), the modeling approach and testing provided information on Bacteroidales ecology. This is the first example of a set of successful statistical

Gamma-glutamyl-transpeptidase to platelet ratio is not superior to APRI,FIB-4 and RPR for diagnosing liver fibrosis in CHB patients in China.

PubMed

Huang, Rui; Wang, Guiyang; Tian, Chen; Liu, Yong; Jia, Bei; Wang, Jian; Yang, Yue; Li, Yang; Sun, Zhenhua; Yan, Xiaomin; Xia, Juan; Xiong, Yali; Song, Peixin; Zhang, Zhaoping; Ding, Weimao; Wu, Chao

2017-08-17

The gamma-glutamyl transpeptidase to platelet ratio (GPR) is a novel index to estimate liver fibrosis in chronic hepatitis B (CHB). Few studies compared diagnostic accuracy of GPR with other non-invasive fibrosis tests based on blood parameters. We analyzed diagnostic values of GPR for detecting liver fibrosis and compared diagnostic performances of GPR with APRI (aspartate aminotransferase-to-platelet ratio index), FIB-4 (fibrosis index based on the four factors), NLR (neutrophil-to-lymphocyte ratio), AAR (aspartate aminotransferase/alanine aminotransferase ratio) and RPR (red cell distribution width-to-platelet ratio) in HBeAg positive CHB and HBeAg negative CHB. We found AUROCs of GPR in predicting significant liver fibrosis, advanced liver fibrosis and liver cirrhosis were 0.732 (95% CI 0.663 to 0.801), 0.788 (95% CI 0.729 to 0.847) and 0.753 (95% CI 0.692 to 0.814), respectively. Further comparisons showed the diagnostic performance of GPR was not significantly different with APRI, FIB-4 and RPR in identifying significant fibrosis, advanced fibrosis and cirrhosis, but it was significantly superior to AAR and NLR in both HBeAg positive CHB and HBeAg negative CHB. In conclusion, GPR does not show advantages than APRI, FIB-4 and RPR in identifying significant liver fibrosis, advanced liver fibrosis and liver cirrhosis in both HBeAg positive CHB and HBeAg negative CHB in China.

Promotion by humus-reducing bacteria for the degradation of UV254 absorbance in reverse-osmosis concentrates pretreated with O3-assisted UV-Fenton method.

PubMed

Xia, Jiaohui; Zhang, Hui; Ding, Shaoxuan; Li, Changyu; Ding, Jincheng; Lu, Jie

2017-07-12

The primary pollutants in reverse-osmosis concentrates (ROC) are the substances with the UV absorbance at 254 nm (UV 254 ), which is closely related to humic substances that can be degraded by humus-reducing bacteria. This work studied the degradation characteristics of humus-reducing bacteria in ROC treatment. The physiological and biochemical characteristics of humus-reducing bacteria were investigated, and the effects of pH values and electron donors on the reduction of humic analog, antraquinone-2, 6-disulfonate were explored to optimize the degradation. Furthermore, the O 3 -assisted UV-Fenton method was applied for the pretreatment of ROC, and the degradation of UV 254 absorbance was apparently promoted with their removal rate, reaching 84.2% after 10 days of degradation by humus-reducing bacteria.

Variation in bacterial ATP concentration during rapid changes in extracellular pH and implications for the activity of attached bacteria.

PubMed

Albert, Lynal S; Brown, Derick G

2015-08-01

In this study we investigated the relationship between a rapid change in extracellular pH and the alteration of bacterial ATP concentration. This relationship is a key component of a hypothesis indicating that bacterial bioenergetics - the creation of ATP from ADP via a proton gradient across the cytoplasmic membrane - can be altered by the physiochemical charge-regulation effect, which results in a pH shift at the bacteria's surface upon adhesion to another surface. The bacterial ATP concentration was measured during a rapid change in extracellular pH from a baseline pH of 7.2 to pH values between 3.5 and 10.5. Experiments were conducted with four neutrophilic bacterial strains, including the Gram-negative Escherichia coli and Pseudomonas putida and the Gram-positive Bacillus subtilis and Staphylococcus epidermidis. A change in bulk pH produced an immediate response in bacterial ATP, demonstrating a direct link between changes in extracellular pH and cellular bioenergetics. In general, the shifts in ATP were similar across the four bacterial strains, with results following an exponential relationship between the extracellular pH and cellular ATP concentration. One exception occurred with S. epidermidis, where there was no variation in cellular ATP at acidic pH values, and this finding is consistent with this species' ability to thrive under acidic conditions. These results provide insight into obtaining a desired bioenergetic response in bacteria through (i) the application of chemical treatments to vary the local pH and (ii) the selection and design of surfaces resulting in local pH modification of attached bacteria via the charge-regulation effect. Copyright © 2015 Elsevier B.V. All rights reserved.

Removal of H2S in down-flow GAC biofiltration using sulfide oxidizing bacteria from concentrated latex wastewater.

PubMed

Rattanapan, Cheerawit; Boonsawang, Piyarat; Kantachote, Duangporn

2009-01-01

A biofiltration system with sulfur oxidizing bacteria immobilized on granular activated carbon (GAC) as packing materials had a good potential when used to eliminate H(2)S. The sulfur oxidizing bacteria were stimulated from concentrated latex wastewater with sulfur supplement under aerobic condition. Afterward, it was immobilized on GAC to test the performance of cell-immobilized GAC biofilter. In this study, the effect of inlet H(2)S concentration, H(2)S gas flow rate, air gas flow rate and long-term operation on the H(2)S removal efficiency was investigated. In addition, the comparative performance of sulfide oxidizing bacterium immobilized on GAC (biofilter A) and GAC without cell immobilization (biofilter B) systems was studied. It was found that the efficiency of the H(2)S removal was more than 98% even at high concentrations (200-4000 ppm) and the maximum elimination capacity was about 125 g H(2)S/m(3)of GAC/h in the biofilter A. However, the H(2)S flow rate of 15-35 l/h into both biofilters had little influence on the efficiency of H(2)S removal. Moreover, an air flow rate of 5.86 l/h gave complete removal of H(2)S (100%) in biofilter A. During the long-term operation, the complete H(2)S removal was achieved after 3-days operation in biofilter A and remained stable up to 60-days.

USING PUBLIC-DOMAIN MODELS TO ESTIMATE BEACH BACTERIA CONCENTRATIONS

EPA Science Inventory

Stretches of beach along popular Huntington Beach, California are occassionally closed to swimming due to high levels of bacteria. One hypothesized source is the treated wastewater plume from the Orange County Sanitation District's (OCSD) ocean outfall. While three independent sc...

Short-term effect of ammonia concentration and salinity on activity of ammonia oxidizing bacteria.

PubMed

Claros, J; Jiménez, E; Borrás, L; Aguado, D; Seco, A; Ferrer, J; Serralta, J

2010-01-01

A continuously aerated SHARON (single reactor high activity ammonia removal over nitrite) system has been operated to achieve partial nitritation. Two sets of batch experiments were carried out to study the effect of ammonia concentration and salinity on the activity of ammonia-oxidizing bacteria (AOB). Activity of AOB raised as free ammonia concentration was increased reaching its maximum value at 4.5 mg NH3-N l(-1). The half saturation constant for free ammonia was determined (K(NH3)=0.32 mg NH3-N l(-1)). Activity decreased at TAN (total ammonium-nitrogen) concentration over 2,000 mg NH4-N l(-1). No free ammonia inhibition was detected. The effect of salinity was studied by adding different concentrations of different salts to the biomass. No significant differences were observed between the experiments carried out with a salt containing or not containing NH4. These results support that AOB are inhibited by salinity, not by free ammonia. A mathematical expression to represent this inhibition is proposed. To compare substrate affinity and salinity inhibitory effect on different AOB populations, similar experiments were carried out with biomass from a biological nutrient removal pilot plant. The AOB activity reached its maximum value at 0.008 mg NH3-N l(-1) and decreased at TAN concentration over 400 mg NH4-N l(-1). These differences can be explained by the different AOB predominating species: Nitrosomonas europaea and N. eutropha in the SHARON biomass and Nitrosomonas oligotropha in the pilot plant.

A single exposure of sediment sulphate-reducing bacteria to oxytetracycline concentrations relevant to aquaculture enduringly disturbed their activity, abundance and community structure.

PubMed

Fernández, M L; Granados-Chinchilla, F; Rodríguez, C

2015-08-01

Although feed medicated with antibiotics is widely used in animal production to prevent and treat bacterial infections, the effect of these drugs on nontarget anaerobic bacteria is unknown. We aimed to clarify whether a single exposure of sulphate-reducing bacteria (SRB) from a tilapia pond to oxytetracycline (OTC) concentrations relevant to aquaculture impacts their function, abundance and community structure. To demonstrate changes in SO4(2-) content, SRB abundance, dsrB copy number and SRB diversity, sediment mesocosms were spiked with 5, 25, 50 and 75 mg OTC kg(-1) and examined for 30 days by means of ion chromatography, qPCR, cultivation and fluorescent in situ hybridization (FISH). On day 3, we measured higher SO4(2-) concentrations (ca. two-fold) and a reduction in dsrB copy numbers of approximately 50% in the treatments compared to the controls. After 30 days, a subtle yet measurable enrichment of bacteria from the order Desulfovibrionales occurred in mesocosms receiving ≥ 50 mg OTC kg(-1), notwithstanding that SRB counts decreased two orders of magnitude. OTC was dynamically and reversibly converted into 4-epioxytetracycline and other related compounds in a dose-dependent manner during the experiment. A single exposure to rather high OTC concentrations triggered functional and structural changes in a SRB community that manifested quickly and persisted for a month. This study improves our limited knowledge on the ecotoxicology of antibiotics in anaerobic environments. © 2015 The Society for Applied Microbiology.

Linked Hydrologic-Hydrodynamic Model Framework to Forecast Impacts of Rivers on Beach Water Quality

NASA Astrophysics Data System (ADS)

Anderson, E. J.; Fry, L. M.; Kramer, E.; Ritzenthaler, A.

2014-12-01

The goal of NOAA's beach quality forecasting program is to use a multi-faceted approach to aid in detection and prediction of bacteria in recreational waters. In particular, our focus has been on the connection between tributary loads and bacteria concentrations at nearby beaches. While there is a clear link between stormwater runoff and beach water quality, quantifying the contribution of river loadings to nearshore bacterial concentrations is complicated due to multiple processes that drive bacterial concentrations in rivers as well as those processes affecting the fate and transport of bacteria upon exiting the rivers. In order to forecast potential impacts of rivers on beach water quality, we developed a linked hydrologic-hydrodynamic water quality framework that simulates accumulation and washoff of bacteria from the landscape, and then predicts the fate and transport of washed off bacteria from the watershed to the coastal zone. The framework includes a watershed model (IHACRES) to predict fecal indicator bacteria (FIB) loadings to the coastal environment (accumulation, wash-off, die-off) as a function of effective rainfall. These loadings are input into a coastal hydrodynamic model (FVCOM), including a bacteria transport model (Lagrangian particle), to simulate 3D bacteria transport within the coastal environment. This modeling system provides predictive tools to assist local managers in decision-making to reduce human health threats.

FibroScan, aspartate aminotransferase and alanine aminotransferase ratio (AAR), aspartate aminotransferase to platelet ratio index (APRI), fibrosis index based on the 4 factor (FIB-4), and their combinations in the assessment of liver fibrosis in patients with hepatitis B.

PubMed

Ding, Deping; Li, Hongbing; Liu, Ping; Chen, Lingli; Kang, Jian; Zhang, Yinhua; Ma, Deqiang; Chen, Yue; Luo, Jie; Meng, Zhongji

2015-01-01

The aim of this study was to assess the effects of FibroScan, aspartate aminotransferase and alanine aminotransferase ratio (AAR), aspartate aminotransferase to platelet ratio index (APRI), fibrosis index based on the 4 factor (FIB-4) and their combinations on liver fibrosis in patients with hepatitis B. 406 hospitalized patients with chronic hepatitis B (CHB) and cirrhosis in our hospital were analyzed retrospectively and collected patients clinical indicators, including liver stiffness (LS), AAR, APRI and FIB-4, and then compared the differences of these indicators between CHB group and hepatitis B with cirrhosis group. Receiver operating curve (ROC) was used to evaluate the differentiating capacity of these indicators on CHB and liver cirrhosis. Four indicators related to liver cirrhosis had a statistical significance between two groups (P < 0.01); the under ROC curve areas of LS, AAR, APRI and FIB-4 for differential diagnosis of CHB and liver cirrhosis were 0.866, 0.772, 0.632 and 0.885, respectively. The under ROC curve areas of LS, AAR, APRI and FIB-4 for differential diagnosis of liver cirrhosis at compensatory stage and de-compensatory stage were 0.627, 0.666, 0.795 and 0.820, respectively. LS, AAR, APRI and FIB-4 were good indicators as clinical diagnosis and differential diagnosis on hepatitis B related cirrhosis.

Occurrence and trends in the concentrations of fecal-indicator bacteria and the relation to field water-quality parameters in the Allegheny, Monongahela, and Ohio Rivers and selected tributaries, Allegheny County, Pennsylvania, 2001–09

USGS Publications Warehouse

Fulton, John W.; Koerkle, Edward H.; McCoy, Jamie L.; Zarr, Linda F.

2016-01-21

A total of 1,742 water samples were collected at 52 main-stem and tributary sites. Quantifiable concentrations of Escherichia coli (E. coli) were reported in 1,667 samples, or 97.0 percent of 1,719 samples; concentrations in 853 samples (49.6 percent) exceeded the U.S. Environmental Protection Agency (EPA) recreational water-quality criterion of 235 colonies per 100 milliliters (col/100 mL). Quantifiable concentrations of fecal coliform (FC) bacteria were reported in 1,693 samples, or 98.8 percent of 1,713 samples; concentrations in 780 samples (45.5 percent) exceeded the Commonwealth of Pennsylvania water contact criterion of 400 col/100 mL. Quantifiable concentrations of enterococci bacteria were reported in 912 samples, or 87.5 percent of 1,042 samples; concentrations in 483 samples (46.4 percent) exceeded the EPA recreational water-quality criterion of 61 col/100 mL. The median percentage of samples in which bacteria concentrations exceeded recreational water-quality standards across all sites with five or more samples was 48 for E. coli, 43 for FC, and 75 for enterococci. E. coli, FC, and enterococci concentrations at main-stem sites had significant positive correlations with streamflow under all weather conditions, with rho values ranging from 0.203 to 0.598. Seasonal Kendall and logistic regression were evaluated to determine whether statistically significant trends were present during the period 2001–09. In general, Seasonal Kendall tests for trends in E. coli and FC bacteria were inconclusive. Results of logistic regression showed no significant trends in dry-weather exceedance of the standards; however, significant decreases in the likelihood that wet-weather E. coli and FC bacteria concentrations will exceed EPA recreational standards were found at the USGS streamgaging station Allegheny River at 9th Street Bridge. Nonparametric correlation analysis, including Spearman’s rho and the paired Prentice-Wilcoxon test, was used to screen for associations

Three dimensional microstructural characterization of nanoscale precipitates in AA7075-T651 by focused ion beam (FIB) tomography

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

Singh, Sudhanshu S.; Loza, Jose J.

2016-08-15

The size and distribution of precipitates in Al 7075 alloys affects both the mechanical and corrosion behavior (including stress corrosion cracking and fatigue corrosion) of the alloy. Three dimensional (3D) quantitative microstructural analysis of Al 7075 in the peak aged condition (T651) allows for a better understanding of these behaviors. In this study, Focused ion beam (FIB) tomography was used to characterize the microstructure in three dimensions. Analysis of grains and precipitates was performed in terms of volume, size, and morphology. It was found that the precipitates at the grain boundaries are larger in size, higher in aspect ratios andmore » maximum Feret diameter compared to the precipitates inside the grains, due to earlier nucleation of the precipitates at the grain boundaries. Our data on the precipitates at the interface between grains and Mg{sub 2}Si inclusion show that the surfaces of inclusion (impurity) particles can serve as a location for heterogeneous nucleation of precipitates. - Highlights: •Focused ion beam (FIB) tomography was used to characterize the microstructure of Al 7075 in three dimensions. •Analysis of grains and precipitates was performed in terms of volume, size, and morphology. •Precipitates at the grain boundaries have larger size and aspect ratio compared to the precipitates inside the grains.« less

Oil recovery test using bio surfactants of indigenous bacteria in variation concentration of carbon source

NASA Astrophysics Data System (ADS)

Yudono, B.; Purwaningrum, W.; Estuningsih, S. P.; Kaffah, S.

2017-05-01

Recovery tests of crude oil by using bio surfactant of indigenous bacteria Pseudomonas peli, Pseudomonas citronellolis, Burkholderia glumae and Bacillus firmus. The bio surfactants were prepared with the variation concentrations of molasses carbon source; 0, 5, 10, 15, 20, and 25 %. The results showed that 10 g samples, which concentration 18.64% TPH could be dissolved in the bio surfactant 10%. Optimally in the molasses carbon source concentrations for each bacterium at 5, 10, 20 and 15 % with oil recovery as much as 31.92, 17.65, 22.32, and 14.38 % respectively. Oil components which extracted by bio surfactant were analyzed by using GLC (Gas Liquid Chromatography). The bio surfactants of Pseudomonas peli could dissolve oil fraction temperatures; 139.85; 144.69; 149.98; 1.55.03: 174.22 °C, Pseudomonas citronellolis could dissolve oil fraction temperatures; 139.13; 142.64;147.99; 155.03; 159.85; 164.50 °C, Burkholderia glumae could dissolve oil fraction temperatures 144.69; 149.98; 155.03; 159.85; 164.50 °C, and Bacillus firmus could dissolve oil fraction temperatures; 149.98; 155.03; 158.46; 164.50 °C.

Rapid, quantitative determination of bacteria in water. [adenosine triphosphate

NASA Technical Reports Server (NTRS)

Chappelle, E. W.; Picciolo, G. L.; Thomas, R. R.; Jeffers, E. L.; Deming, J. W. (Inventor)

1978-01-01

A bioluminescent assay for ATP in water borne bacteria is made by adding nitric acid to a water sample with concentrated bacteria to rupture the bacterial cells. The sample is diluted with sterile, deionized water, then mixed with a luciferase-luciferin mixture and the resulting light output of the bioluminescent reaction is measured and correlated with bacteria present. A standard and a blank also are presented so that the light output can be correlated to bacteria in the sample and system noise can be substracted from the readings. A chemiluminescent assay for iron porphyrins in water borne bacteria is made by adding luminol reagent to a water sample with concentrated bacteria and measuring the resulting light output of the chemiluminescent reaction.

FIB-based measurement of local residual stresses on microsystems

NASA Astrophysics Data System (ADS)

Vogel, Dietmar; Sabate, Neus; Gollhardt, Astrid; Keller, Juergen; Auersperg, Juergen; Michel, Bernd

2006-03-01

The paper comprises research results obtained for stress determination on micro and nanotechnology components. It meets the concern of controlling stresses introduced to sensors, MEMS and electronics devices during different micromachining processes. The method bases on deformation measurement options made available inside focused ion beam equipment. Removing locally material by ion beam milling existing stresses / residual stresses lead to deformation fields around the milled feature. Digital image correlation techniques are used to extract deformation values from micrographs captured before and after milling. In the paper, two main milling features have been analyzed - through hole and through slit milling. Analytical solutions for stress release fields of in-plane stresses have been derived and compared to respective experimental findings. Their good agreement allows to settle a method for determination of residual stress values, which is demonstrated for thin membranes manufactured by silicon micro technology. Some emphasis is made on the elimination of main error sources for stress determination, like rigid body object displacements and rotations due to drifts of experimental conditions under FIB imaging. In order to illustrate potential application areas of the method residual stress suppression by ion implantation is evaluated by the method and reported here.

Human Occupancy as a Source of Indoor Airborne Bacteria

PubMed Central

Hospodsky, Denina; Qian, Jing; Nazaroff, William W.; Yamamoto, Naomichi; Bibby, Kyle; Rismani-Yazdi, Hamid; Peccia, Jordan

2012-01-01

Exposure to specific airborne bacteria indoors is linked to infectious and noninfectious adverse health outcomes. However, the sources and origins of bacteria suspended in indoor air are not well understood. This study presents evidence for elevated concentrations of indoor airborne bacteria due to human occupancy, and investigates the sources of these bacteria. Samples were collected in a university classroom while occupied and when vacant. The total particle mass concentration, bacterial genome concentration, and bacterial phylogenetic populations were characterized in indoor, outdoor, and ventilation duct supply air, as well as in the dust of ventilation system filters and in floor dust. Occupancy increased the total aerosol mass and bacterial genome concentration in indoor air PM10 and PM2.5 size fractions, with an increase of nearly two orders of magnitude in airborne bacterial genome concentration in PM10. On a per mass basis, floor dust was enriched in bacterial genomes compared to airborne particles. Quantitative comparisons between bacterial populations in indoor air and potential sources suggest that resuspended floor dust is an important contributor to bacterial aerosol populations during occupancy. Experiments that controlled for resuspension from the floor implies that direct human shedding may also significantly impact the concentration of indoor airborne particles. The high content of bacteria specific to the skin, nostrils, and hair of humans found in indoor air and in floor dust indicates that floors are an important reservoir of human-associated bacteria, and that the direct particle shedding of desquamated skin cells and their subsequent resuspension strongly influenced the airborne bacteria population structure in this human-occupied environment. Inhalation exposure to microbes shed by other current or previous human occupants may occur in communal indoor environments. PMID:22529946

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.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

PubMed Central

Sidhu, J. P. S.; Smith, K.; Beale, D. J.; Gyawali, P.; Toze, S.

2015-01-01

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 106 gene copies per ml), followed by those of HF183 (8.0 × 105 gene copies per ml) and Enterococcus spp. (3.6 × 105 gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters. PMID:26682850

Effects of Antiadhesion preparation on free fibrinogen and fibrin degrading products in abdominal exudates of rabbits postoperatively

PubMed Central

Wang, You-Li; Pan, Cheng-En; Yang, Ping-Lin; Tian, Yuan; Pei, Shu-Wen; Dong, Ming

2004-01-01

AIM: To observe effects of ACOL on fibrinogen (FIB), fibrin degrading products (FDP) and changes of FIB and FDP concentration in rabbits with intro-abdominal exudates during 7 d after major abdominal surgery. METHODS: Sixty New Zealand rabbits were randomly divided into 4 groups: ACOL group, the control group, DCT group and the normal group. After being modeled, except the normal group, the other 3 groups were treated with different ways for a week; the intro-abdominal exudates of rabbits in the 4 groups were drawn for FIB and FDP measurement once daily during 7 d after major abdominal surgery. RESULTS: FIB and FDP in the intro-abdominal exudates altered in a regular way and ACOL could change the concentration of FIB and FDP in the intra-abdominal exudates after major abdominal surgery. CONCLUSION: ACOL can prevent intestinal adhesion by reducing the concentration of FIB and raising that of FDP in the intro-abdominal exudates after major abdominal surgery. PMID:15309738

Anti-bacteria effect of active ingredients of siraitia grosvenorii on the spoilage bacteria isolated from sauced pork head meat

NASA Astrophysics Data System (ADS)

Li, X.; Xu, L. Y.; Cui, Y. Q.; Pang, M. X.; Wang, F.; Qi, J. H.

2018-01-01

Extraction and anti-bacteria effect of active ingredients of Siraitia grosvenorii were studied in this paper. Extraction combined with ultrasonic was adopted. The optimum extraction condition was determined by single factor test; the anti-bacteria effect of active ingredients and minimum inhibitory concentration (MIC) were valued by Oxford-cup method. The results indicated that optimum extraction condition of active ingredients extracted from Siraitia grosvenorii were described as follows: ethanol concentrations of sixty-five percent and twenty minutes with ultrasonic assisted extraction; the active ingredients of Siraitia grosvenorii had anti-bacteria effect on Staphylococcus epidermidis, Proteus vulgaris, Bacillus sp, Serratia sp and MIC was 0.125g/mL, 0.0625g/mL, 0.125g/mL and 0.125g/mL. The active constituent of Siraitia grosvenorii has obvious anti-bacteria effect on the spoilage bacteria isolated from Sauced pork head meat and can be used as a new natural food preservation to prolong the shelf-life of Low-temperature meat products.

Differential Decay of Enterococci and Escherichia coli Originating from Two Fecal Pollution Sources

PubMed Central

Harwood, Valerie J.; Shanks, Orin C.; Fout, G. Shay; Ashbolt, Nicholas J.

2013-01-01

Using in situ subtropical aquatic mesocosms, fecal source (cattle manure versus sewage) was shown to be the most important contributor to differential loss in viability of fecal indicator bacteria (FIB), specifically enterococci in freshwater and Escherichia coli in marine habitats. In this study, sunlight exposure and indigenous aquatic microbiota were also important contributors, whose effects on FIB also differed between water types. PMID:23377944

Factors related to occurrence and distribution of selected bacterial and protozoan pathogens in Pennsylvania streams

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Donna A. Crouse,; Isaacs, Natasha M.

2013-01-01

The occurrence and distribution of fecal indicator bacteria (FIB) and bacterial and protozoan pathogens are controlled by diverse factors. To investigate these factors in Pennsylvania streams, 217 samples were collected quarterly from a 27-station water-quality monitoring network from July 2007 through August 2009. Samples were analyzed for concentrations of Escherichia coli (EC) and enterococci (ENT) indicator bacteria, concentrations of Cryptosporidium oocysts and Giardia cysts, and the presence of four genes related to pathogenic types of EC (eaeA, stx2, stx1, rfbO157) plus three microbial source tracking (MST) gene markers that are also associated with pathogenic ENT and EC (esp, LTIIa, STII). Water samples were concurrently analyzed for basic water chemistry, physical measures of water quality, nutrients, metals, and a suite of 79 organic compounds that included hormones, pharmaceuticals, and antibiotics. For each sample location, stream discharge was measured by using standardized methods at the time of sample collection, and ancillary sample site information, such as land use and geological characteristics, was compiled. Samples exceeding recreational water quality criteria were more likely to contain all measured pathogen genes but notCryptosporidium or Giardia (oo)cysts. FIB and Giardia density and frequency of eaeA gene occurrence were significantly related to season. When discharge at a sampling location was high (>75th percentile of daily mean discharge), there were greater densities of FIB and Giardia, and the stx2, rfbO157, STII, and esp genes were found more frequently than at other discharge conditions. Giardia occurrence was likely related to nonpoint sources, which are highly influential during seasonal overland transport resulting from snowmelt and elevated precipitation in late winter and spring in Pennsylvania. When MST markers of human, swine, or bovine origin were present, samples more frequently carried the eaeA, stx2

[Establishment of Assessment Method for Air Bacteria and Fungi Contamination].

PubMed

Zhang, Hua-ling; Yao, Da-jun; Zhang, Yu; Fang, Zi-liang

2016-03-15

In this paper, in order to settle existing problems in the assessment of air bacteria and fungi contamination, the indoor and outdoor air bacteria and fungi filed concentrations by impact method and settlement method in existing documents were collected and analyzed, then the goodness of chi square was used to test whether these concentration data obeyed normal distribution at the significant level of α = 0.05, and combined with the 3σ principle of normal distribution and the current assessment standards, the suggested concentrations ranges of air microbial concentrations were determined. The research results could provide a reference for developing air bacteria and fungi contamination assessment standards in the future.

Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania.

PubMed

Lupan, Iulia; Carpa, Rahela; Oltean, Andreea; Kelemen, Beatrice Simona; Popescu, Octavian

2017-09-27

The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98-99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.

Sorption of lead onto two gram-negative marine bacteria in seawater

USGS Publications Warehouse

Harvey, Ronald W.; Leckie, James O.

1985-01-01

Laboratory adsorption experiments performed at environmentally significant lead (Pb) and cell concentrations indicate that the marine bacteria examined have significant binding capacities for Pb. However, the behavior governing Pb sorption onto gram-negative bacteria in seawater may be quite complex. The sorption kinetics appear to involve two distinct phases, i.e., a rapid removal of Pb from solution within the first few minutes, followed by a slow but nearly constant removal over many hours. Also, the average binding coefficient, calculated for Pb sorption onto bacteria and a measure of binding intensity, increases with decreasing sorption density (amounts of bacteria-associated Pb per unit bacterial surface) at low cell concentrations (105 cells ml−1), but decreases with decreasing sorption density at higher cell concentrations (107 cells ml−1). The latter effect is apparently due to the production of significant amounts of extra-cellular organics at high cell concentrations that compete directly with bacterial surfaces for available lead. Lead toxicity and active uptake by marine bacteria did not appear significant at the Pb concentrations used.

Anti-bacteria Effect of Active Ingredients of Cacumen Platycladi on the Spoilage Bacteria of Sauced Pork Head Meat

NASA Astrophysics Data System (ADS)

Li, Xiao; Xu, Lingyi; Cui, Yuqian; Pang, Meixia; Wang, Fang; Qi, Jinghua

2017-12-01

Extraction and anti-bacteria effect of active ingredients of Cacumen Platycladi were studied in this paper. Extraction combined with ultrasonic was adopted. The optimum extraction condition was determined by single factor test; the anti-bacteria effect of active ingredients and minimum inhibitory concentration(MIC) were valued by Oxford-cup method. The results indicated that kaempferol was the active ingredients of Cacumen Platycladi whose optimum extraction condition for ethanol concentrations were sixty-five percent and twenty minutes with ultrasonic assisted extraction.; the active ingredients of Cacumen Platycladi had anti-bacteria effect on Staphylococcus, Proteus, Bacillus, Serratia and MIC was 0.5 g/mL,0.5 g/mL,0.0313 g/mL and 0.0625 g/mL. The active constituent of Cacumen Platycladi is kaempferol which has obvious anti-bacteria effect and can be used to prolong the shelf-life of Low-temperature meat products.

Impact of an intense combined sewer overflow event on the microbiological water quality of the Seine River.

PubMed

Passerat, Julien; Ouattara, Nouho Koffi; Mouchel, Jean-Marie; Rocher, Vincent; Servais, Pierre

2011-01-01

For a better understanding of the short and mid-term impacts of a combined sewer overflow (CSO) on the microbiological quality of the receiving river, we studied the composition of a CSO discharge and monitored during several hours the changes in the concentration of fecal indicator bacteria (FIB) in the impacted river water mass. The CSO occurred at the Clichy outfall (Paris agglomeration, France) in summer 2008 as a result of the most intense rainfall of the year. In 6h, 578, 705 m(3) of sewage and 124 t of suspended matter (SM) were discharged into the Seine River. The CSO contained 1.5 × 10(6)E. coli and 4.0 × 10(5) intestinal enterococci per 100 mL on average, and 77% of the E. coli were attached to SM. It was estimated that 89% of the CSO discharge was contributed by surface water runoff, and that resuspension of sewer sediment contributed to ∼75% of the SM, 10-70% of the E. coli and 40-80% of the intestinal enterococci. Directly downstream from the CSO outfall, FIB concentrations in the impacted water mass of the Seine River (2.9 × 10(5)E. coli and 7.6 × 10(4) intestinal enterococci per 100 mL) exceeded by two orders of magnitude the usual dry weather concentrations. After 13-14 h of transit, these concentrations had decreased by 66% for E. coli and 79% for intestinal enterococci. This decline was well accounted for by our estimations of dilution, decay resulting from mortality or loss of culturability and sedimentation of the attached fraction of FIB. Copyright © 2010 Elsevier Ltd. All rights reserved.

Methanotrophic bacteria.

PubMed Central

Hanson, R S; Hanson, T E

1996-01-01

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

Screening and biological characteristics of fufenozide degrading bacteria

NASA Astrophysics Data System (ADS)

Xu, Chenhao; Gong, Mingfu; Guan, Qinlan; Deng, Xia; Deng, Hongyan; Huang, Jiao

2018-04-01

Fufenozide was a novel pesticide for the control of Lepidoptera pests, which was highly toxic to silkworm. Fufenozide-contaminated soil samples were collected and the bacteria that degrade fufenozide were isolated and screened by selective medium. The colony characteristics, cell characteristics and degradation characteristics in different concentrations fufenozide of the fufenozide degrading bacteria were studied. The results indicated that seven strains of fufenozide degradeing bacteria, named as DDH01, DDH03, DDH04, DDH04, DDH05, DDH07 and DDH07 respectively, were isolated from soil contaminated with fufenozide. DDH01, DDH02, DDH04 and DDH05 of seven fufenozide degrading bacteria, was gram-positive bacteria, and DDH03, DDH06 and DDH07 was gram-negative bacteria. All of seven strains of fufenozide degrading bacteria were not spores, weeks flagella, rod-shaped bacteria. DDH06 and DDH07 had capsules, and the remaining five strains had not capsule. The colonies formed by seven strains of fufenozide degradation bacteria on beef extract peptone medium plate were milky white colonies with irregular edges, thinner lawn, smaller colony with smooth surface. The growth of 7 strains of fufenozide degradation bacteria was significantly affected by the concentration of fufenozide, All of 7 strains grown in the range from 0.00025 g/mL to 1 g/mL of 10% fufenozide suspension. DDH2 was the best among the 7 strains of fufenozide degrading bacteria grown in 10% fufenozide suspension medium.

Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter.

PubMed

Liu, Huan; Zhang, Xu; Zhang, Hao; Yao, Xiangwu; Zhou, Meng; Wang, Jiaqi; He, Zhanfei; Zhang, Huihui; Lou, Liping; Mao, Weihua; Zheng, Ping; Hu, Baolan

2018-02-01

In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers. Copyright © 2017 Elsevier Ltd

Deployable micro-traps to sequester motile bacteria

NASA Astrophysics Data System (ADS)

di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-04-01

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria.

Deployable micro-traps to sequester motile bacteria

PubMed Central

Di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-01-01

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria. PMID:28378786

Deployable micro-traps to sequester motile bacteria.

PubMed

Di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-04-05

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria.

Integral strategy for evaluation of fecal indicator performance in bird-influenced saline inland waters.

PubMed

Kirschner, Alexander K T; Zechmeister, Thomas C; Kavka, Gerhard G; Beiwl, Christian; Herzig, Alois; Mach, Robert L; Farnleitner, Andreas H

2004-12-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems.

Integral Strategy for Evaluation of Fecal Indicator Performance in Bird-Influenced Saline Inland Waters

PubMed Central

Kirschner, Alexander K. T.; Zechmeister, Thomas C.; Kavka, Gerhard G.; Beiwl, Christian; Herzig, Alois; Mach, Robert L.; Farnleitner, Andreas H.

2004-01-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems. PMID:15574941

Status of faecal pollution in ports: A basin-wide investigation in the Adriatic Sea.

PubMed

Luna, Gian Marco; Manini, Elena; Turk, Valentina; Tinta, Tinkara; D'Errico, Giuseppe; Baldrighi, Elisa; Baljak, Vanja; Buda, Donatella; Cabrini, Marina; Campanelli, Alessandra; Cenov, Arijana; Del Negro, Paola; Drakulović, Dragana; Fabbro, Cinzia; Glad, Marin; Grilec, Dolores; Grilli, Federica; Jokanović, Sandra; Jozić, Slaven; Kauzlarić, Vesna; Kraus, Romina; Marini, Mauro; Mikuš, Josip; Milandri, Stefania; Pećarević, Marijana; Perini, Laura; Quero, Grazia Marina; Šolić, Mladen; Lušić, Darija Vukić; Zoffoli, Silvia

2018-04-07

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of hydrologic, biological, and environmental processes on sources and concentrations of fecal bacteria in the Cuyahoga River, with implications for management of recreational waters in Summit and Cuyahoga Counties, Ohio

USGS Publications Warehouse

Myers, Donna N.; Koltun, G.F.; Francy, Donna S.

1998-01-01

Discharges of fecal bacteria (fecal coliform bacteria and Escherichia coli ) to the middle main stem of the Cuyahoga River from storm water, combined sewers, and incompletely disinfected wastewater have resulted in frequent exceedances of bacteriological water-quality standards in a 23-mile reach of the river that flows through the Cuyahoga Valley National Recreation Area. Contamination of the middle main stem of the Cuyahoga River by bacteria of fecal origin and subsequent transport to downstream areas where water-contact recreation is an important use of the river are a concern because of the potential public-health risk from the presence of enteric pathogens. Independent field investigations of bacterial decay, dilution, dispersion, transport, and sources, and bacterial contamination of streambed sediments, were completed in 1991-93 during periods of rainfall and runoff. The highest concentration of fecal coliform bacteria observed in the middle main stem during three transport studies exceeded the single-sample fecal coliform standard applicable to primary-contact recreation by a factor of approximately 1,300 and exceeded the Escherichia coli standard by a factor of approximately 8,000. The geometric-mean concentrations of fecal bacteria in the middle main stem were 6.7 to 12.3 times higher than geometric-mean concentrations in the monitored tributaries, and 1.8 to 7.0 times larger than the geometric-mean concentrations discharged from the Akron Water Pollution Control Station. Decay rates of fecal bacteria measured in field studies in 1992 ranged from 0.0018 per hour to 0.0372 per hour for fecal coliform bacteria and from 0.0022 per hour to 0.0407 per hour for Escherichia coli. Most of the decay rates measured in June and August were significantly higher than decay rates measured in April and October. Results of field studies demonstrated that concentrations of fecal coliform bacteria were 1.2 to 58 times higher in streambed sediments than in the overlying

2006 Pathogen and Toxin Concentration Systems for Water Monitoring

DTIC Science & Technology

2012-07-24

design and construct a compact, portable automated device enabling the simultaneous concentration of protozoa , bacteria, bacterial spores, algae and...portable automated device enabling the simultaneous concentration of protozoa , bacteria, bacterial spores, algae and viruses from large volumes of various...construct a compact, portable automated device enabling the simultaneous concentration of protozoa , bacteria, bacterial spores, algae and viruses

Quantitative risk analysis for potentially resistant E. coli in surface waters caused by antibiotic use in agricultural systems.

PubMed

Limayem, Alya; Martin, Elizabeth M

2014-01-01

Antibiotics are frequently used in agricultural systems to promote livestock health and to control bacterial contaminants. Given the upsurge of the resistant fecal indicator bacteria (FIB) in the surface waters, a novel statistical method namely, microbial risk assessment (MRA) was performed, to evaluate the probability of infection by resistant FIB on populations exposed to recreational waters. Diarrheagenic Escherichia coli, except E. coli O157:H7, were selected for their prevalence in aquatic ecosystem. A comparative study between a typical E. coli pathway and a case scenario aggravated by antibiotic use has been performed via Crystal Ball® software in an effort to analyze a set of available inputs provided by the US institutions including E. coli concentrations in US Great Lakes through using random sampling and probability distributions. Results from forecasting a possible worst-case scenario dose-response, accounted for an approximate 50% chance for 20% of the exposed human populations to be infected by recreational water in the U.S. However, in a typical scenario, there is a 50% chance of infection for only 1% of the exposed human populations. The uncertain variable, E. coli concentration accounted for approximately 92.1% in a typical scenario as the major contributing factor of the dose-response model. Resistant FIB in recreational waters that are exacerbated by a low dose of antibiotic pollutants would increase the adverse health effects in exposed human populations by 10 fold.

Airborne Bacteria in an Urban Environment

PubMed Central

Mancinelli, Rocco L.; Shulls, Wells A.

1978-01-01

Samples were taken at random intervals over a 2-year period from urban air and tested for viable bacteria. The number of bacteria in each sample was determined, and each organism isolated was identified by its morphological and biochemical characteristics. The number of bacteria found ranged from 0.013 to 1.88 organisms per liter of air sampled. Representatives of 19 different genera were found in 21 samples. The most frequently isolated organisms and their percent of occurence were Micrococcus (41%), Staphylococcus (11%), and Aerococcus (8%). The bacteria isolated were correlated with various weather and air pollution parameters using the Pearson product-moment correlation coefficient method. Statistically significant correlations were found between the number of viable bacteria isolated and the concentrations of nitric oxide (−0.45), nitrogen dioxide (+0.43), and suspended particulate pollutants (+0.56). Calculated individually, the total number of Micrococcus, Aerococcus, and Staphylococcus, number of rods, and number of cocci isolated showed negative correlations with nitric oxide and positive correlations with nitrogen dioxide and particulates. Statistically significant positive correlations were found between the total number of rods isolated and the concentration of nitrogen dioxide (+0.54) and the percent relative humidity (+0.43). The other parameters tested, sulfur dioxide, hydrocarbons, and temperature, showed no significant correlations. Images PMID:677875

Acoustic impedance matched buffers enable separation of bacteria from blood cells at high cell concentrations.

PubMed

Ohlsson, Pelle; Petersson, Klara; Augustsson, Per; Laurell, Thomas

2018-06-14

Sepsis is a common and often deadly systemic response to an infection, usually caused by bacteria. The gold standard for finding the causing pathogen in a blood sample is blood culture, which may take hours to days. Shortening the time to diagnosis would significantly reduce mortality. To replace the time-consuming blood culture we are developing a method to directly separate bacteria from red and white blood cells to enable faster bacteria identification. The blood cells are moved from the sample flow into a parallel stream using acoustophoresis. Due to their smaller size, the bacteria are not affected by the acoustic field and therefore remain in the blood plasma flow and can be directed to a separate outlet. When optimizing for sample throughput, 1 ml of undiluted whole blood equivalent can be processed within 12.5 min, while maintaining the bacteria recovery at 90% and the blood cell removal above 99%. That makes this the fastest label-free microfluidic continuous flow method per channel to separate bacteria from blood with high bacteria recovery (>80%). The high throughput was achieved by matching the acoustic impedance of the parallel stream to that of the blood sample, to avoid that acoustic forces relocate the fluid streams.

Use of magnetic beads for Gram staining of bacteria in aqueous suspension.

PubMed

Yazdankhah, S P; Sørum, H; Larsen, H J; Gogstad, G

2001-12-01

A Gram staining technique was developed using monodisperse magnetic beads in concentrating bacteria in suspension for downstream application. The technique does not require heat fixation of organisms, electrical power, or a microscope. Gram-negative and Gram-positive bacteria were identified macroscopically based on the colour of the suspension. The bacteria concentrated on magnetic beads may also be identified microscopically.

Accuracy of transient elastography-FibroScan®, acoustic radiation force impulse (ARFI) imaging, the enhanced liver fibrosis (ELF) test, APRI, and the FIB-4 index compared with liver biopsy in patients with chronic hepatitis C.

PubMed

Ragazzo, Taisa Grotta; Paranagua-Vezozzo, Denise; Lima, Fabiana Roberto; de Campos Mazo, Daniel Ferraz; Pessoa, Mário Guimarães; Oliveira, Claudia Pinto; Alves, Venancio Avancini Ferreira; Carrilho, Flair José

2017-10-01

Although liver biopsy is the gold standard for determining the degree of liver fibrosis, issues regarding its invasiveness and the small amount of liver tissue evaluated can limit its applicability and interpretation in clinical practice. Non-invasive evaluation methods for liver fibrosis can address some of these limitations. The aim of this study was to evaluate the accuracy of transient elastography-FibroScan®, acoustic radiation force impulse (ARFI), enhanced liver fibrosis (ELF), the aspartate aminotransferase-to-platelet ratio index (APRI), and the FIB-4 index compared with liver biopsy in hepatitis C. We evaluated chronic hepatitis C patients who were followed at the Division of Clinical Gastroenterology and Hepatology, Hospital das Clínicas, Department of Gastroenterology of University of São Paulo School of Medicine, São Paulo, Brazil, and who underwent liver biopsy. The accuracy of each method was determined by a receiver operating characteristic (ROC) curve analysis, and fibrosis was classified as significant fibrosis (≥F2), advanced fibrosis (≥F3), or cirrhosis (F4). The Obuchowski method was also used to determine the diagnostic accuracy of each method at the various stages of fibrosis. In total, 107 FibroScan®, 51 ARFI, 68 ELF, 106 APRI, and 106 FIB-4 analyses were performed. A total of 107 patients were included in the study. The areas under the ROC curve (AUROCs) according to fibrosis degree were as follows: significant fibrosis (≥F2): FibroScan®: 0.83, FIB-4: 0.76, ELF: 0.70, APRI: 0.69, and ARFI: 0.67; advanced fibrosis (≥F3): FibroScan®: 0.85, ELF: 0.82, FIB-4: 0.77, ARFI: 0.74, and APRI: 0.71; and cirrhosis (F4): APRI: 1, FIB-4: 1, FibroScan®: 0.99, ARFI: 0.96, and ELF: 0.94. The accuracies of transient elastography, ARFI, ELF, APRI and FIB-4 determined by the Obuchowski method were F0-F1: 0.81, 0.78, 0.44, 0.72 and 0.67, respectively; F1-F2: 0.73, 0.53, 0.62, 0.60, and 0.68, respectively; F2-F3: 0.70, 0.64, 0.77, 0.60, and 0

Noninvasive Assessment of Liver Fibrosis By Transient Elastography and FIB4/APRI for Prediction of Treatment Response in Chronic Hepatitis C-An Experience from a Tertiary Care Hospital.

PubMed

Taneja, Sunil; Tohra, Sunil; Duseja, Ajay; Dhiman, Radha Krishan; Chawla, Yogesh Kumar

2016-12-01

Liver fibrosis and its sequel cirrhosis represent a major health care burden, and assessment of fibrosis by biopsy is gradually being replaced by noninvasive methods. In clinical practice, the determination of fibrosis stage is important, since patients with advanced fibrosis have faster progression to cirrhosis and antiviral therapy is indicated in these patients. To assess the role of transient elastography (TE) and compare it with APRI and FIB4 for predicting liver fibrosis and assessing the effect of host and viral factors on fibrosis and treatment outcome in CHC patients. In a retrospective analysis, 330 CHC patients underwent liver stiffness measurement (LSM) by TE and tests needed for calculating APRI and FIB4 scores at baseline. 228 patients received a combination of Pegylated IFN-based antiviral therapy and were analyzed for therapeutic response. The study included 330 patients (median age 39 years [range 18-67]), predominantly males ( n  = 227, 68.8%) with baseline LSMs. The median liver stiffness was 7.8 kPa (range 3.2-69.1 kPa). LSMs and its thresholds for severe fibrosis progression (≥9.5 kPa) and cirrhosis (≥12.5 kPa) were significantly higher in patients with age ≥40 years, diabetes mellitus, and patients with significant alcohol intake ( P  = 0.003 to P  < 0.001). By taking TE as a reference, the diagnostic accuracy of FIB4 scores for predicting cirrhosis (AUROC 0.896) was good (+LR 13.4) compared to APRI (AUROC 0.823) with moderate likelihood ratio (+LR 6.9). Among 228 treated patients the SVR rate in genotype 3 was 70% versus 57.8% in genotype 1. Fibrosis score F4 ( P  = 0.023) and HCV genotype ( P  = 0.008) were independent predictors of SVR. The study shows that LSM by TE and fibrosis assessment by FIB4/APRI scores can be used with fair reliability to predict fibrosis and treatment response in patients with CHC infection.

Antibiotic-induced population fluctuations and stochastic clearance of bacteria

PubMed Central

Le, Dai; Şimşek, Emrah; Chaudhry, Waqas

2018-01-01

Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria. PMID:29508699

Bacteria, biofilm and honey: a study of the effects of honey on 'planktonic' and biofilm-embedded chronic wound bacteria.

PubMed

Merckoll, Patricia; Jonassen, Tom Øystein; Vad, Marie Elisabeth; Jeansson, Stig L; Melby, Kjetil K

2009-01-01

Chronically infected wounds are a costly source of suffering. An important factor in the failure of a sore to heal is the presence of multiple species of bacteria, living cooperatively in highly organized biofilms. The biofilm protects the bacteria from antibiotic therapy and the patient's immune response. Honey has been used as a wound treatment for millennia. The components responsible for its antibacterial properties are now being elucidated. The study aimed to determine the effects of different concentrations of 'Medihoney' therapeutic honey and Norwegian Forest Honey 1) on the real-time growth of typical chronic wound bacteria; 2) on biofilm formation; and 3) on the same bacteria already embedded in biofilm. Reference strains of MRSE, MRSA, ESBL Klebsiella pneumoniae and Pseudomonas aeruginosa were incubated with dilution series of the honeys in microtitre plates for 20 h. Growth of the bacteria was assessed by measuring optical density every 10 min. Growth curves, biofilm formation and minimum bactericidal concentrations are presented. Both honeys were bactericidal against all the strains of bacteria. Biofilm was penetrated by biocidal substances in honey. Reintroduction of honey as a conventional wound treatment may help improve individual wound care, prevent invasive infections, eliminate colonization, interrupt outbreaks and thereby preserve current antibiotic stocks.

External concentration of organic acid anions and pH: key independent variables for studying how organic acids inhibit growth of bacteria in mildly acidic foods.

PubMed

Carpenter, C E; Broadbent, J R

2009-01-01

Although the mechanisms by which organic acids inhibit growth of bacteria in mildly acidic foods are not fully understood, it is clear that intracellular accumulation of anions is a primary contributor to inhibition of bacterial growth. We hypothesize that intracellular accumulation of anions is driven by 2 factors, external anion concentration and external acidity. This hypothesis follows from basic chemistry principles that heretofore have not been fully applied to studies in the field, and it has led us to develop a novel approach for predicting internal anion concentration by controlling the external concentration of anions and pH. This approach overcomes critical flaws in contemporary experimental design that invariably target concentration of either protonated acid or total acid in the growth media thereby leaving anion concentration to vary depending on the pK(a) of the acids involved. Failure to control external concentration of anions has undoubtedly confounded results, and it has likely led to misleading conclusions regarding the antimicrobial action of organic acids. In summary, we advocate an approach for directing internal anion levels by controlling external concentration of anions and pH because it presents an additional opportunity to study the mechanisms by which organic acids inhibit bacterial growth. Knowledge gained from such studies would have important application in the control of important foodborne pathogens such as Listeria monocytogenes, and may also facilitate efforts to promote the survival in foods or beverages of desirable probiotic bacteria.

Three-dimensional characterization of ODS ferritic steel using by FIB-SEM serial sectioning method.

PubMed

Endo, T; Sugino, Y; Ohono, N; Ukai, S; Miyazaki, N; Wang, Y; Ohnuki, S

2014-11-01

Considerable attention has been paid to the research of the electron tomography due to determine the three-dimensional (3D) structure of materials [1]. One of the electron tomography techniques, focused ion beam/scanning electron microscopy (FIB-SEM) imaging has advantages of high resolutions (10 nm), large area observation (μm order) and simultaneous energy dispersive x- ray microanalysis (EDS)/ electron backscatter diffraction (EBSD) analysis. The purpose of this study, three-dimensional EBSD analysis of ODS ferritic steel which carried out cold work using FIB-SEM equipment was conducted, and it aimed at analyzing the microstructure obtained there. The zone annealing tests were conducted for ferritic steel [2,3], which were produced through mechanical alloying and hot-extrusion. After zone annealing, specimens were mechanically polished with #400∼4000 emery paper, 1 µm diamond paste and alumina colloidal silica. The serial sectioning and the 3D-electron backscattering diffraction (3D-EBSD) analysis were carried out. We made the micro pillar (30 x 30 x 15 µm). The EBSD measurements were carried out in each layer after serial sectioning at a step size and milling depth was 80 nm with 30 slices. After EBSD analysis, the series of cross-sectional images were aligned according to arbitrarily specified areas and then stacked up to form a volume. Consequently, we obtained the 3D-IPF maps for ODS ferritic steel. In this specimen, the {111} and {001} grains are layered by turns. In addition, the volume fraction value of both plane are similar. The aspect ratio increases with specimen depth. The 3D-EBSD mapping is useful to analysis of the bulk material since this method obtain many microstructure information, such a shape, volume and orientation of the crystal, grain boundary. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bioretention column study of bacteria community response to salt-enriched artificial stormwater.

PubMed

Endreny, Theodore; Burke, David J; Burchhardt, Kathleen M; Fabian, Mark W; Kretzer, Annette M

2012-01-01

Cold climate cities with green infrastructure depend on soil bacteria to remove nutrients from road salt-enriched stormwater. Our research examined how bacterial communities in laboratory columns containing bioretention media responded to varying concentrations of salt exposure from artificial stormwater and the effect of bacteria and salt on column effluent concentrations. We used a factorial design with two bacteria treatments (sterile, nonsterile) and three salt concentrations (935, 315, and 80 ppm), including a deionized water control. Columns were repeatedly saturated with stormwater or deionized and then drained throughout 5 wk, with the last week of effluent analyzed for water chemistry. To examine bacterial communities, we extracted DNA from column bioretention media at time 0 and at week 5 and used molecular profiling techniques to examine bacterial community changes. We found that bacterial community taxa changed between time 0 and week 5 and that there was significant separation between taxa among salt treatments. Bacteria evenness was significantly affected by stormwater treatment, but there were no differences in bacterial richness or diversity. Soil bacteria and salt treatments had a significant effect on the effluent concentration of NO, PO, Cu, Pb, and Zn based on ANOVA tests. The presence of bacteria reduced effluent NO and Zn concentrations by as much as 150 and 25%, respectively, while having a mixed effect on effluent PO concentrations. Our results demonstrate how stormwater can affect bacterial communities and how the presence of soil bacteria improves pollutant removal by green infrastructure. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Diversity and Distribution of Heavy Metal-Resistant Bacteria in Polluted Sediments of the Araça Bay, São Sebastião (SP), and the Relationship Between Heavy Metals and Organic Matter Concentrations.

PubMed

Zampieri, Bruna Del Busso; Pinto, Aline Bartelochi; Schultz, Leonardo; de Oliveira, Marcos Antonio; de Oliveira, Ana Julia Fernandes Cardoso

2016-10-01

Heavy metals influence the population size, diversity, and metabolic activity of bacteria. In turn, bacteria can develop heavy metal resistance mechanisms, and this can be used in bioremediation of contaminated areas. The purpose of the present study was to understand how heavy metals concentration influence on diversity and distribution of heavy metal-resistant bacteria in Araça Bay, São Sebastião, on the São Paulo coast of Brazil. The hypothesis is that activities that contribute for heavy metal disposal and the increase of metals concentrations in environment can influence in density, diversity, and distribution of heavy metal-resistant bacteria. Only 12 % of the isolated bacteria were sensitive to all of the metals tested. We observed that the highest percentage of resistant strains were in areas closest to the São Sebastião channel, where port activity occurs and have bigger heavy metals concentrations. Bacterial isolated were most resistant to Cr, followed by Zn, Cd, and Cu. Few strains resisted to Cd levels greater than 200 mg L(-1). In respect to Cr, 36 % of the strains were able to grow in the presence of as much as 3200 mg L(-1). Few strains were able to grow at concentrations of Zn and Cu as high as 1600 mg L(-1), and none grew at the highest concentration of 3200 mg L(-1). Bacillus sp. was most frequently isolated and may be the dominant genus in heavy metal-polluted areas. Staphylococcus sp., Planococcus maritimus, and Vibrio aginolyticus were also isolated, suggesting their potential in bioremediation of contaminated sites.

Microbiological quality assessment of sand and water from three selected beaches of South Coast, São Paulo State, Brazil.

PubMed

Pinto, K C; Hachich, E M; Sato, M I Z; Di Bari, M; Coelho, M C L S; Matté, M H; Lamparelli, C C; Razzolini, M T P

2012-01-01

This study aimed to assess the sanitary quality of water, and wet and dry sand from three beaches located in the South Coast region of São Paulo State, Brazil, selected taking into account the frequency of tourists and the water quality (good, fair and poor). Thirty-six water samples each of wet and dry sand and seawater were collected monthly over a period of one year and analyzed for fecal indicator bacteria (FIB: thermotolerant coliforms, Escherichia coli, and enterococci), presumptive Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans and dermatophytes. The results revealed FIB concentrations more elevated in dry sand followed by wet sand and water. P. aeruginosa and presumptive S. aureus were detected with a similar frequency in water and sand samples, but maximum concentrations and geometric means were higher in dry sand. C. albicans was detected only in water samples whereas the dermatophyte Microsporum sp. was isolated exclusively from dry and wet sand samples. This evaluation showed also that the environment had a significant influence on P. aeruginosa but not on presumptive S. aureus concentrations. According to threshold values proposed in the literature for E. coli and enterococci dry sand densities, none of the beaches would be considered of sufficient quality for recreational activities.

Comparison of FIB-4 index, NAFLD fibrosis score and BARD score for prediction of advanced fibrosis in adult patients with non-alcoholic fatty liver disease: A meta-analysis study.

PubMed

Sun, Wenjing; Cui, Hongli; Li, Ning; Wei, Yanling; Lai, Shujie; Yang, Yang; Yin, Xinru; Chen, Dong-Feng

2016-08-01

Non-alcoholic fatty liver disease (NAFLD)-related advanced hepatic fibrosis is associated with liver and cardiovascular morbidity and mortality. This study aims to compare the FIB-4 index, NAFLD fibrosis score (NFS) and BARD score for prediction of advanced liver fibrosis. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), summary receiver-operator curves (SROC) and Spearman's rank correlation coefficient were used to examine the accuracy of each non-invasive scoring system for predicting NAFLD-related advanced fibrosis. Four studies with 1038 adult patients were included in this meta-analysis. A total of 135 patients (13.0%) had advanced fibrosis. In the FIB-4 index group, pooled sensitivity and specificity with 95% confidence interval (CI), and the area under the ROC (AUROC) were 0.844 (0.772-0.901), 0.685 (0.654-0.716) and 0.8496 ± 0.0680, respectively, at a cut-off of 1.30. At a threshold of 3.25, the same parameters were 0.38 (0.30-0.47), 0.96 (0.95-0.98) and 0.8445 ± 0.0981. At a cut-off of -1.455, values were 0.77 (0.69-0.84), 0.70 (0.67-0.73) and 0.8355 ± 0.0667, respectively. At a 0.676 cut-off, pooled sensitivity and specificity with 95% CI were 0.27 (0.19-0.35) and 0.98 (0.96-0.98), respectively; and the AUROC was 0.647 ± 0.2208. In the BARD score group, pooled sensitivity and specificity with 95% CI were 0.74 (0.66-0.81) and 0.66 (0.63-0.69), respectively; and the AUROC was 0.7625 ± 0.0285. FIB-4 index with a 1.30 cut-off has better diagnostic accuracy than the FIB-4 index with a 3.25 cut-off, NFS and BARD score, despite showing its limited value for predicting NAFLD-related advanced fibrosis. © 2016 The Japan Society of Hepatology.

Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium.

PubMed

Lefèvre, Christopher T; Howse, Paul A; Schmidt, Marian L; Sabaty, Monique; Menguy, Nicolas; Luther, George W; Bazylinski, Dennis A

2016-12-01

Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O 2 . For example, SRB remain viable in many aerobic environments while some even reduce O 2 to H 2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O 2 concentration gradient formed, or under O 2 -free N 2 gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O 2 as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gardnerella vaginalis and anaerobic bacteria in genital disease.

PubMed Central

Tabaqchali, S; Wilks, M; Thin, R N

1983-01-01

In a study of Gardnerella vaginalis and anaerobic bacteria in non-specific vaginitis (NSV) and other genital disease 89 patients attending a genital medicine clinic had vaginal samples examined for conventional pathogens and for quantitative analysis of G vaginalis and aerobic and anaerobic bacterial flora. The overall incidence of G vaginalis was 20%; G vaginalis (mean concentration 7.0 log10/g of secretion) occurred predominantly in patients with NSV (57%) but also in sexual contacts of non-specific urethritis (NSU) (37.5%) and in patients with other conditions (11.8%). G vaginalis is therefore a relatively common isolate in patients with vaginal discharge. The concentration of aerobic and anaerobic bacteria ranged from 4.9-11.0 log10/g of secretion with an anaerobe-to-aerobe ratio of 10:1. Anaerobic bacteria, particularly anaerobic Gram-positive cocci (mean concentrations 7.7 log10/g), were present in patients with NSV and in association with G vaginalis, but they also occurred in other clinical groups and with other pathogens, particularly Trichomonas vaginalis. Anaerobic bacteria may therefore play an important role in the pathogenesis of vaginal infections. PMID:6600955

Vibrio bacteria in raw oysters: managing risks to human health.

PubMed

Froelich, Brett A; Noble, Rachel T

2016-03-05

The human-pathogenic marine bacteria Vibrio vulnificus and V. parahaemolyticus are strongly correlated with water temperature, with concentrations increasing as waters warm seasonally. Both of these bacteria can be concentrated in filter-feeding shellfish, especially oysters. Because oysters are often consumed raw, this exposes people to large doses of potentially harmful bacteria. Various models are used to predict the abundance of these bacteria in oysters, which guide shellfish harvest policy meant to reduce human health risk. Vibrio abundance and behaviour varies from site to site, suggesting that location-specific studies are needed to establish targeted risk reduction strategies. Moreover, virulence potential, rather than simple abundance, should be also be included in future modeling efforts. © 2016 The Author(s).

Traditional and Host-Associated Fecal Indicator Bacterial Patterns in Southern California Watersheds: Field Source Identification Studies and Laboratory Microcosms Investigating Presence and Persistence in Water and Sediments

NASA Astrophysics Data System (ADS)

Mika, Kathryn Beth

Overall, recreational beach water quality remains an issue of concern in Southern California and across the globe. Many factors come into play when determining water quality, including physical issues such as the myriad sources that contribute pollution to the site and financial and political issues that control the way water quality is monitored and determined. Current national regulations require the monitoring of fecal indicator bacteria in order to determine recreational water quality. However, it is also important to identify biological and geographical sources of pollution to consistently impaired locations. A commonly applied approach to meet the goals of source identification is to sample sites that have been high in FIB for further study. A tiered approach such as this, however, assumes a correlation between FIB and the sources of interest in the watershed. The research described in this dissertation tests this assumption in two Southern California watersheds, Santa Monica Canyon and Ventura Harbor. In both cases, a tiered approach to sampling using FIB as a first tier to guide sampling would have failed to identify sources of human fecal pollution (as identified by the presence of the human-associated Bacteroides marker HF183). Every watershed is a distinct environment that has different potential sources of bacteria and many factors contributing to the persistence of the bacteria. Rather than attempting to apply an indicator that has worked as a first tier in other watersheds, it would be better to have as a first tier an in-depth study of the watershed using historical data or local experts to provide information on the most likely sources of pollution in the watershed. Using this information it would be possible to design a study using FIB and one or more source-associated parameters to identify specific sources of pollution in the watershed. In addition, sampling FIB and other parameters such as HF183 allow the application of other

Survival of soil bacteria during prolonged desiccation.

NASA Technical Reports Server (NTRS)

Chen, M.; Alexander, M.

1973-01-01

A determination was made of the kinds and numbers of bacteria surviving when two soils were maintained in the laboratory under dry conditions for more than half a year. Certain non-spore-forming bacteria were found to survive in the dry condition for long periods. A higher percentage of drought-tolerant than drought-sensitive bacteria was able to grow at low water activities. When they were grown in media with high salt concentrations, bacteria generally became more tolerant of prolonged drought and they persisted longer. The percent of cells in a bacterial population that remained viable when exposed to drought stress varied with the stage of growth.

Antimicrobial copper alloys decreased bacteria on stethoscope surfaces.

PubMed

Schmidt, Michael G; Tuuri, Rachel E; Dharsee, Arif; Attaway, Hubert H; Fairey, Sarah E; Borg, Keith T; Salgado, Cassandra D; Hirsch, Bruce E

2017-06-01

Stethoscopes may serve as vehicles for transmission of bacteria among patients. The aim of this study was to assess the efficacy of antimicrobial copper surfaces to reduce the bacterial concentration associated with stethoscope surfaces. A structured prospective trial involving 21 health care providers was conducted at a pediatric emergency division (ED) (n = 14) and an adult medical intensive care unit located in tertiary care facilities (n = 7). Four surfaces common to a stethoscope and a facsimile instrument fabricated from U.S. Environmental Protection Agency-registered antimicrobial copper alloys (AMCus) were assessed for total aerobic colony counts (ACCs), methicillin-resistant Staphylococcus aureus, gram-negative bacteria, and vancomycin-resistant enterococci for 90 days. The mean ACCs collectively recovered from all stethoscope surfaces fabricated from the AMCus were found to carry significantly lower concentrations of bacteria (pediatric ED, 11.7 vs 127.1 colony forming units [CFU]/cm 2 , P < .00001) than their control equivalents. This observation was independent of health care provider or infection control practices. Absence of recovery of bacteria from the AMCu surfaces (66.3%) was significantly higher (P < .00001) than the control surfaces (22.4%). The urethane rim common to the stethoscopes was the most heavily burdened surface; mean concentrations exceeded the health care-associated infection acquisition concentration (5 CFU/cm 2 ) by at least 25×, supporting that the stethoscope warrants consideration in plans mitigating microbial cross-transmission during patient care. Stethoscope surfaces fabricated with AMCus were consistently found to harbor fewer bacteria. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Rapid separation of bacteria from blood — Chemical aspects

PubMed Central

Alizadeh, Mahsa; Wood, Ryan L.; Buchanan, Clara M.; Bledsoe, Colin G.; Wood, Madison E.; McClellan, Daniel S.; Blanco, Rae; Ravsten, Tanner V.; Husseini, Ghaleb A.; Hickey, Caroline L.; Robison, Richard A.; Pitt, William G.

2017-01-01

To rapidly diagnose infectious organisms causing blood sepsis, bacteria must be rapidly separated from blood, a very difficult process considering that concentrations of bacteria are many orders of magnitude lower than concentrations of blood cells. We have successfully separated bacteria from red and white blood cells using a sedimentation process in which the separation is driven by differences in density and size. Seven mL of whole human blood spiked with bacteria is placed in a 12-cm hollow disk and spun at 3000 rpm for 1 min. The red and white cells sediment more than 30-fold faster than bacteria, leaving much of the bacteria in the plasma. When the disk is slowly decelerated, the plasma flows to a collection site and the red and white cells are trapped in the disk. Analysis of the recovered plasma shows that about 36% of the bacteria is recovered in the plasma. The plasma is not perfectly clear of red blood cells, but about 94% have been removed. This paper describes the effects of various chemical aspects of this process, including the influence of anticoagulant chemistry on the separation efficiency and the use of wetting agents and platelet aggregators that may influence the bacterial recovery. In a clinical scenario, the recovered bacteria can be subsequently analyzed to determine their species and resistance to various antibiotics. PMID:28365426

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms.

PubMed

Ho, Van Thi Thuy; Fleet, Graham H; Zhao, Jian

2018-08-20

Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of the bean pulp by microorganisms is essential for developing the precursors of chocolate flavour. Currently, the cocoa fermentation is still conducted by an uncontrolled traditional process via a consortium of indigenous species of yeasts, lactic acid bacteria and acetic acid bacteria. Although the essential contribution of yeasts to the production of good quality beans and, typical chocolate character is generally agreed, the roles of lactic acid bacteria and acetic acid bacteria are less certain. The objective of this study was to investigate the contribution of LAB and AAB in cocoa bean fermentation by conducting small scale laboratory fermentations under aseptic conditions, inoculated with different groups of microorganisms previously isolated from spontaneous cocoa fermentations. The inoculation protocols were: (1) four yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae; (2) four yeasts plus the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum; (3) four yeasts plus the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateuri and (4) four yeasts plus two lactic acid bacteria and two acetic acid bacteria. Only the inoculated species were detected in the microbiota of their respective fermentations. Beans from the inoculated fermentations showed no significant differences in colour, shell weights and concentrations of residual sugars, alcohols and esters (p>0.05), but they were slightly different in contents of lactic acid and acetic acid (p<0.05). All beans were fully brown and free of mould. Residual sugar levels were less than 2.6 mg/g while the shell contents and ethanol were in the range of 11-13.4% and 4.8-7 mg/g, respectively. Beans fermented in the presence of LAB contained higher levels of lactic acid (0.6-1.2 mg/g) whereas higher concentrations of acetic acid

Raman spectroscopy of oral bacteria

NASA Astrophysics Data System (ADS)

Berger, Andrew J.; Zhu, Qingyuan; Quivey, Robert G.

2003-10-01

Raman spectroscopy has been employed to measure the varying concentrations of two oral bacteria in simple mixtures. Evaporated droplets of centrifuged mixtures of Streptococcus sanguis and Streptococcus mutans were analyzed via Raman microspectroscopy. The concentration of s. sanguis was determined based upon the measured Raman spectrum, using partial least squares cross-validation, with an r2 value of 0.98.

Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria

DOEpatents

Ooteghem, Suellen Van

2005-09-13

A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

Optimization of a reusable hollow-fiber ultrafilter for simultaneous concentration of enteric bacteria, protozoa, and viruses from water.

PubMed

Morales-Morales, Hugo A; Vidal, Guadalupe; Olszewski, John; Rock, Channah M; Dasgupta, Debanjana; Oshima, Kevin H; Smith, Geoffrey B

2003-07-01

The detection and identification of pathogens from water samples remain challenging due to variations in recovery rates and the cost of procedures. Ultrafiltration offers the possibility to concentrate viral, bacterial, and protozoan organisms in a single process by using size-exclusion-based filtration. In this study, two hollow-fiber ultrafilters with 50,000-molecular-weight cutoffs were evaluated to concentrate microorganisms from 2- and 10-liter water samples. When known quantities (10(5) to 10(6) CFU/liter) of two species of enteric bacteria were introduced and concentrated from 2 liters of sterile water, the addition of 0.1% Tween 80 increased Escherichia coli strain K-12 recoveries from 70 to 84% and Salmonella enterica serovar Enteritidis recoveries from 36 to 72%. An E. coli antibiotic-resistant strain, XL1-Blue, was recovered at a level (87%) similar to that for strain K-12 (96%) from 10 liters of sterile water. When E. coli XL1-Blue was introduced into 10 liters of nonsterile Rio Grande water with higher turbidity levels (23 to 29 nephelometric turbidity units) at two inoculum levels (9 x 10(5) and 2.4 x 10(3) per liter), the recovery efficiencies were 89 and 92%, respectively. The simultaneous addition of E. coli XL1-Blue (9 x 10(5) CFU/liter), Cryptosporidium parvum oocysts (10 oocysts/liter), phage T1 (10(5) PFU/liter), and phage PP7 (10(5) PFU/liter) to 10 liters of Rio Grande surface water resulted in mean recoveries of 96, 54, 59, and 46%, respectively. Using a variety of surface waters from around the United States, we obtained recovery efficiencies for bacteria and viruses that were similar to those observed with the Rio Grande samples, but recovery of Cryptosporidium oocysts was decreased, averaging 32% (the site of collection of these samples had previously been identified as problematic for oocyst recovery). Results indicate that the use of ultrafiltration for simultaneous recovery of bacterial, viral, and protozoan pathogens from variable

Porosity and permeability determination of organic-rich Posidonia shales based on 3-D analyses by FIB-SEM microscopy

NASA Astrophysics Data System (ADS)

Grathoff, Georg H.; Peltz, Markus; Enzmann, Frieder; Kaufhold, Stephan

2016-07-01

The goal of this study is to better understand the porosity and permeability in shales to improve modelling fluid and gas flow related to shale diagenesis. Two samples (WIC and HAD) were investigated, both mid-Jurassic organic-rich Posidonia shales from Hils area, central Germany of different maturity (WIC R0 0.53 % and HAD R0 1.45 %). The method for image collection was focused ion beam (FIB) microscopy coupled with scanning electron microscopy (SEM). For image and data analysis Avizo and GeoDict was used. Porosity was calculated from segmented 3-D FIB based images and permeability was simulated by a Navier Stokes-Brinkman solver in the segmented images. Results show that the quantity and distribution of pore clusters and pores (≥ 40 nm) are similar. The largest pores are located within carbonates and clay minerals, whereas the smallest pores are within the matured organic matter. Orientation of the pores calculated as pore paths showed minor directional differences between the samples. Both samples have no continuous connectivity of pore clusters along the axes in the x, y, and z direction on the scale of 10 to 20 of micrometer, but do show connectivity on the micrometer scale. The volume of organic matter in the studied volume is representative of the total organic carbon (TOC) in the samples. Organic matter does show axis connectivity in the x, y, and z directions. With increasing maturity the porosity in organic matter increases from close to 0 to more than 5 %. These pores are small and in the large organic particles have little connection to the mineral matrix. Continuous pore size distributions are compared with mercury intrusion porosimetry (MIP) data. Differences between both methods are caused by resolution limits of the FIB-SEM and by the development of small pores during the maturation of the organic matter. Calculations show no permeability when only considering visible pores due to the lack of axis connectivity. Adding the organic matter with a

Population of Nitrifying Bacteria and Nitrification in Ammonium Saturated Clinoptilolite

NASA Technical Reports Server (NTRS)

McGilloway, R. L.; Weaver, R. W.; Ming, Douglas W.; Gruener, J.

1999-01-01

As humans begin to spend longer periods of time in space, plants will be incorporated into life support systems. Ammonium saturated clinoptilolite is one plant growth substrate but a balance between ammonium and nitrate is needed. A laboratory study was conducted to determine effects of nitrifying bacteria on ammonium concentrations and kinetics of nitrification. Columns containing clinoptilolite substrate amended with nitrifying bacteria obtained from soil enrichment were analyzed weekly for a 90 day period. The enrichment culture initially contained 1 x 10(exp 5) ammonium oxidizing bacteria and 1 x 10(exp 2) nitrite oxidizing bacteria per gram of substrate. Populations of ammonium oxidizing bacteria increased to 1 x 10(exp 6) and nitrite oxidizing bacteria increased to 1 x 10(exp 3) per gram of substrate. The nitrification rate was approximately 0.25mg NO3(-)-N/kg.hr. Experiments were also conducted to enumerate nitrifying bacteria in a clinoptilolite substrate used to grow wheat (Triticum aestivum L.). Seventy days following the initial inoculation with an unknown number of commercial nitrifying bacteria, 1 x 10(exp 5) ammonium oxidizing bacteria per gram of substrate were present. The number of nitrite oxidizing bacteria was between 1 x 10(exp 3) to 10(exp 4) per gram of substrate as measured by the most probable number method. Nitrification rates were approximately 0.20mg NO3(-)-N/kg.hr. Clinoptilolite readily exchanged sufficient concentrations of ammonium to support nitrifying bacteria and they survived well in this medium.

The impact of bacteria of circulating water on apatite-nepheline ore flotation.

PubMed

Evdokimova, G A; Gershenkop, A Sh; Fokina, N V

2012-01-01

A new phenomenon has been identified and studied-the impact of bacteria on the benefication process of non-sulphide ores using circulating water supply-a case study of apatite-nepheline ore. It is shown that bacteria deteriorate the floatability of apatite due to their interaction with active centres of calcium-containing minerals and intense flocculation, resulting in a decrease of the flotation process selectivity thus deteriorating the quality of concentrate. Based on the comparative analysis of primary sequences of 16S rRNA genes, there have been identified dominating bacteria species, recovered from the circulating water used at apatite-nepheline concentrating mills, and their phylogenetic position has been determined. All the bacteria were related to γ-Proteobacteria, including the Acinetobacter species, Pseudomonas alcaliphila, Ps. plecoglossicida, Stenotrophomonas rhizophila. A method of non-sulphide ores flotation has been developed with consideration of the bacterial factor. It consists in use of small concentrations of sodium hypochlorite, which inhibits the development of bacteria in the flotation of apatite-nepheline ores.

Monitoring of airborne bacteria and aerosols in different wards of hospitals - Particle counting usefulness in investigation of airborne bacteria.

PubMed

Mirhoseini, Seyed Hamed; Nikaeen, Mahnaz; Khanahmd, Hossein; Hatamzadeh, Maryam; Hassanzadeh, Akbar

2015-01-01

The presence of airborne bacteria in hospital environments is of great concern because of their potential role as a source of hospital-acquired infections (HAI). The aim of this study was the determination and comparison of the concentration of airborne bacteria in different wards of four educational hospitals, and evaluation of whether particle counting could be predictive of airborne bacterial concentration in different wards of a hospital. The study was performed in an operating theatre (OT), intensive care unit (ICU), surgery ward (SW) and internal medicine (IM) ward of four educational hospitals in Isfahan, Iran. A total of 80 samples were analyzed for the presence of airborne bacteria and particle levels. The average level of bacteria ranged from 75-1194 CFU/m (3) . Mean particle levels were higher than class 100,000 cleanrooms in all wards. A significant correlation was observed between the numbers of 1-5 µm particles and levels of airborne bacteria in operating theatres and ICUs. The results showed that factors which may influence the airborne bacterial level in hospital environments should be properly managed to minimize the risk of HAIs especially in operating theaters. Microbial air contamination of hospital settings should be performed by the monitoring of airborne bacteria, but particle counting could be considered as a good operative method for the continuous monitoring of air quality in operating theaters and ICUs where higher risks of infection are suspected.

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

Bacteria in non-woven textile filters for domestic wastewater treatment.

PubMed

Spychała, Marcin; Starzyk, Justyna

2015-01-01

The objective of this study was preliminary identification of heterotrophic and ammonia oxidizing bacteria (AOB) cell concentration in the cross-sectional profile of geotextile filters for wastewater treatment. Filters of thicknesses 3.6 and 7.2 mm, made of non-woven textile TS20, were supplied with septic tank effluent and intermittently dosed and filtered under hydrostatic pressure. The cumulative loads of chemical oxygen demand (COD) and total solids were about 1.36 and 1.06 kg/cm2, respectively. The filters under analysis reached a relatively high removal efficiency for organic pollution 70-90% for biochemical oxygen demand (BOD5) and 60-85% for COD. The ammonia nitrogen removal efficiency level proved to be unstable (15-55%). Biomass samples for dry mass identification were taken from two regions: continuously flooded with wastewater and intermittently flooded with wastewater. The culturable heterotrophic bacteria were determined as colony-forming units (CFUs) on microbiological-selective media by means of the plate method. AOB and nitrite oxidizing bacteria (NOB) were examined using the FISH technique. A relatively wide range of heterotrophic bacteria was observed from 7.4×10(5)/cm2 to 3.8×10(6)/cm2 in geotextile layers. The highest concentration of heterotrophic bacteria (3.8×10(6)/cm2) was observed in the first layer of the textile filter. AOB were identified occasionally--about 8-15% of all bacteria colonizing the last filter layer, but occasionally much higher concentrations and ammonia nitrogen efficiency were achieved. Bacteria oxidizing nitrite to nitrate were not observed. The relation of total and organic fraction of biomass to culturable heterotrophic bacteria was also found.

Mutations and Misconceptions: The Isolation and Study of Mutant Bacteria.

ERIC Educational Resources Information Center

Corner, Thomas R.

1992-01-01

Describes simple, inexpensive activities for teaching students about mutants and mutations in bacteria. Explains how to isolate bacteria from soil and leaves and how to grow bacteria on agar or in broth. Describes how to construct a gradient plate for finding the minimum inhibitory concentration of a substance and how to use this set up to find…

Tolerance of anaerobic bacteria to chlorinated solvents.

PubMed

Koenig, Joanna C; Groissmeier, Kathrin D; Manefield, Mike J

2014-01-01

The aim of this research was to evaluate the effects of four chlorinated aliphatic hydrocarbons (CAHs), perchloroethene (PCE), carbon tetrachloride (CT), chloroform (CF) and 1,2-dichloroethane (1,2-DCA), on the growth of eight anaerobic bacteria: four fermentative species (Escherichia coli, Klebsiella sp., Clostridium sp. and Paenibacillus sp.) and four respiring species (Pseudomonas aeruginosa, Geobacter sulfurreducens, Shewanella oneidensis and Desulfovibrio vulgaris). Effective concentrations of solvents which inhibited growth rates by 50% (EC50) were determined. The octanol-water partition coefficient or log Po/w of a CAH proved a generally satisfactory measure of its toxicity. Most species tolerated approximately 3-fold and 10-fold higher concentrations of the two relatively more polar CAHs CF and 1,2-DCA, respectively, than the two relatively less polar compounds PCE and CT. EC50 values correlated well with growth rates observed in solvent-free cultures, with fast-growing organisms displaying higher tolerance levels. Overall, fermentative bacteria were more tolerant to CAHs than respiring species, with iron- and sulfate-reducing bacteria in particular appearing highly sensitive to CAHs. These data extend the current understanding of the impact of CAHs on a range of anaerobic bacteria, which will benefit the field of bioremediation.

Reconstructing the microstructure of polyimide-silicalite mixed-matrix membranes and their particle connectivity using FIB-SEM tomography.

PubMed

Diblíková, P; Veselý, M; Sysel, P; Čapek, P

2018-03-01

Properties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused-ion beam scanning electron microscope (FIB-SEM) tomography data, we reconstructed three mixed-matrix membrane samples made of 6FDA-ODA polyimide and silicalite-1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite-1. Second, after spatial alignment of the stacked FIB-SEM data, the 3D image was smoothed using adaptive median and anisotropic nonlinear diffusion filters. Third, the image was segmented using the power watershed method coupled with a seeding algorithm based on geodesic reconstruction from the markers. If the resulting volume fraction did not match the target value quantified by chemical analysis of the sample, the BSE and SE signals were mixed in another ratio and the procedure was repeated until the target volume fraction was achieved. Otherwise, the segmented 3D image (replica) was accepted and its microstructure was thoroughly characterized with special attention paid to connectivity of the silicalite phase. In terms of the phase connectivity, Monte Carlo simulations based on the pure-phase permeability values enabled us to calculate the effective permeability tensor, the main diagonal elements of which were compared with the experimental permeability. In line with the hypothesis proposed in our recent paper (Čapek, P. et al. (2014) Comput. Mater. Sci. 89, 142-156), the results confirmed that the existence of particle clusters was a key microstructural feature determining effective permeability. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Chemical and microstructural characterization of a 9 cycle Zircaloy-2 cladding using EPMA and FIB tomography

NASA Astrophysics Data System (ADS)

Baris, A.; Restani, R.; Grabherr, R.; Chiu, Y.-L.; Evans, H. E.; Ammon, K.; Limbäck, M.; Abolhassani, S.

2018-06-01

A high burn-up Zircaloy-2 cladding is characterised in order to correlate its microstructure and composition to the change of oxidation and hydrogen uptake behaviour during long term service in the reactor. After 9 cycle of service, the chemical analysis of the cladding segment shows that most secondary phase particles (SPPs) have dissolved into the matrix. Fe and Ni are distributed homogenously in the metal matrix. Cr-containing clusters, remnants of the original Zr(Fe, Cr)2 type precipitates, are still present. Hydrides are observed abundantly in the metal side close to the metal-oxide interface. These hydrides have lower Fe and Ni concentration than that in the metal matrix. The three-dimensional (3D) reconstruction of the oxide and the metal-oxide interface obtained by Focused Ion Beam (FIB) tomography shows how the oxide microstructure has evolved with the number of cycles. The composition and microstructural changes in the oxide and the metal can be correlated to the oxidation kinetics and the H-uptake. It is observed that there is an increase in the oxidation kinetics and in the H-uptake between the third and the fifth cycles, as well as during the last two cycles. At the same time the volume fraction of cracks in the oxide significantly increased. Many fine cracks and pores exist in the oxide formed in the last cycle. Furthermore, the EPMA results confirm that this oxide formed at the last cycle reflects the composition of the metal at the metal-oxide interface after the long residence time in the reactor.

Occurrence of squalene in methanol-grown bacteria.

PubMed Central

Goldberg, I; Shechter, I

1978-01-01

The nonpolar lipids of methanol-grown bacteria which utilize one-carbon (C1) compounds via the RMP pathway (Pseudomonas C, Pseudomonas methylotropha, and Methylomonas methanolica) were found to contain squalene in concentrations between 0.1 to 1.16 mg/g of cell (dry weight). Squalene could not be detected in lipid extracts of methanol-grown bacteria which utilize C1 compounds via the serine pathway. PMID:98521

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review.

PubMed

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

PubMed Central

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Biodegradation of PAHs in Soil: Influence of Initial PAHs Concentration

NASA Astrophysics Data System (ADS)

Kamil, N. A. F. M.; Talib, S. A.

2016-07-01

Most studies on biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) evaluate the effect of initial PAHs concentration in liquid medium. There are limited studies on evaluation in solid medium such as contaminated soil. This study investigated the potential of the bacteria, Corynebacterium urealyticum isolated from municipal sludge in degrading phenanthrene contaminated soil in different phenanthrene concentration. Batch experiments were conducted over 20 days in reactors containing artificially contaminated phenanthrene soil at different concentration inoculated with a bacterial culture. This study established the optimum condition for phenanthrene degradation by the bacteria under nonindigenous condition at 500 mg/kg of initial phenanthrene concentration. High initial concentration required longer duration for biodegradation process compared to low initial concentration. The bacteria can survive for three days for all initial phenanthrene concentrations.

Genes indicative of zoonotic and swine pathogens are persistent in stream water and sediment following a swine manure spill

USGS Publications Warehouse

Haack, Sheridan K.; Duris, Joseph W.; Kolpin, Dana W.; Fogarty, Lisa R.; Johnson, Heather E.; Gibson, Kristen E.; Focazio, Michael J.; Schwab, Kellogg J.; Hubbard, Laura E.; Foreman, William T.

2015-01-01

Manure spills to streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for: fecal indicator bacteria (FIB); the fecal indicator chemicals cholesterol and coprostanol; 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence polymerase chain reaction (PCR) for viable cells; one swine-specific Escherichia coli toxin gene (STII) by quantitative PCR (qPCR); and nine human and animal viruses by qPCR, or reverse-transcriptase qPCR. Twelve days post-spill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1-2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli, were detected in water or sediment. STII increased from undetectable before, or above the spill, to 105 copies/100 mL water 12 days post-spill. Thirteen of 14 water (8/9 sediment) samples had viable STII-carrying cells post-spill. Eighteen days post-spill porcine adenovirus and teschovirus were detected 5.6 km downstream. Sediment FIB concentrations (per gram wet weight) were greater than in water, and sediment was a continuous reservoir of genes and chemicals post-spill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days post-spill) following manure application, although the swine-associated STII and stx2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes, and the potential for human and veterinary health consequences.

Presence of Pathogens and Indicator Microbes at a Non-Point Source Subtropical Recreational Marine Beach ▿ †

PubMed Central

Abdelzaher, Amir M.; Wright, Mary E.; Ortega, Cristina; Solo-Gabriele, Helena M.; Miller, Gary; Elmir, Samir; Newman, Xihui; Shih, Peter; Bonilla, J. Alfredo; Bonilla, Tonya D.; Palmer, Carol J.; Scott, Troy; Lukasik, Jerzy; Harwood, Valerie J.; McQuaig, Shannon; Sinigalliano, Chris; Gidley, Maribeth; Plano, Lisa R. W.; Zhu, Xiaofang; Wang, John D.; Fleming, Lora E.

2010-01-01

Swimming in ocean water, including ocean water at beaches not impacted by known point sources of pollution, is an increasing health concern. This study was an initial evaluation of the presence of indicator microbes and pathogens and the association among the indicator microbes, pathogens, and environmental conditions at a subtropical, recreational marine beach in south Florida impacted by non-point sources of pollution. Twelve water and eight sand samples were collected during four sampling events at high or low tide under elevated or reduced solar insolation conditions. The analyses performed included analyses of fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli, enterococci, and Clostridium perfringens), human-associated microbial source tracking (MST) markers (human polyomaviruses [HPyVs] and Enterococcus faecium esp gene), and pathogens (Vibrio vulnificus, Staphylococcus aureus, enterovirus, norovirus, hepatitis A virus, Cryptosporidium spp., and Giardia spp.). The enterococcus concentrations in water and sand determined by quantitative PCR were greater than the concentrations determined by membrane filtration measurement. The FIB concentrations in water were below the recreational water quality standards for three of the four sampling events, when pathogens and MST markers were also generally undetectable. The FIB levels exceeded regulatory guidelines during one event, and this was accompanied by detection of HPyVs and pathogens, including detection of the autochthonous bacterium V. vulnificus in sand and water, detection of the allochthonous protozoans Giardia spp. in water, and detection of Cryptosporidium spp. in sand samples. The elevated microbial levels were detected at high tide and under low-solar-insolation conditions. Additional sampling should be conducted to further explore the relationships between tidal and solar insolation conditions and between indicator microbes and pathogens in subtropical recreational marine waters impacted

Modeling of Cd adsorption to goethite-bacteria composites

DOE PAGES

Qu, Chenchen; Ma, Mingkai; Chen, Wenli; ...

2017-11-21

The accurate modeling of heavy metal adsorption in complex systems is fundamental for risk assessments in soils and associated environments. Bacteria-iron (hydr)oxide associations in soils and sediments play a critical role in heavy metal immobilization. The reduced adsorption of heavy metals on these composites have been widely reported using the component additivity (CA) method. However, there is a lack of a mechanism model to account for these deviations. In this study, we established models for Cd adsorption on goethite-Pseudomonas putida composites at 1:1 and 5:1 mass ratios. Cadmium adsorption on the 5:1 composite was consistent with the additivity method. But,more » the CA method over predicted Cd adsorption by approximately 8% on the 1:1 composite at high Cd concentration. The deviation was corrected by adding the site blockage reactions between P. putida and goethite. Both CA and “CA-site masking” models for Cd adsorption onto the composites were in line with the ITC data. These results indicate that CA method in simulating Cd adsorption on bacteria-iron oxides composites is limited to low bacterial and Cd concentrations. Thus the interfacial complexation reactions that occur between iron (hydr)oxides and bacteria should be taken into account when high concentrations of bacteria and heavy metals are present.« less

Modeling of Cd adsorption to goethite-bacteria composites

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

Qu, Chenchen; Ma, Mingkai; Chen, Wenli

The accurate modeling of heavy metal adsorption in complex systems is fundamental for risk assessments in soils and associated environments. Bacteria-iron (hydr)oxide associations in soils and sediments play a critical role in heavy metal immobilization. The reduced adsorption of heavy metals on these composites have been widely reported using the component additivity (CA) method. However, there is a lack of a mechanism model to account for these deviations. In this study, we established models for Cd adsorption on goethite-Pseudomonas putida composites at 1:1 and 5:1 mass ratios. Cadmium adsorption on the 5:1 composite was consistent with the additivity method. But,more » the CA method over predicted Cd adsorption by approximately 8% on the 1:1 composite at high Cd concentration. The deviation was corrected by adding the site blockage reactions between P. putida and goethite. Both CA and “CA-site masking” models for Cd adsorption onto the composites were in line with the ITC data. These results indicate that CA method in simulating Cd adsorption on bacteria-iron oxides composites is limited to low bacterial and Cd concentrations. Thus the interfacial complexation reactions that occur between iron (hydr)oxides and bacteria should be taken into account when high concentrations of bacteria and heavy metals are present.« less

Monitoring and evaluation of antibiotic-resistant bacteria at a municipal wastewater treatment plant in China.

PubMed

Huang, Jing-Jing; Hu, Hong-Ying; Lu, Sun-Qin; Li, Yi; Tang, Fang; Lu, Yun; Wei, Bin

2012-07-01

The prevalence of antibiotic-resistant bacteria in municipal wastewater treatment plants (WWTPs) is becoming a concern of public health. In order to acquire information on the emission of antibiotic-resistant bacteria from WWTP effluents into natural waters, both average antibiotic tolerance and concentrations of antibiotic-resistant bacteria in the effluent of a WWTP in Beijing, China were investigated. A new index of IC(50)/MIC ratio (the antibiotic concentration required to inhibit 50% of total heterotrophic bacteria compared to the highest minimum inhibitory concentration value of a group of pathogens according to a specific antibiotic, as defined by CLSI) was used to reflect the average antibiotic tolerance of total heterotrophic bacteria in the secondary effluent. The results showed that the IC(50)/MIC ratios of heterotrophic bacteria in the secondary effluent to penicillin, ampicillin, cephalothin, chloramphenicol and rifampicin were >2, >1, >1, and 1.08, respectively, which reflected a significantly high general level of heterotrophic bacteria found in the secondary effluent resistant to these five antibiotics. The concentrations of penicillin-, ampicillin-, cephalothin-, and chloramphenicol-resistant bacteria were as high as 1.5×10(4)-1.9×10(5), 1.2×10(4)-1.5×10(5), 8.9×10(3)-1.9×10(5) and 2.6×10(4)-2.0×10(5) CFU/mL, and the average percentages in relation to total heterotrophic bacteria were 63%, 47%, 55%, and 69%, respectively. The concentrations of tetracycline- and rifampicin-resistant bacteria were 840-6.1×10(3) and 310-6.1×10(4) CFU/mL with average percentages of 2.6% and 11%, respectively. Furthermore, our study found that five- and six-antibiotic-resistant bacteria were widely distributed in four types of enterobacteria from the secondary effluent. The presence of multiple-antibiotic-resistant bacteria from effluents of WWTPs into natural waters could pose a serious problem as a secondary pollutant of drinking water. Copyright © 2011

The inhibitory effects of free ammonia on ammonia oxidizing bacteria and nitrite oxidizing bacteria under anaerobic condition.

PubMed

Qian, Wenting; Peng, Yongzhen; Li, Xiyao; Zhang, Qiong; Ma, Bin

2017-11-01

The free ammonia (FA) inhibition on ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) under anaerobic condition was investigated in this study. The results indicated that NOB was more sensitive to the FA anaerobic treatment than AOB. The FA anaerobic inhibition on nitrifier gradually heightened with the increase of FA concentration. Accompanied with FA concentration increase from 0 to 16.82mgNH 3 -N·L -1 (the highest concentration adopted in this study), the activity of AOB reduced by 15.9%, while NOB decreased by 29.2%. After FA anaerobic treatment, nitrite was accumulated during nitrification. However, the nitrite accumulation disappeared on the sixth cycle of activity recovery tests with excessive aeration. Based on this result, a novel strategy for achieving nitritation is proposed, which involves recirculating a portion of the activated sludge through a side-line sludge treatment unit, where the sludge is subjected to treatment with FA under anaerobic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Observation of thermally etched grain boundaries with the FIB/TEM technique

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

Palizdar, Y., E-mail: y.palizdar@merc.ac.ir; San Martin, D.; Ward, M.

2013-10-15

Thermal etching is a method which is able to reveal and characterize grain boundaries, twins or dislocation structures and determine parameters such as grain boundary energies, surface diffusivities or study phase transformations in steels, intermetallics or ceramic materials. This method relies on the preferential transfer of matter away from grain boundaries on a polished sample during heating at high temperatures in an inert/vacuum atmosphere. The evaporation/diffusion of atoms at high temperatures results in the formation of grooves at the intersections of the planes of grain/twin boundaries with the polished surface. This work describes how the combined use of Focussed Ionmore » Beam and Transmission Electron Microscopy can be used to characterize not only the grooves and their profile with the surface, but also the grain boundary line below the groove, this method being complementary to the commonly used scanning probe techniques. - Highlights: • Thermally etched low-carbon steel samples have been characterized by FIB/TEM • Grain boundary (GB) lines below the groove have been characterized in this way • Absence of ghost traces and large θ angle suggests that GB are not stationary but mobile • Observations correlate well with previous works and Mullins' investigations [22].« less

Amino acid composition of rumen bacteria and protozoa in cattle.

PubMed

Sok, M; Ouellet, D R; Firkins, J L; Pellerin, D; Lapierre, H

2017-07-01

Because microbial crude protein (MCP) constitutes more than 50% of the protein digested in cattle, its AA composition is needed to adequately estimate AA supply. Our objective was to update the AA contributions of the rumen microbial AA flowing to the duodenum using only studies from cattle, differentiating between fluid-associated bacteria (FAB), particle-associated bacteria (PAB), and protozoa, based on published literature (53, 16, and 18 treatment means were used for each type of microorganism, respectively). In addition, Cys and Met reported concentrations were retained only when an adequate protection of the sulfur groups was performed before the acid hydrolysis. The total AA (or true protein) fraction represented 82.4% of CP in bacteria. For 10 AA, including 4 essential AA, the AA composition differed between protozoa and bacteria. The most noticeable differences were a 45% lower Lys concentration and 40% higher Ala concentration in bacteria than in protozoa. Differences between FAB and PAB were less pronounced than differences between bacteria and protozoa. Assuming 33% FAB, 50% PAB, and 17% of protozoa in MCP duodenal flow, the updated concentrations of AA would decrease supply estimates of Met, Thr, and Val originating from MCP and increase those of Lys and Phe by 5 to 10% compared with those calculated using the FAB composition reported previously. Therefore, inclusion of the contribution of PAB and protozoa to the duodenal MCP flow is needed to adequately estimate AA supply from microbial origin when a factorial method is used to estimate duodenal AA flow. Furthermore, acknowledging the fact that hydrolysis of 1 kg of true microbial protein yields 1.16 kg of free AA substantially increases the estimates of AA supply from MCP. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Highly Effective Polyphosphate Synthesis, Phosphate Removal, and Concentration Using Engineered Environmental Bacteria Based on a Simple Solo Medium-Copy Plasmid Strategy.

PubMed

Wang, Xin; Wang, Xiaomeng; Hui, Kaimin; Wei, Wei; Zhang, Wen; Miao, Aijun; Xiao, Lin; Yang, Liuyan

2018-01-02

Microbial polyphosphate (polyP) production is vital to the removal of phosphate from wastewater. However, to date, engineered polyP synthesis using genetically accessible environmental bacteria remains a challenge. This study develops a simple solo medium-copy plasmid-based polyphosphate kinase (PPK1) overexpression strategy for achieving maximum intracellular polyphosphate accumulation by environmental bacteria. The polyP content of the subsequently engineered Citrobacter freundii (CPP) could reach as high as 12.7% of its dry weight. The biomass yield of CPP was also guaranteed because of negligible metabolic burden effects resulting from the medium plasmid copy number. Consequently, substantial removal of phosphate (P i ) from the ambient environment was achieved simultaneously. Because of the need for exogenous P i for in vivo ATP regeneration, CPP could thoroughly remove P i from synthetic municipal wastewater when it was applied for the "one-step" removal of P i with a bench-scale sequence batch membrane reactor. Almost all the phosphorus except for that assimilated by CPP for cellular growth could be recovered in the form of more concentrated P i . Overall, engineering environmental bacteria to overexpress PPK1 via a solo medium-copy plasmid strategy may represent a valuable general option for not only biotechnological research based on sufficient intracellular polyP production but also removal of P i from wastewater and P i enrichment.

A new challenge: in-situ investigation of the elusive nanostructures in wet halite and clay using BIB/FIB-cryo-SEM methods

NASA Astrophysics Data System (ADS)

Desbois, G.; Urai, J. L.

2009-04-01

Mudrocks and saltrocks form seals for hydrocarbon accumulations, aquitards and chemical barriers. The sealing capacity is controlled either by the rock microstructure or by chemical interactions between minerals and the permeating fluid. A detailed knowledge about the sealing characteristics is of particular interest in Petroleum Sciences. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. A key factor to the understanding of sealing by mudstones and saltrocks is the study of their porosity. However, Halite and clay are so fluids sensitive that investigation on dried samples required by traditional methods of investigations (metal injection methods [6],[3]; magnetic susceptibility measurement [4]; SEM imaging of broken surfaces [5] and CT scanner computing [7]) are critical for robust interpretation. In one hand, none of these methods is able to directly describe the in-situ porosity at the pore scale and on the other hand, most of these methods require dried samples in which the natural structure of pores could be damaged due to the desiccation, dehydration and dissolution-recrystallisation of the fabric. SEM imaging is certainly the most direct approach to investigate the porosity but it is generally limited by the poor quality of the mechanically prepared surfaces. This problem is solved by the recent development of ion milling tools (FIB: Focussed Ion Beam or BIB: Broad Ion Beam, which allows producing in-situ high quality polished cross-sections suitable for high resolution pores SEM imaging at nano-scale. More over, new and innovative developments of the cryo-SEM approach in the Geosciences allow investigating samples under wet natural conditions. Thus, we are developing the combination of FIB/BIB-cryo-SEM methods ([1],[2]), which combine in one machine the vitrification of the pore fluids by very rapid cooling, the excavation of the sample by ion milling tool and SEM imaging. By these, we

Fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers and selected tributaries, Allegheny County, Pennsylvania, 2001-2005

USGS Publications Warehouse

Buckwalter, Theodore F.; Zimmerman, Tammy M.; Fulton, John W.

2006-01-01

Concentrations of fecal-indicator bacteria were determined in 1,027 water-quality samples collected from July 2001 through August 2005 during dry- (72-hour dry antecedent period) and wet-weather (48-hour dry antecedent period and at least 0.3 inch of rain in a 24-hour period) conditions in the Allegheny, Monongahela, and Ohio Rivers (locally referred to as the Three Rivers) and selected tributaries in Allegheny County. Samples were collected at five sampling sites on the Three Rivers and at eight sites on four tributaries to the Three Rivers having combined sewer overflows. Water samples were analyzed for three fecal-indicator organisms fecal coliform, Escherichia coli (E. coli), and enterococci bacteria. Left-bank and right-bank surface-water samples were collected in addition to a cross-section composite sample at each site. Concentrations of fecal coliform, E. coli, and enterococci were detected in 98.6, 98.5, and 87.7 percent of all samples, respectively. The maximum fecal-indicator bacteria concentrations were collected from Sawmill Run, a tributary to the Ohio River; Sawmill Run at Duquesne Heights had concentrations of fecal coliform, E. coli, and enterococci of 410,000, 510,000, and 180,000 col/100 mL, respectively, following a large storm. The samples collected in the Three Rivers and selected tributaries frequently exceeded established recreational standards and criteria for bacteria. Concentrations of fecal coliform exceeded the Pennsylvania water-quality standard (200 col/100 mL) in approximately 63 percent of the samples. Sample concentrations of E. coli and enterococci exceeded the U.S. Environmental Protection Agency (USEPA) water-quality criteria (235 and 61 col/100 mL, respectively) in about 53 and 47 percent, respectively, of the samples. Fecal-indicator bacteria were most strongly correlated with streamflow, specific conductance, and turbidity. These correlations most frequently were observed in samples collected from tributary sites. Fecal

Tolerance of Anaerobic Bacteria to Chlorinated Solvents

PubMed Central

Koenig, Joanna C.; Groissmeier, Kathrin D.; Manefield, Mike J.

2014-01-01

The aim of this research was to evaluate the effects of four chlorinated aliphatic hydrocarbons (CAHs), perchloroethene (PCE), carbon tetrachloride (CT), chloroform (CF) and 1,2-dichloroethane (1,2-DCA), on the growth of eight anaerobic bacteria: four fermentative species (Escherichia coli, Klebsiella sp., Clostridium sp. and Paenibacillus sp.) and four respiring species (Pseudomonas aeruginosa, Geobacter sulfurreducens, Shewanella oneidensis and Desulfovibrio vulgaris). Effective concentrations of solvents which inhibited growth rates by 50% (EC50) were determined. The octanol-water partition coefficient or log Po/w of a CAH proved a generally satisfactory measure of its toxicity. Most species tolerated approximately 3-fold and 10-fold higher concentrations of the two relatively more polar CAHs CF and 1,2-DCA, respectively, than the two relatively less polar compounds PCE and CT. EC50 values correlated well with growth rates observed in solvent-free cultures, with fast-growing organisms displaying higher tolerance levels. Overall, fermentative bacteria were more tolerant to CAHs than respiring species, with iron- and sulfate-reducing bacteria in particular appearing highly sensitive to CAHs. These data extend the current understanding of the impact of CAHs on a range of anaerobic bacteria, which will benefit the field of bioremediation. PMID:24441515

Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

USGS Publications Warehouse

Hyer, Kenneth; Moyer, Douglas

2003-01-01

Surface-water impairment by fecal coliform bacteria is a water-quality issue of national scope and importance. In Virginia, more than 175 stream segments are on the Commonwealth's 1998 303(d) list of impaired waters because of elevated concentrations of fecal coliform bacteria. These fecal coliform-impaired stream segments require the development of total maximum daily load (TMDL) and associated implementation plans, but accurate information on the sources contributing these bacteria usually is lacking. The development of defendable fecal coliform TMDLs and management plans can benefit from reliable information on the bacteria sources that are responsible for the impairment. Bacterial source tracking (BST) recently has emerged as a powerful tool for identifying the sources of fecal coliform bacteria that impair surface waters. In a demonstration of BST technology, three watersheds on Virginia's 1998 303(d) list with diverse land-use practices (and potentially diverse bacteria sources) were studied. Accotink Creek is dominated by urban land uses, Christians Creek by agricultural land uses, and Blacks Run is affected by both urban and agricultural land uses. During the 20-month field study (March 1999?October 2000), water samples were collected from each stream during a range of flow conditions and seasons. For each sample, specific conductance, dissolved oxygen concentration, pH, turbidity, flow, and water temperature were measured. Fecal coliform concentrations of each water sample were determined using the membrane filtration technique. Next, Escherichia coli (E. coli) were isolated from the fecal coliform bacteria and their sources were identified using ribotyping (a method of 'genetic fingerprinting'). Study results provide enhanced understanding of the concentrations and sources of fecal coliform bacteria in these three watersheds. Continuum sampling (sampling along the length of the streams) indicated that elevated concentrations of fecal coliform bacteria

Bacteria foraging in turbulent waters

NASA Astrophysics Data System (ADS)

Taylor, John; Tang, Wenbo; Stocker, Roman

2009-11-01

Marine bacteria are the Ocean's recyclers, contributing to as much as 50% of the productivity of the marine food web. Bacteria forage on patches of dissolved nutrients using chemotaxis, the ability to swim up chemical gradients. As turbulence is ubiquitous in the Ocean, it is important to understand how turbulent flow conditions affect bacterial foraging. We used three-dimensional, isotropic direct numerical simulations coupled with a bacterial transport equation to address this problem. After the flow is continuously forced until it reaches a steady state, microscale nutrient patches are injected into the turbulent flow, and stirring produces thin nutrient filaments. Two populations of bacteria compete against each other: one population is motile and chemotactic (`active'), the other is non-motile (`passive'). The distribution of both populations is initially uniform. Chemotaxis allows active bacteria to cluster near the center of the nutrient filaments, increasing their nutrient uptake relative to passive bacteria. Increasing the turbulence intensity increases the short-term chemotactic advantage by quickly producing large gradients in the nutrient concentration, but also leads to rapid mixing of the nutrient field, which makes the chemotactic advantage short-lived. The results suggest that the evolutionary advantage of chemotaxis, based on the increase in nutrient uptake relative to the energetic cost of swimming, strongly depends on the turbulence level.

Enrichment of viable bacteria in a micro-volume by free-flow electrophoresis.

PubMed

Podszun, Susann; Vulto, Paul; Heinz, Helene; Hakenberg, Sydney; Hermann, Carsten; Hankemeier, Thomas; Urban, Gerald A

2012-02-07

Macro- to micro-volume concentration of viable bacteria is performed in a microfluidic chip. The enrichment principle is based on free flow electrophoresis and is demonstrated for Gram positive bacteria. Bacteria from a suspension flow are trapped on a gel interface that separates the trapping location from integrated actuation electrodes in order to enable non-destructive trapping. The microfluidic chip contains integrated electrolytic gas expulsion structures and phaseguides for gel and liquid handling. Trapping efficiency is systematically optimized to reach 25 times the initial concentration from a theoretical maximum of 30. Finally, enrichment from analytically relevant concentrations down to 3 × 10(2) colony forming units per millilitre is demonstrated with a trapping efficiency of 80% which represents the most important parameter in enrichment.

Exchange of E. coli from the foreshore reservoir to surface waters during intensified wave conditions

NASA Astrophysics Data System (ADS)

Malott, S. S.; Vogel, L. J.; Edge, T.; O'Carroll, D. M.; Robinson, C. E.

2014-12-01

In recent years a number of studies have suggested that foreshore sand and porewater can act as a non-point source of microbial contamination to adjacent surface waters. Fecal indicator bacteria (FIB) can be released from the sand into the surface water through sand erosion or wave-induced porewater flows leading to FIB detachment. Although regression models often show that there is a strong correlation between wave events and high E. coli in surface waters, there is limited understanding of the mechanisms by which E. coli is transported from the subsurface foreshore reservoir (sand and porewater) to surface waters during wave events. An improved understanding of the transport mechanisms will facilitate the development of better water quality exceedences predictions. Detailed groundwater flow, sand level and E. coli measurements were conducted at Ipperwash Beach, Lake Huron (Ontario) for three wave events during the 2014 bathing season to evaluate the relative contribution of sand erosion and wave-induced pore water flow in transporting E. coli from the subsurface reservoir to the shallow waters. As expected, results indicate increased E. coli concentrations in ankle and waist deep surface water during periods of increased wave activity (wave height > 0.5m). Considerable sand erosion from the foreshore may have contributed to these increased surface water concentrations. The E. coli concentrations in the foreshore reservoir generally decreased as the wave height intensified, while E. coli concentrations in upshore sand and porewater locations increased.

Acute sensitivity of activated sludge bacteria to erythromycin.

PubMed

Alighardashi, A; Pandolfi, D; Potier, O; Pons, M N

2009-12-30

The presence of antibiotics in water resources has been disturbing news for the stakeholders who are responsible for public health and the drinking water supply. In many cases, biological wastewater treatment plants are the final opportunity in the water cycle to trap these substances. The sensitivity of activated sludge bacteria to erythromycin, a macrolide widely used in human medicine was investigated in batch toxicity tests using a concentration range of 1-300 mg L(-1). Erythromycin, a protein synthesis inhibitor, has been found to significantly inhibit ammonification, nitritation and nitratation at concentrations higher than 20 mg L(-1). The degree of inhibition increased with greater concentrations of the antibiotic. Exposure to erythromycin also clearly affected heterotrophs, particularly filamentous bacteria, causing floc disintegration and breakage of filaments. Cell lysis was observed with the concomitant release of organic nitrogen (intracellular proteins) and soluble COD. Although erythromycin exhibits properties of a surfactant, this characteristic alone cannot explain the damage to heterotrophs: the effects from erythromycin were greater than those of Tween 80, a commonly used surfactant. Floc disruption can lead to the release of isolated bacteria, and possibly antibiotic resistance genes, into the environment.

Freeze-drying of lactic acid bacteria.

PubMed

Fonseca, Fernanda; Cenard, Stéphanie; Passot, Stéphanie

2015-01-01

Lactic acid bacteria are of great importance for the food and biotechnology industry. They are widely used as starters for manufacturing food (e.g., yogurt, cheese, fermented meats, and vegetables) and probiotic products, as well as for green chemistry applications. Freeze-drying or lyophilization is a convenient method for preservation of bacteria. By reducing water activity to values below 0.2, it allows long-term storage and low-cost distribution at suprazero temperatures, while minimizing losses in viability and functionality. Stabilization of bacteria via freeze-drying starts with the addition of a protectant solution to the bacterial suspension. Freeze-drying includes three steps, namely, (1) freezing of the concentrated and protected cell suspension, (2) primary drying to remove ice by sublimation, and (3) secondary drying to remove unfrozen water by desorption. In this chapter we describe a method for freeze-drying of lactic acid bacteria at a pilot scale, thus allowing control of the process parameters for maximal survival and functionality recovery.

Effects of Interactions of Auxin-Producing Bacteria and Bacterial-Feeding Nematodes on Regulation of Peanut Growths

PubMed Central

Xu, Li; Xu, Wensi; Jiang, Ying; Hu, Feng; Li, Huixin

2015-01-01

The influences of an IAA (indole-3-acetic acid)-producing bacterium (Bacillus megaterium) and two bacterial-feeding nematodes (Cephalobus sp. or Mesorhabditis sp.) on the growth of peanut (Arachis hypogaea L. cv. Haihua 1) after various durations of time were investigated in natural soils. The addition of bacteria and nematodes and incubation time all significantly affected plant growth, plant root growth, plant nutrient concentrations, soil nutrient concentrations, soil microorganisms and soil auxin concentration. The addition of nematodes caused greater increases in these indices than those of bacteria, while the addition of the combination of bacteria and nematodes caused further increases. After 42-day growth, the increases in soil respiration differed between the additions of two kinds of nematodes because of differences in their life strategies. The effects of the bacteria and nematodes on the nutrient and hormone concentrations were responsible for the increases in plant growth. These results indicate the potential for promoting plant growth via the addition of nematodes and bacteria to soil. PMID:25867954

Effects of interactions of auxin-producing bacteria and bacterial-feeding nematodes on regulation of peanut growths.

PubMed

Xu, Li; Xu, Wensi; Jiang, Ying; Hu, Feng; Li, Huixin

2015-01-01

The influences of an IAA (indole-3-acetic acid)-producing bacterium (Bacillus megaterium) and two bacterial-feeding nematodes (Cephalobus sp. or Mesorhabditis sp.) on the growth of peanut (Arachis hypogaea L. cv. Haihua 1) after various durations of time were investigated in natural soils. The addition of bacteria and nematodes and incubation time all significantly affected plant growth, plant root growth, plant nutrient concentrations, soil nutrient concentrations, soil microorganisms and soil auxin concentration. The addition of nematodes caused greater increases in these indices than those of bacteria, while the addition of the combination of bacteria and nematodes caused further increases. After 42-day growth, the increases in soil respiration differed between the additions of two kinds of nematodes because of differences in their life strategies. The effects of the bacteria and nematodes on the nutrient and hormone concentrations were responsible for the increases in plant growth. These results indicate the potential for promoting plant growth via the addition of nematodes and bacteria to soil.

Plasma Deactivation of Oral Bacteria Seeded on Hydroxyapatite Disks as Tooth Enamel Analogue

PubMed Central

Blumhagen, Adam; Singh, Prashant; Mustapha, Azlin; Chen, Meng; Wang, Yong; Yu, Qingsong

2014-01-01

Purpose To study the plasma treatment effects on deactivation of oral bacteria seeded on a tooth enamel analogue. Methods A non-thermal atmospheric pressure argon plasma brush was used to treat two different Gram-positive oral bacteria including Lactobacillus acidophilus (L. acidophilus) and Streptococcus mutans (S. mutans). The bacteria were seeded on hydroxyapatite (HA) disks used as tooth enamel analogue with three initial bacterial seeding concentrations: a low inoculum concentration between 2.1×108 and 2.4×108 cfu/mL, a medium inoculum concentration between 9.8×108 and 2.4×109 cfu/mL, and a high inoculum concentration between 1.7×1010 and 3.5×1010 cfu/mL. The bacterial survivability upon plasma exposure was examined in terms of plasma exposure time and oxygen addition into the plasmas. SEM was performed to examine bacterial morphological changes after plasma exposure. Results The experimental data indicated that 13 second plasma exposure time completely killed all the bacteria when initial bacterial seeding density on HA surfaces were less than 6.9×106 cfu/cm2 for L. acidophilus and 1.7×107 cfu/cm2 for S. mutans, which were resulted from low initial seeding inoculum concentration between 2.1×108 and 2.4×108 cfu/mL. Plasma exposure of the bacteria at higher initial bacterial seeding density obtained with high initial seeding inoculum concentration, however, only resulted in ~ 1.5 to 2 log reduction and ~ 2 to 2.5 log reduction for L. acidophilus and S. mutans, respectively. It was also noted that oxygen addition into the argon plasma brush did not affect the plasma deactivation effectiveness. SEM images showed that plasma deactivation mainly occurred with the top layer bacteria, while shadowing effects from the resulting bacterial debris reduced the plasma deactivation of the underlying bacteria. Clinical Significance The experimental results indicate that, with direct contact, nonthermal atmospheric pressure argon plasmas could rapidly and

Effects of sulfate-reducing bacteria on methylmercury at the sediment-water interface.

PubMed

Zeng, Lingxia; Luo, Guangjun; He, Tianrong; Guo, Yanna; Qian, Xiaoli

2016-08-01

Sediment cores (containing sediment and overlying water) from Baihua Reservoir (SW China) were cultured under different redox conditions with different microbial activities, to understand the effects of sulfate-reducing bacteria (SRB) on mercury (Hg) methylation at sediment-water interfaces. Concentrations of dissolved methyl mercury (DMeHg) in the overlying water of the control cores with bioactivity maintained (BAC) and cores with only sulfate-reducing bacteria inhibited (SRBI) and bacteria fully inhibited (BACI) were measured at the anaerobic stage followed by the aerobic stage. For the BAC and SRBI cores, DMeHg concentrations in waters were much higher at the anaerobic stage than those at the aerobic stage, and they were negatively correlated to the dissolved oxygen concentrations (r=-0.5311 and r=-0.4977 for BAC and SRBI, respectively). The water DMeHg concentrations of the SRBI cores were 50% lower than those of the BAC cores, indicating that the SRB is of great importance in Hg methylation in sediment-water systems, but there should be other microbes such as iron-reducing bacteria and those containing specific gene cluster (hgcAB), besides SRB, causing Hg methylation in the sediment-water system. Copyright © 2016. Published by Elsevier B.V.

Rhizosphere Bacteria Enhance Selenium Accumulation and Volatilization by Indian Mustard1

PubMed Central

de Souza, Mark P.; Chu, Dara; Zhao, May; Zayed, Adel M.; Ruzin, Steven E.; Schichnes, Denise; Terry, Norman

1999-01-01

Indian mustard (Brassica juncea L.) accumulates high tissue Se concentrations and volatilizes Se in relatively nontoxic forms, such as dimethylselenide. This study showed that the presence of bacteria in the rhizosphere of Indian mustard was necessary to achieve the best rates of plant Se accumulation and volatilization of selenate. Experiments with the antibiotic ampicillin showed that bacteria facilitated 35% of plant Se volatilization and 70% of plant tissue accumulation. These results were confirmed by inoculating axenic plants with rhizosphere bacteria. Compared with axenic controls, plants inoculated with rhizosphere bacteria had 5-fold higher Se concentrations in roots (the site of volatilization) and 4-fold higher rates of Se volatilization. Plants with bacteria contained a heat-labile compound in their root exudate; when this compound was added to the rhizosphere of axenic plants, Se accumulation in plant tissues increased. Plants with bacteria had an increased root surface area compared with axenic plants; the increased area was unlikely to have caused their increased tissue Se accumulation because they did not accumulate more Se when supplied with selenite or selenomethionine. Rhizosphere bacteria also possibly increased plant Se volatilization because they enabled plants to overcome a rate-limiting step in the Se volatilization pathway, i.e. Se accumulation in plant tissues. PMID:9952452

Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa.

PubMed

Gonzales-Gustavson, Eloy; Cárdenas-Youngs, Yexenia; Calvo, Miquel; da Silva, Marcelle Figueira Marques; Hundesa, Ayalkibet; Amorós, Inmaculada; Moreno, Yolanda; Moreno-Mesonero, Laura; Rosell, Rosa; Ganges, Llilianne; Araujo, Rosa; Girones, Rosina

2017-03-01

In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and Cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E. coli), 30% (H. pylori) and 21% (Acanthamoeba castellanii). When testing the infectivity, the mean recoveries were 59% (HAdV 35), 12% (MS2), 26% (RoV SA-11) and 0.7% (BVDV). The protozoa Giardia lamblia and Cryptosporidium parvum were studied by immunofluorescence with recoveries of 18% and 13%, respectively. Although q(RT)PCR consistently showed higher quantification values (as expected), q(RT)PCR and the infectivity assays showed similar recoveries for HAdV 35 and RoV SA-11. Additionally, we investigated modelling the variability and uncertainty of the recovery with this method to extrapolate the quantification obtained by q(RT)PCR and estimate the real concentration. The 95% prediction intervals of the real concentration of the microorganisms inoculated were calculated using a general non-parametric bootstrap procedure adapted in our context to estimate the technical error of the measurements. SMF shows recoveries with a low variability that permits the use of a mathematical approximation to predict the concentration of the pathogen and indicator with acceptable low intervals. The values of uncertainty may be used for a quantitative microbial risk analysis or diagnostic purposes. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

MG Isotopic Measurement of FIB-Isolated Presolar Silicate Grains

NASA Technical Reports Server (NTRS)

Messenger, Scott R.; Nguyen, A.; Ito, M.; Rahman, Z.

2010-01-01

The majority of presolar oxide and silicate grains are ascribed to origins in low-mass red giant and asymptotic giant branch (AGB) stars based on their O isotopic ratios. However, a minor population of these grains (< 10%) has O isotopic ratios incompatible with these sources. Two principle alternative sources are higher-than-solar metallicity (Z) stars or, more likely, supernovae (SN) [1-3]. These rare (Group 4) grains [3] are characterized by enrichments in O-18, and typically also enrichments in O-17. An even rarer subset of grains with extremely large enrichments in O-17 and smaller depletions in O-18 were suggested to come from binary star systems [2]. To establish the origins of these isotopically unusual grains, it is necessary to examine isotopic systems in addition to O. Presolar silicates offer several elements diagnostic of their stellar sources and nuclear processes, including O, Si, Mg, Fe and Ca. However, the database for minor element isotopic compositions in silicates is seriously lacking. To date only two silicate grains have been analyzed for Mg [4] or Fe [5]. One major complicating factor is their small size (average 230 nm), which greatly limits the number of measurements that can be performed on any one grain and makes it more difficult to obtain statistically relevant data. This problem is compounded because the grains are identified among isotopically solar silicates, which contribute a diluting signal in isotopic measurements [1]. Thus, relatively small isotopic anomalies are missed due to this dilution effect. By applying focused ion beam (FIB) milling, we obtain undiluted Mg isotopic ratios of isolated rare presolar silicate grains to investigate their sources.

The Gamma-Glutamyl-Transpeptidase to Platelet Ratio Does not Show Advantages than APRI and Fib-4 in Diagnosing Significant Fibrosis and Cirrhosis in Patients With Chronic Hepatitis B: A Retrospective Cohort Study in China.

PubMed

Li, Qiang; Song, Jie; Huang, Yuxian; Li, Xinyan; Zhuo, Qibin; Li, Weixia; Chen, Chong; Lu, Chuan; Qi, Xun; Chen, Liang

2016-04-01

The gamma-glutamyl-transpeptidase to platelet ratio (GPR) is a new liver fibrosis model, which is reported to be more accurate than aspartate transaminase (AST) to platelet ratio index (APRI) and fibrosis index based on the four factors (Fib-4) for diagnosing significant fibrosis and cirrhosis in patients with chronic hepatitis B (CHB) in West Africa. The aim of this study is to assess the diagnostic accuracy of GPR for significant fibrosis and cirrhosis in Chinese CHB patients, and explore whether GPR deserves to be popularized in China. A total of 372 CHB patients who underwent liver biopsies and routine laboratory tests were retrospectively studied. The Scheuer scoring system was adopted as the pathological standard of liver fibrosis. Using liver histology as a gold standard, the diagnostic accuracies of GPR, APRI, and Fib-4 for significant fibrosis and cirrhosis are evaluated and compared by the receiver operating characteristic (ROC) curves and the area under the ROC curves (AUROCs). Of these 372 patients, 176 (47.3%), 129 (34.7%), and 72 (19.4%) were classified as having significant fibrosis (≥ S2), severe fibrosis (≥ S3), and cirrhosis (S4), respectively. The AUROCs of GPR for significant fibrosis (0.72 vs. 0.78; P = 0.01), severe fibrosis (0.75 vs. 0.80; P = 0.04), and cirrhosis (0.78 vs. 0.83; P = 0.02) were lower than those of APRI. The AUROCs of GPR and Fib-4 for diagnosing significant fibrosis (0.72 vs. 0.70; P = 0.29), severe fibrosis (0.75 vs. 0.73; P = 0.33), and cirrhosis (0.78 vs. 0.75; P = 0.38) were comparable. GPR is a new serum diagnostic model for liver fibrosis and cirrhosis, but does not show advantages than APRI and Fib-4 in identifying significant fibrosis, severe fibrosis, and cirrhosis in CHB patients in China.

Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California.

PubMed

Steele, Joshua A; Blackwood, A Denene; Griffith, John F; Noble, Rachel T; Schiff, Kenneth C

2018-06-01

Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater

Synthesis and characterization of alginate beads encapsulated zinc oxide nanoparticles for bacteria disinfection in water.

PubMed

Motshekga, Sarah Constance; Sinha Ray, Suprakas; Maity, Arjun

2018-02-15

The use of polymer nanocomposites as novel materials for water remediation has emerged as a promising alternative for disinfection of bacteria contaminated water. Sodium alginate, a natural biopolymer has been investigated in this study by encapsulating antimicrobial zinc oxide nanoparticles supported bentonite. The confirmation of the alginate nanocomposites was done by use of TEM, SEM-EDS and XRD. The antimicrobial activity of the alginate nanocomposites was investigated by batch studies using surface water and synthetic bacteria contaminated water containing Staphylococcus aureus. The effect of nanocomposite amount and initial bacteria concentration has been studied. The inactivation results indicated that the nanocomposite effectively inactivated bacteria in both the synthetic and surface water. With an amount of 0.5 g of the nanocomposites, no bacteria was observed in the water after 70 min of contact time with initial bacteria concentration of 200 cfu/ml for synthetic water and within a min, no bacteria was observed in the water for surface water. It is worth noting that 200 cfu/ml is the bacteria concentration range in which environmental water is likely to contain. Therefore, the results of this study have indicated that the alginate nanocomposites can be deemed as a potential antimicrobial agent for water disinfection. Copyright © 2017 Elsevier Inc. All rights reserved.

Chapter A7. Section 7.1. Fecal Indicator Bacteria

USGS Publications Warehouse

Myers, Donna N.; Sylvester, Marc A.

1997-01-01

Fecal indicator bacteria are used to assess the microbiological quality of water because, although not typically disease causing, they are correlated with the presence of several waterborne disease-causing organisms. The concentration of indicator bacteria is a measure of water safety for body-contact recreation or for consumption. This report provides information on the equipment, sampling protocols, and identification, enumeration, and calculation procedures that are in standard use by U.S. Geological Survey (USGS) personnel for the collection of data on fecal indicator bacteria.

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources.

PubMed

Mika, K B; Imamura, G; Chang, C; Conway, V; Fernandez, G; Griffith, J F; Kampalath, R A; Lee, C M; Lin, C-C; Moreno, R; Thompson, S; Whitman, R L; Jay, J A

2009-07-01

Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills. Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0.23 and -1.02 per day, and for enterococci between -0.5 and -1.0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall. Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels. Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent.

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.

Anaerobic bacteria in wastewater treatment plant.

PubMed

Cyprowski, Marcin; Stobnicka-Kupiec, Agata; Ławniczek-Wałczyk, Anna; Bakal-Kijek, Aleksandra; Gołofit-Szymczak, Małgorzata; Górny, Rafał L

2018-03-28

The objective of this study was to assess exposure to anaerobic bacteria released into air from sewage and sludge at workplaces from a wastewater treatment plant (WWTP). Samples of both sewage and sludge were collected at six sampling points and bioaerosol samples were additionally collected (with the use of a 6-stage Andersen impactor) at ten workplaces covering different stages of the technological process. Qualitative identification of all isolated strains was performed using the biochemical API 20A test. Additionally, the determination of Clostridium pathogens was carried out using 16S rRNA gene sequence analysis. The average concentration of anaerobic bacteria in the sewage samples was 5.49 × 10 4 CFU/mL (GSD = 85.4) and in sludge-1.42 × 10 6 CFU/g (GSD = 5.1). In turn, the average airborne bacterial concentration was at the level of 50 CFU/m 3 (GSD = 5.83) and the highest bacterial contamination (4.06 × 10 3  CFU/m 3 ) was found in winter at the bar screens. In total, 16 bacterial species were determined, from which the predominant strains belonged to Actinomyces, Bifidobacterium, Clostridium, Propionibacterium and Peptostreptococcus genera. The analysis revealed that mechanical treatment processes were responsible for a substantial emission of anaerobic bacteria into the air. In both the sewage and air samples, Clostridium perfringens pathogen was identified. Anaerobic bacteria were widely present both in the sewage and in the air at workplaces from the WWTP, especially when the technological process was performed in closed spaces. Anaerobic bacteria formed small aggregates with both wastewater droplets and dust particles of sewage sludge origin and as such may be responsible for adverse health outcomes in exposed workers.

Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators.

PubMed

Shahryari, A; Nikaeen, M; Khiadani Hajian, M; Nabavi, F; Hatamzadeh, M; Hassanzadeh, A

2014-11-01

Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs.

Selective pressure of antibiotic pollution on bacteria of importance to public health.

PubMed

Tello, Alfredo; Austin, Brian; Telfer, Trevor C

2012-08-01

Many bacteria of clinical importance survive and may grow in different environments. Antibiotic pollution may exert on them a selective pressure leading to an increase in the prevalence of resistance. In this study we sought to determine whether environmental concentrations of antibiotics and concentrations representing action limits used in environmental risk assessment may exert a selective pressure on clinically relevant bacteria in the environment. We used bacterial inhibition as an assessment end point to link antibiotic selective pressures to the prevalence of resistance in bacterial populations. Species sensitivity distributions were derived for three antibiotics by fitting log-logistic models to end points calculated from minimum inhibitory concentration (MIC) distributions based on worldwide data collated by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). To place bacteria represented in these distributions in a broader context, we performed a brief phylogenetic analysis. The potentially affected fraction of bacterial genera at measured environmental concentrations of antibiotics and environmental risk assessment action limits was used as a proxy for antibiotic selective pressure. Measured environmental concentrations and environmental risk assessment action limits were also directly compared to wild-type cut-off values. The potentially affected fraction of bacterial genera estimated based on antibiotic concentrations measured in water environments is ≤ 7%. We estimated that measured environmental concentrations in river sediments, swine feces lagoons, liquid manure, and farmed soil inhibit wild-type populations in up to 60%, 92%, 100%, and 30% of bacterial genera, respectively. At concentrations used as action limits in environmental risk assessment, erythromycin and ciprofloxacin were estimated to inhibit wild-type populations in up to 25% and 76% of bacterial genera. Measured environmental concentrations of antibiotics, as

Modeling Studying the Role of Bacteria on ice Nucleation Processes

NASA Astrophysics Data System (ADS)

Sun, J.

2006-12-01

Certain air-borne bacteria have been recognized as active ice nuclei at the temperatures warm than - 10°C. Ice nucleating bacteria commonly found in plants and ocean surface. These ice nucleating bacteria are readily disseminated into the atmosphere and have been observed in clouds and hailstones, and their importance in cloud formation process and precipitation, as well as causing diseases in plants and animal kingdom, have been considered for over two decades, but their significance in atmospheric processes are yet to be understood. A 1.5-D non-hydrostatic cumulus cloud model with bin-resolved microphysics is developed and is to used to examine the relative importance of sulphate aerosol concentrations on the evolution of cumulus cloud droplet spectra and ice multiplication process, as well as ice initiation process by ice nucleating bacteria in the growing stage of cumulus clouds and the key role of this process on the ice multiplication in the subsequent dissipating stage of cumulus clouds. In this paper, we will present some sensitivity test results of the evolution of cumulus cloud spectra, ice concentrations at various concentrations of sulfate aerosols, and at different ideal sounding profiles. We will discuss the implication of our results in understanding of ice nucleation processes.

Interaction of aerobic soil bacteria with plutonium(VI)

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

Panak, Petra J.; Nitsche, Heino

2000-08-22

We studied the interaction of Pu(VI) with Pseudomonas stutzeri ATCC 17588 and Bacillus sphaericus ATCC 14577, representatives of the main aerobic groups of soil bacteria present in the upper soil layers. The accumulation studies have shown that these soil bacteria accumulate high amounts of Pu(VI). The sorption efficiency toward Pu(VI) decreased with increasing biomass concentration due to increased agglomeration of the bacteria resulting in a decreased total surface area and number of available complexing groups. Spores of Bacillus sphaericus showed a higher biosorption than the vegetative cells at low biomass concentration which decreased significantly with increasing biomass concentration. At highermore » biomass concentrations (> 0.7 g/L), the vegetative cells of both strains and the spores of B. sphaericus showed comparable sorption efficiencies. Investigations on the pH dependency of the biosorption and extraction studies with 0.01 M EDTA solution have shown that the biosorption of plutonium is a reversible process and the plutonium is bound by surface complexation. Optical absorption spectroscopy showed that one third of the initially present Pu(VI) was reduced to Pu(V) after 24 hours. Kinetic studies and solvent extraction to separate different oxidation states of Pu after contact with the biomass provided further information on the yield and the kinetics of the bacteria-mediated reduction. Long-term studies showed that also 16% of Pu(IV) was formed after one month. The comparison of the amount of Pu(IV) formed during that time period with literature data of the Pu(V) disproportionation, indicated that the Pu(IV) seemed to be rather the result of the disproportionation of the formed Pu(V) than of a further microbial reduction.« less

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing.

PubMed

Pumphrey, Graham M; Ranchou-Peyruse, Anthony; Spain, Jim C

2011-07-01

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

Contribution of bacteria-like particles to PM2.5 aerosol in urban and rural environments

NASA Astrophysics Data System (ADS)

Wolf, R.; El-Haddad, I.; Slowik, J. G.; Dällenbach, K.; Bruns, E.; Vasilescu, J.; Baltensperger, U.; Prévôt, A. S. H.

2017-07-01

We report highly time-resolved estimates of airborne bacteria-like particle concentrations in ambient aerosol using an Aerodyne aerosol mass spectrometer (AMS). AMS measurements with a newly developed PM2.5 and the standard (PM1) aerodynamic lens were performed at an urban background site (Zurich) and at a rural site (Payerne) in Switzerland. Positive matrix factorization using the multilinear engine (ME-2) implementation was used to estimate the contribution of bacteria-like particles to non-refractory organic aerosol. The success of the method was evaluated by a size-resolved analysis of the organic mass and the analysis of single particle mass spectra, which were detected with a light scattering system integrated into the AMS. Use of the PM2.5 aerodynamic lens increased measured bacteria-like concentrations, supporting the analysis method. However, at all sites, the low concentrations of this component suggest that airborne bacteria constitute a minor fraction of non-refractory PM2.5 organic aerosol mass. Estimated average mass concentrations were below 0.1 μg/m3 and relative contributions were lower than 2% at both sites. During rainfall periods, concentrations of the bacteria-like component increased considerably reaching a short-time maximum of approximately 2 μg/m3 at the Payerne site in summer.

Relationships and trends of E. Coli, human-associated Bacteroides, and pathogens in the Proctor Creek Watershed

EPA Science Inventory

Urban surface waters can be impacted by anthropogenic sources such as impervious surfaces, sanitary and storm sewers, and failing infrastructure. Fecal indicator bacteria (FIB) and microbial source tracking (MST) markers are common gauges of stream water quality, however, little...

What have we learned after more than 30 years of research into the effects of sunlight, water type, nutrients, temperature and biotic interactions on decay of fecal indicators and pathogens?

EPA Science Inventory

Many waterborne pathogens originate in the gastrointestinal tract of humans or other animals (the primary habitat), and enter water bodies (secondary habitat) via direct fecal deposition, runoff, or sewage discharges. Fecal indicator bacteria (FIB) such as fecal coliforms, entero...

*A FASTER METHOD OF MEASURING RECREATIONAL WATER QUALITY FOR BETTER PROTECTION OF SWIMMER'S HEALTH

EPA Science Inventory

We previously reported that a faster method (< 2 hours) of measuring fecal indicator bacteria (FIB), based on Quantitative Polymerase Chain Reaction (QPCR), was predictive of swimming associated gastrointestinal illness. Using data from two additional beaches, we examined the re...

Influence of surfaces on sulphidogenic bacteria.

PubMed

Bass, C J; Webb, J S; Sanders, P F; Lappin-Scott, H M

1996-01-01

Sulphidogenic bacteria in oil reservoirs are of great economic importance in terms of souring, fouling and corrosion. Mixed cultures containing these bacteria were isolated from chalk formations in North Sea oil reservoirs. These were thermophilic cultures, growing optimally at 60°C. Oil formations are porous matrices, providing a very large surface area and ideal conditions for bacterial attachment, survival and growth. This study included assessments of sulphide production rates of thermophilic (t-)sulphidogen consortia with and without additional surfaces. The availability of a surface contributed significantly to the rate and extent of sulphide generation. Surfaces were offered in varying amounts to growing planktonic cultures: significantly more sulphide was produced from cultures in contact with a surface than from identical cultures in the absence of a surface. In another series of experiments, t-sulphidogens were added to chalk rock chips in the presence of nutrients and incubated for several months. This resulted in rapid sulphide generation, the final concentration being related to the initial nutrient concentration. Subsequent nutrient addition resulted in renewed sulphide generation. It is suggested that bacteria in reservoirs can withstand long periods of nutrient deprivation while attached within the porous rock matrix and opportunistically utilise nutrients when they become available.

Improving water quality through California's Clean Beach Initiative: an assessment of 17 projects.

PubMed

Dorsey, John H

2010-07-01

California's Clean Beach Initiative (CBI) funds projects to reduce loads of fecal indicator bacteria (FIB) impacting beaches, thus providing an opportunity to judge the effectiveness of various CBI water pollution control strategies. Seventeen initial projects were selected for assessment to determine their effectiveness on reducing FIB in the receiving waters along beaches nearest to the projects. Control strategies included low-flow diversions, sterilization facilities, sewer improvements, pier best management practices (BMPs), vegetative swales, and enclosed beach BMPs. Assessments were based on statistical changes in pre- and postproject mean densities of FIB at shoreline monitoring stations targeted by the projects. Most low-flow diversions and the wetland swale project were effective in removing all contaminated runoff from beaches. UV sterilization was effective when coupled with pretreatment filtration and where effluent was released within a few hundred meters of the beach to avoid FIB regrowth. Other BMPs were less effective because they treated only a portion of contaminant sources impacting their target beach. These findings should be useful to other coastal states and agencies faced with similar pollution control problems.