Growth inhibition and stimulation of Shewanella oneidensis MR-1 by surfactants and calcium polysulfide.

PubMed

Bailey, Kathryn L; Tilton, Fred; Jansik, Danielle P; Ergas, Sarina J; Marshall, Matthew J; Miracle, Ann L; Wellman, Dawn M

2012-06-01

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation of microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 μM were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS > CPS > NINOL 40-CO>SLES≥CAPB. Dose dependent growth decreases (20-100mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45-7.25 mM CPS). Both SLES (20-100mM) and SDS at lower concentrations (20-500 μM) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface microorganisms. This benchtop

Evaluation of the effects of various culture condition on Cr (VI)reduction by Shewanella oneidensis MR-1 in a novel high-throughputmini-bioreactor

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

Tang, Yinjie J.; Laidlaw, David; Gani, Kishen

2006-03-16

The growth and Cr(VI) reduction by Shewanella oneidensisMR-1 was examined using a mini-bioreactor system that independentlymonitors and controls pH, dissolved oxygen, and temperature for each ofits 24, 10-mL reactors. Independent monitoring and control of eachreactor in the cassette allows the exploration of a matrix ofenvironmental conditions known to influence S. oneidensis chromiumreduction. S. oneidensis MR-1 grew in minimal medium without amino acidor vitamin supplementation under aerobic conditions but required serineand glycine supplementation under anaerobic conditions. Growth wasinhibited by dissolved oxygen concentrations>80 percent. Lactatetransformation to acetate was enhanced by low concentration of dissolvedoxygen during the logarithmic growth phase. Between 11 andmore » 35oC, thegrowth rate obeyed the Arrhenius reaction rate-temperature relationship,with a maximum growth rate occurring at 35oC. S. oneidensis MR-1 was ableto grow over a wide range of pH (6-9). At neutral pH and temperaturesranging from 30-35oC, S. oneidensis MR-1 reduced 100 mu M Cr(VI) toCr(III) within 20 minutes in the exponential growth phase, and the growthrate was not affected by the addition of chromate; it reduced chromateeven faster at temperatures between 35 and 39oC. At low temperatures(<25oC), acidic (pH<6.5), or alkaline (pH>8.5) conditions, 100mu M Cr(VI) strongly inhibited growth and chromate reduction. Themini-bioreactor system enabled the rapid determination of theseparameters reproducibly and easily by performing very few experiments.Besides its use for examining parameters of interest to environmentalremediation, the device will also allow one to quickly assess parametersfor optimal production of recombinant proteins or secondarymetabolites« less

Growth Inhibition and Stimulation of Shewanella oneidensis MR-1 by Surfactants and Calcium Polysulfide

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

Bailey, Kathryn L.; Tilton, Fred A.; Jansik, Danielle P.

2012-06-14

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation ofmore » microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 {micro}M were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES-CAPB. Dose dependent growth decreases (20 to 100 mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45 to 7.25 mM CPS). Both SLES (20 to 100 mM) and SDS at lower concentrations (20 to 500 {micro}M) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components

PubMed Central

Pirbadian, Sahand; Barchinger, Sarah E.; Leung, Kar Man; Byun, Hye Suk; Jangir, Yamini; Bouhenni, Rachida A.; Reed, Samantha B.; Romine, Margaret F.; Saffarini, Daad A.; Shi, Liang; Gorby, Yuri A.; Golbeck, John H.; El-Naggar, Mohamed Y.

2014-01-01

Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic–abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution. PMID:25143589

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components.

PubMed

Pirbadian, Sahand; Barchinger, Sarah E; Leung, Kar Man; Byun, Hye Suk; Jangir, Yamini; Bouhenni, Rachida A; Reed, Samantha B; Romine, Margaret F; Saffarini, Daad A; Shi, Liang; Gorby, Yuri A; Golbeck, John H; El-Naggar, Mohamed Y

2014-09-02

Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic-abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.

Purification and Characterization of [NiFe]-Hydrogenase of Shewanella oneidensis MR-1

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

Shi, Liang; Belchik, Sara M.; Plymale, Andrew E.

2011-08-02

The γ-proteobacterium Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that was implicated in both H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned into a protein expression vector. The resulting plasmid was transformed into a MR-1 mutant deficient in H2 formation. Expression of MR-1 [NiFe]-H2ase in trans restored the mutant’s ability to produce H2 at 37% of that for wild type. Following expression, MR-1 [NiFe]-H2ase was purified to near homogeneity. The purified MR-1 [NiFe]-H2ase could couplemore » H2 oxidation to reduction of Tc(VII) and methyl viologen directly. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated Tc(VII) but not methyl viologen reductions. Under the conditions tested, Tc(VII) reduction was complete in Tris buffer but not in HEPES buffer. The reduced Tc(IV) was soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc(IV) precipitates formed in HEPES buffer were packed with crystallites. Although X-ray absorption near-edge spectroscopy measurements confirmed that the reduction products found in both buffers were Tc(IV), extended X-ray adsorption fine-structure measurements revealed that these products were very different. While the product in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2•nH2O. These results shows for the first time that MR-1 [NiFe]-H2ase is a bidirectional enzyme that catalyzes both H2 formation and oxidation as well as Tc(VII) reduction directly by coupling H2 oxidation.« less

Probing Electron Transfer Mechanisms in Shewanella oneidensis MR-1 using a Nanoelectrode Platform and Single-Cell Imaging

DTIC Science & Technology

2010-01-01

investigate extracellu- lar electron transfer in Shewanella oneidensisMR-1,where an array of nanoholes precludes or single window allows for direct...the single-cell level (Fig. 1B) highlights the re- lative sizes of the nanohole and window openings in the insulating layer deposited over electrodes...relative to individual bacteria such as Shewanella. The nanoholes are sufficiently small to preclude direct contact of the bacterial cell body to the

Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

NASA Astrophysics Data System (ADS)

Cooper, Rebecca Elizabeth; Eusterhues, Karin; Wegner, Carl-Eric; Totsche, Kai Uwe; Küsel, Kirsten

2017-11-01

The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron

Purification and Characterization of the [NiFe]-Hydrogenase of Shewanella oneidensis MR-1 ▿

PubMed Central

Shi, Liang; Belchik, Sara M.; Plymale, Andrew E.; Heald, Steve; Dohnalkova, Alice C.; Sybirna, Kateryna; Bottin, Hervé; Squier, Thomas C.; Zachara, John M.; Fredrickson, James K.

2011-01-01

Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H2ase in trans restored the mutant's ability to produce H2 at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2 oxidation to reduction of Tc(VII)O4− and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated reduction of Tc(VII)O4− but not methyl viologen. Under the conditions tested, all Tc(VII)O4− used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O4− was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2·nH2O, which was also the product of Tc(VII)O4− reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H2ase catalyzes Tc(VII)O4− reduction directly by coupling to H2 oxidation. PMID:21724888

Role of outer membrane c-type cytochromes MtrC and OmcA in Shewanella oneidensis MR-1 cell production, accumulation and detachment during respiration on hematite

USDA-ARS?s Scientific Manuscript database

The iron-reducing bacterium Shewanella oneidensis MR-1 has the capacity to contribute to iron cycling over the long term by respiring on crystalline iron oxides such as hematite when poorly crystalline phases are depleted. The ability of outer membrane cytochromes OmcA and MtrC of MR-1 to bind to an...

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

PubMed

Clark, Iain C; Melnyk, Ryan A; Youngblut, Matthew D; Carlson, Hans K; Iavarone, Anthony T; Coates, John D

2015-05-19

Despite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth. The ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of

Comparative c-type cytochrome expression analysis in Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C grown with soluble and insoluble oxidised metal electron acceptors

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

Nissen, Silke; Liu, Xiaoxin; Chourey, Karuna

2012-01-01

The genomes of Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C encode 40 and 69 putative c-type cytochrome genes, respectively. Deletion mutant and biochemical studies have assigned specific functions to a few c-type cytochromes involved in electron transfer to oxidised metals in Shewanella oneidensis strain MR-1. Although promising, the genetic approach is limited to gene deletions that produce a distinct phenotype, and organism for which a genetic system is available. To more comprehensively investigate and compare c-type cytochrome expression in Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C, proteomic measurements were used to characterise lysates of cells grownmore » with soluble Fe(III) (as ferric citrate) and insoluble Mn(IV) (as MnO2) as electron acceptors. Strain MR-1 expressed 19 and 20, and strain 2CP-C expressed 27 and 25 c-type cytochromes when grown with Fe(III) and Mn(IV), respectively. The majority of c-type cytochromes (77% for strain MR-1 and 63% for strain 2CP-C) were expressed under both growth conditions; however, the analysis also revealed unique c-type cytochromes that were specifically expressed in cells grown with soluble Fe(III) or insoluble Mn(IV). Proteomic characterisation proved to be a promising approach for determining the c-type cytochrome complement expressed under different growth conditions, and will help elucidating the specific functions of more c-type cytochromes that are the basis for Shewanella and Anaeromyxobacter respiratory versatility.« less

Enhanced performance of hexavalent chromium reducing cathodes in the presence of Shewanella oneidensis MR-1 and lactate.

PubMed

Xafenias, Nikolaos; Zhang, Yue; Banks, Charles J

2013-05-07

Biocathodes for the reduction of the highly toxic hexavalent chromium (Cr(VI)) were investigated using Shewanella oneidensis MR-1 (MR-1) as a biocatalyst and performance was assessed in terms of current production and Cr(VI) reduction. Potentiostatically controlled experiments (-500 mV vs Ag/AgCl) showed that a mediatorless MR-1 biocathode started up under aerated conditions in the presence of lactate, received 5.5 and 1.7 times more electrons for Cr(VI) reduction over a 4 h operating period than controls without lactate and with lactate but without MR-1, respectively. Cr(VI) reduction was also enhanced, with a decrease in concentration over the 4 h operating period of 9 mg/L Cr(VI), compared to only 1 and 3 mg/L, respectively, in the controls. Riboflavin, an electron shuttle mediator naturally produced by MR-1, was also found to have a positive impact in potentiostatically controlled cathodes. Additionally, a microbial fuel cell (MFC) with MR-1 and lactate present in both anode and cathode produced a maximum current density of 32.5 mA/m(2) (1000 Ω external load) after receiving a 10 mg/L Cr(VI) addition in the cathode, and cathodic efficiency increased steadily over an 8 day operation period with successive Cr(VI) additions. In conclusion, effective and continuous Cr(VI) reduction with associated current production were achieved when MR-1 and lactate were both present in the biocathodes.

Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1

PubMed Central

Syed, Mustafa H; Karpinets, Tatiana V; Leuze, Michael R; Kora, Guruprasad H; Romine, Margaret R; Uberbacher, Edward C

2009-01-01

Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression, and, a visualization environment that enables integration of these data types. The regulatory information in the database includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators. Availability http://shewanella-knowledgebase.org:8080/Shewanella/gbrowserLanding.jsp PMID:20198195

Transcriptome and metabolome responses of Shewanella oneidensis MR-1 to methyl orange under microaerophilic and aerobic conditions.

PubMed

Cao, Xinhua; Qi, Yueling; Xu, Chen; Yang, Yuyi; Wang, Jun

2017-04-01

Shewanella oneidensis MR-1 degrades various azo dyes under microaerophilic and anaerobic conditions, but this process is inhibited under aerobic conditions. The mechanisms underlying azo dye biodegradation and inhibition remain unknown. Therefore, we investigated metabolic and transcriptional changes in strain MR-1, which was cultured under different conditions, to elucidate these mechanisms. At the transcriptional level, genes involved in certain metabolic processes, particularly the tricarboxylic acid (TCA) cycle, amino acid biodegradation, and the electron transfer system, were significantly altered (M ≧ 2, p > 0.8 ) in the presence of methyl orange (MO). Moreover, a high concentration of dissolved oxygen heavily impacted the expression levels of genes involved in fatty acid biodegradation. Metabolome analysis revealed significant alteration (p < 0.05) in the concentrations of nine metabolites when strain MR-1 was cultured under aerobic conditions; the majority of these metabolites were closely associated with amino acid metabolism and DNA replication. Accordingly, we propose a possible pathway for MO biodegradation and discuss the most likely causes of biodegradation inhibition due to dissolved oxygen.

Cell density related H2 consumption in relation to anoxic Fe(0) corrosion and precipitation of corrosion products by Shewanella oneidensis MR-1.

PubMed

De Windt, Wim; Boon, Nico; Siciliano, Steven D; Verstraete, Willy

2003-11-01

In the absence of oxygen, a protective H2 film is formed around an Fe(0) surface, inhibiting the electron flow from this surface. Our study of anoxic corrosion of Fe(0) beads revealed that, in the presence of Shewanella oneidensis MR-1, H2 removal and precipitation of Fe mineral particles on the cell surface are determining processes for corrosion. These two biologically mediated processes were governed by cell density. H2 removal by Shewanella oneidensis was detected at cell concentrations of 1.0 x 10(6) live cells ml-1 and higher and H2 was electron donor for denitrification of NO3-. The removal of the protective H2 layer from Fe(0) beads by Shewanella oneidensis, resulted in an increase of Fe release out of the Fe(0) beads from 153 +/- 25 mg l(-1) to 196 +/- 7 mg l-1 after 20 h. When the cell concentration exceeded 1.0 x 10(8) live cells ml-1, precipitation of iron minerals on the cell surface was characteristic for the greatest percentage of MR-1 cells, whereas micrometre-scale iron precipitates not associated with culturable cell biomass significantly decreased in number. Addition of supernatant of a corrosion assay with high cell concentration induced metabolic activity in a corrosion assay with low cell concentration, resulting in increased H2 consumption and Fe release from Fe(0) beads. Homoserine lactone-like molecules were detected in the supernatant by a bio-assay, suggesting the involvement of a quorum-sensing regulatory mechanism.

Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway.

PubMed

Yang, Yun; Ding, Yuanzhao; Hu, Yidan; Cao, Bin; Rice, Scott A; Kjelleberg, Staffan; Song, Hao

2015-07-17

Flavins regulate the rate and direction of extracellular electron transfer (EET) in Shewanella oneidensis. However, low concentration of endogenously secreted flavins by the wild-type S. oneidensis MR-1 limits its EET efficiency in bioelectrochemical systems (BES). Herein, a synthetic flavin biosynthesis pathway from Bacillus subtilis was heterologously expressed in S. oneidensis MR-1, resulting in ∼25.7 times' increase in secreted flavin concentration. This synthetic flavin module enabled enhanced bidirectional EET rate of MR-1, in which its maximum power output in microbial fuel cells increased ∼13.2 times (from 16.4 to 233.0 mW/m(2)), and the inward current increased ∼15.5 times (from 15.5 to 255.3 μA/cm(2)).

Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms.

PubMed

McLean, Jeffrey S; Majors, Paul D; Reardon, Catherine L; Bilskis, Christina L; Reed, Samantha B; Romine, Margaret F; Fredrickson, James K

2008-07-01

Biofilms possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. This results in varying growth environments that may ultimately drive species diversity, determine biofilm structure and the spatial distribution of the community members. Using non-invasive nuclear magnetic resonance (NMR) microscopic imaging/spectroscopy and confocal imaging, we investigated the kinetics and stratification of anaerobic metabolism within live biofilms of the dissimilatory metal-reducing bacterium Shewanella oneidensis strain MR-1. Biofilms were pre-grown using a defined minimal medium in a constant-depth film bioreactor and subsequently transferred to an in-magnet sample chamber under laminar flow for NMR measurements. Biofilms generated in this manner were subjected to changing substrate/electron acceptor combinations (fumarate, dimethyl sulfoxide, and nitrate) and the metabolic responses measured. Localized NMR spectroscopy was used to non-invasively measure hydrogen-containing metabolites at high temporal resolution (4.5 min) under O(2)-limited conditions. Reduction of electron acceptor under anaerobic conditions was immediately observed upon switching feed solutions indicating that no gene induction (transcriptional response) was needed for MR-1 to switch metabolism from O(2) to fumarate, dimethyl sulfoxide or nitrate. In parallel experiments, confocal microscopy was used with constitutively expressed fluorescent reporters to independently investigate changes in population response to the availability of electron acceptor and to probe metabolic competition under O(2)-limited conditions. A clearer understanding of the metabolic diversity and plasticity of the biofilm mode of growth as well as how these factors relate to environmental fitness is made possible through the use of non-invasive and non-destructive techniques such as described herein.

Microbial fuel cells equipped with an iron-plated carbon-felt anode and Shewanella oneidensis MR-1 with corn steep liquor as a fuel.

PubMed

Phansroy, Nichanan; Khawdas, Wichean; Watanabe, Keigo; Aso, Yuji; Ohara, Hitomi

2018-05-12

A single chamber type microbial fuel cell (MFC) with 100 mL of chamber volume and 50 cm 2 of air-cathode was developed in this study wherein a developed iron-plated carbon-felt anode and Shewanella oneidensis MR-1 were used. The performance of the iron-plated carbon-felt anode and the possibility of corn steep liquor (CSL) as a fuel, which was the byproduct of corn wet milling and contained lactic acid, was investigated here. MFCs equipped with iron-plated or non-plated carbon-felt anodes exhibited maximum current densities of 443 or 302 mA/m 2 using 10 g/L of reagent-grade lactic acid, respectively. In addition, using centrifuged CSL without insoluble ingredients or non-centrifuged CSL as a fuel, the maximum current densities of the MFCs with iron-plated carbon-felt anode were 321 or 158 mA/m 2 , respectively. This report demonstrated the effect of iron-plated carbon-felt anode for electricity generation of MFC using S. oneidensis MR-1 and the performance of CSL as a fuel. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli.

PubMed

Kataeva, Irina; Chang, Jessie; Xu, Hao; Luan, Chi-Hao; Zhou, Jizhong; Uversky, Vladimir N; Lin, Dawei; Horanyi, Peter; Liu, Z J; Ljungdahl, Lars G; Rose, John; Luo, Ming; Wang, Bi-Cheng

2005-01-01

Low solubility of proteins overexpressed in E. coli is a frequent problem in high-throughput structural genomics. To improve solubility of proteins from mesophilic Shewanella oneidensis MR-1 and thermophilic Clostridium thermocellum JW20, an approach was attempted that included a fusion of the target protein to a maltose-binding protein (MBP) and a decrease of induction temperature. The MBP was selected as the most efficient solubilizing carrier when compared to a glutathione S-transferase and a Nus A protein. A tobacco etch virus (TEV) protease recognition site was introduced between fused proteins using a double polymerase-chain reaction and four primers. In this way, 79 S. oneidensis proteins have been expressed in one case with an N-terminal 30-residue tag and in another case as a fusion protein with MBP. A foreign tag might significantly affect the properties of the target polypeptide. At 37 degrees C and 18 degrees C induction temperatures, only 5 and 17 tagged proteins were soluble, respectively. In fusion with MBP 4, 34, and 38 proteins were soluble upon induction at 37 degrees, 28 degrees, and 18 degrees C, respectively. The MBP is assumed to increase stability and solubility of a target protein by changing both the mechanism and the cooperativity of folding/unfolding. The 66 C. thermocellum proteins were expressed as fusion proteins with MBP. Induction at 37 degrees, 28 degrees, and 18 degrees C produced 34, 57, and 60 soluble proteins, respectively. The higher solubility of C. thermocellum proteins in comparison with the S. oneidensis proteins under similar conditions of induction correlates with the thermophilicity of the host. The two-factor Wilkinson-Harrison statistical model was used to identify soluble and insoluble proteins. Theoretical and experimental data showed good agreement for S. oneidensis proteins; however, the model failed to identify soluble/insoluble Clostridium proteins. A suggestion has been made that the Wilkinson-Harrison model is

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1

PubMed Central

Clark, Iain C.; Melnyk, Ryan A.; Youngblut, Matthew D.; Carlson, Hans K.; Iavarone, Anthony T.

2015-01-01

ABSTRACT Despite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth. PMID:25991681

Shewanella oneidensis MR-1 chemotaxis proteins and electron-transport chain components essential for congregation near insoluble electron acceptors.

PubMed

Harris, H Wayne; El-Naggar, Mohamed Y; Nealson, Kenneth H

2012-12-01

Shewanella oneidensis MR-1 cells utilize a behaviour response called electrokinesis to increase their speed in the vicinity of IEAs (insoluble electron acceptors), including manganese oxides, iron oxides and poised electrodes [Harris, El-Naggar, Bretschger, Ward, Romine, Obraztsova and Nealson (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 326-331]. However, it is not currently understood how bacteria remain in the vicinity of the IEA and accumulate both on the surface and in the surrounding medium. In the present paper, we provide results indicating that cells that have contacted the IEAs swim faster than those that have not recently made contact. In addition, fast-swimming cells exhibit an enhancement of swimming reversals leading to rapid non-random accumulation of cells on, and adjacent to, mineral particles. We call the observed accumulation near IEAs 'congregation'. Congregation is eliminated by the loss of a critical gene involved with EET (extracellular electron transport) (cymA, SO_4591) and is altered or eliminated in several deletion mutants of homologues of genes that are involved with chemotaxis or energy taxis in Escherichia coli. These genes include chemotactic signal transduction protein (cheA-3, SO_3207), methyl-accepting chemotaxis proteins with the Cache domain (mcp_cache, SO_2240) or the PAS (Per/Arnt/Sim) domain (mcp_pas, SO_1385). In the present paper, we report studies of S. oneidensis MR-1 that lend some insight into how microbes in this group can 'sense' the presence of a solid substrate such as a mineral surface, and maintain themselves in the vicinity of the mineral (i.e. via congregation), which may ultimately lead to attachment and biofilm formation.

13C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells

PubMed Central

Luo, Shuai; Guo, Weihua; H. Nealson, Kenneth; Feng, Xueyang; He, Zhen

2016-01-01

Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and 13C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the 13C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that 13C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms. PMID:26868848

¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells.

PubMed

Luo, Shuai; Guo, Weihua; Nealson, Kenneth H; Feng, Xueyang; He, Zhen

2016-02-12

Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.

Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions

PubMed Central

Liu, Yongqing; Gao, Weimin; Wang, Yue; Wu, Liyou; Liu, Xueduan; Yan, Tinfeng; Alm, Eric; Arkin, Adam; Thompson, Dorothea K.; Fields, Matthew W.; Zhou, Jizhong

2005-01-01

Whole-genomic expression patterns were examined in Shewanella oneidensis cells exposed to elevated sodium chloride. Genes involved in Na+ extrusion and glutamate biosynthesis were significantly up-regulated, and the majority of chemotaxis/motility-related genes were significantly down-regulated. The data also suggested an important role for metabolic adjustment in salt stress adaptation in S. oneidensis. PMID:15774893

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

PubMed Central

Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Shao, Wenjun; Baumohl, Jason K.; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W.; Arkin, Adam P.

2011-01-01

Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. PMID:22125499

The role of Shewanella oneidensis MR-1 outer surface structures in extracellular electron transfer

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

Bouhenni, Rachida; Vora, Gary J.; Biffinger, Justin C.

2010-04-20

Shewanella oneidensis is a facultative anaerobe that uses more than 14 different terminal electron acceptors for respiration. These include metal oxides and hydroxyoxides, and toxic metals such as uranium and chromium. Mutants deficient in metal reduction were isolated using the mariner transposon derivative, minihimar RB1. These included mutants with transposon insertions in the prepilin peptidase and type II secretion system genes. All mutants were deficient in Fe(III) and Mn(IV) reduction, and exhibited slow growth when DMSO was used as the electron acceptor. The genome sequence of S. oneidensis contains one prepilin peptidase gene, pilD. A similar prepilin peptidase that maymore » function in the processing of type II secretion prepilins was not found. Single and multiple chromosomal deletions of four putative type IV pilin genes did not affect Fe(III) and Mn(IV) reduction. These results indicate that PilD in S. oneidensis is responsible for processing both type IV and type II secretion prepilin proteins. Type IV pili do not appear to be required for Fe(III) and Mn(IV) reduction.« less

Reduction of jarosite by Shewanella oneidensis MR-1 and secondary mineralization

NASA Astrophysics Data System (ADS)

Bingjie, Ouyang; Xiancai, Lu; Huan, Liu; Juan, Li; Tingting, Zhu; Xiangyu, Zhu; Jianjun, Lu; Rucheng, Wang

2014-01-01

Jarosite is a common mineral in a variety of environments formed by the oxidation of iron sulfide normally accompanying with the generation of acid mine drainage (AMD) in mining areas or acid rock drainages (ARD) in many localities. Decomposition of jarosite by dissimilatory iron reducing bacteria (DIRB) influences the mobility of many heavy metals generally accommodated in natural jarosite. This study examined the anaerobic reduction of synthesized jarosite by Shewanella oneidensis strain MR-1, a typical facultative bacteria. The release of ferrous and ferric ion, as well as sulfate and potassium, in the inoculated experimental group lasting 80 days is much higher than that in abiotic control groups. The detection of bicarbonate and acetate in experimental solution further confirms the mechanism of microbial reduction of jarosite, in which lactate acts as the electron donor. The produced ferrous iron stimulates the subsequent secondary mineralization, leading to precipitation and transformation of various iron-containing minerals. Green rust and goethite are the intermediate minerals of the microbial reduction process under anoxic conditions, and the end products include magnetite and siderite. In aerobic environments, goethite, magnetite and siderite were also detected, but the contents were relatively lower. While in abiotic experiments, only goethite has been detected as a product. Thus, the microbial reduction and subsequent mineral transformation can remarkably influence the geochemical cycling of iron and sulfur in supergene environments, as well as the mobility of heavy metals commonly accommodated in jarosite.

The role of riboflavin in decolourisation of Congo red and bioelectricity production using Shewanella oneidensis-MR1 under MFC and non-MFC conditions.

PubMed

Gomaa, Ola M; Fapetu, Segun; Kyazze, Godfrey; Keshavarz, Tajalli

2017-03-01

Dissimilatory metal reducing bacteria can exchange electrons extracellularly and hold great promise for their use in simultaneous wastewater treatment and electricity production. This study investigated the role of riboflavin, an electron carrier, in the decolourisation of Congo red in microbial fuel cells (MFCs) using Shewanella oneidensis MR-1 as a model organism. The contribution of the membrane-bound protein MtrC to the decolourisation process was also investigated. Within the range of riboflavin concentrations tested, 20 µM was found to be the best with >95% of the dye (initial concentration 200 mg/L) decolourised in MFCs within 50 h compared to 90% in the case where no riboflavin was added. The corresponding maximum power density was 45 mW/m 2 . There was no significant difference in the overall decolourisation efficiencies of Shewanela oneidensis MR-1 ΔMtrC mutants compared to the wild type. However, in terms of power production the mutant produced more power (P max 76 mW/m 2 ) compared to the wild type (P max 46 mW/m 2 ) which was attributed to higher levels of riboflavin secreted in solution. Decolourisation efficiencies in non-MFC systems (anaerobic bottles) were similar to those under MFC systems indicating that electricity generation in MFCs does not impair dye decolourisation efficiencies. The results suggest that riboflavin enhances both decolourisation of dyes and simultaneous electricity production in MFCs.

Systematic screening of carbon-based anode materials for microbial fuel cells with Shewanella oneidensis MR-1.

PubMed

Kipf, Elena; Koch, Julia; Geiger, Bettina; Erben, Johannes; Richter, Katrin; Gescher, Johannes; Zengerle, Roland; Kerzenmacher, Sven

2013-10-01

We present a systematic screening of carbon-based anode materials for microbial fuel cells with Shewanella oneidensis MR-1. Under anoxic conditions nanoporous activated carbon cloth is a superior anode material in terms of current density normalized to the projected anode area and anode volume (24.0±0.3 μA cm(-2) and 482±7 μA cm(-3) at -0.2 vs. SCE, respectively). The good performance can be attributed to the high specific surface area of the material, which is available for mediated electron transfer through self-secreted flavins. Under aerated conditions no influence of the specific surface area is observed, which we attribute to a shift from primary indirect electron transfer by mediators to direct electron transfer via adherent cells. Furthermore, we show that an aerated initial growth phase enhances the current density under subsequent anoxic conditions fivefold when compared to a similar experiment that was conducted under permanently anoxic conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Expression of Shewanella oneidensis MR-1 [FeFe]-Hydrogenase Genes in Anabaena sp. Strain PCC 7120

PubMed Central

Gärtner, Katrin; Lechno-Yossef, Sigal; Cornish, Adam J.; Wolk, C. Peter

2012-01-01

H2 generated from renewable resources holds promise as an environmentally innocuous fuel that releases only energy and water when consumed. In biotechnology, photoautotrophic oxygenic diazotrophs could produce H2 from water and sunlight using the cells' endogenous nitrogenases. However, nitrogenases have low turnover numbers and require large amounts of ATP. [FeFe]-hydrogenases found in other organisms can have 1,000-fold higher turnover numbers and no specific requirement for ATP but are very O2 sensitive. Certain filamentous cyanobacteria protect nitrogenase from O2 by sequestering the enzyme within internally micro-oxic, differentiated cells called heterocysts. We heterologously expressed the [FeFe]-hydrogenase operon from Shewanella oneidensis MR-1 in Anabaena sp. strain PCC 7120 using the heterocyst-specific promoter PhetN. Active [FeFe]-hydrogenase was detected in and could be purified from aerobically grown Anabaena sp. strain PCC 7120, but only when the organism was grown under nitrate-depleted conditions that elicited heterocyst formation. These results suggest that the heterocysts protected the [FeFe]-hydrogenase against inactivation by O2. PMID:23023750

Vanadium(V) Reduction by Shewanella oneidensis MR-1 Requires Menaquinone and Cytochromes from the Cytoplasmic and Outer Membranes

PubMed Central

Myers, Judith M.; Antholine, William E.; Myers, Charles R.

2004-01-01

The metal-reducing bacterium Shewanella oneidensis MR-1 displays remarkable anaerobic respiratory plasticity, which is reflected in the extensive number of electron transport components encoded in its genome. In these studies, several cell components required for the reduction of vanadium(V) were determined. V(V) reduction is mediated by an electron transport chain which includes cytoplasmic membrane components (menaquinone and the tetraheme cytochrome CymA) and the outer membrane (OM) cytochrome OmcB. A partial role for the OM cytochrome OmcA was evident. Electron spin resonance spectroscopy demonstrated that V(V) was reduced to V(IV). V(V) reduction did not support anaerobic growth. This is the first report delineating specific electron transport components that are required for V(V) reduction and of a role for OM cytochromes in the reduction of a soluble metal species. PMID:15006760

CRISPRi-sRNA: Transcriptional-Translational Regulation of Extracellular Electron Transfer in Shewanella oneidensis.

PubMed

Cao, Yingxiu; Li, Xiaofei; Li, Feng; Song, Hao

2017-09-15

Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i.e., clustered regularly interspaced short palindromic repeats interference (CRISPRi), in S. oneidensis MR-1 using green fluorescent protein (GFP) as a reporter. We used this CRISPRi technology to repress the expression levels of target genes, individually and in combination, in the EET pathways (e.g., the MtrCAB pathway and genes affecting the formation of electroactive biofilms in S. oneidensis), which in turn enabled the efficient regulation of EET efficiency. We then established a translational regulation technology, i.e., Hfq-dependent small regulatory RNA (sRNA), in S. oneidensis by repressing the GFP reporter and mtrA, which is a critical gene in the EET pathways in S. oneidensis. To achieve coordinated transcriptional and translational regulation at the genomic level, the CRISPRi and Hfq-dependent sRNA systems were incorporated into a single plasmid harbored in a recombinant S. oneidensis strain, which enabled an even higher efficiency of mtrA gene repression in the EET pathways than that achieved by the CRISPRi and Hfq-dependent sRNA system alone, as exhibited by the reduced electricity output. Overall, we developed a combined CRISPRi-sRNA method that enabled the synergistic transcriptional and translational regulation of target genes in S. oneidensis. This technology involving CRISPRi-sRNA transcriptional-translational regulation of gene expression at the genomic level could be applied to other microorganisms.

Viability and metal reduction of Shewanella oneidensis MR-1 under CO2 stress: implications for ecological effects of CO2 leakage from geologic CO2 sequestration.

PubMed

Wu, Bing; Shao, Hongbo; Wang, Zhipeng; Hu, Yandi; Tang, Yinjie J; Jun, Young-Shin

2010-12-01

To study potential ecological impacts of CO(2) leakage to shallow groundwater and soil/sediments from geologic CO(2) sequestration (GCS) sites, this work investigated the viability and metal reduction of Shewanella oneidensis MR-1 under CO(2) stress. While MR-1 could grow under high-pressure nitrogen gas (500 psi), the mix of 1% CO(2) with N(2) at total pressures of 15 or 150 psi significantly suppressed the growth of MR-1, compared to the N(2) control. When CO(2) partial pressures were over 15 psi, the growth of MR-1 stopped. The reduced bacterial viability was consistent with the pH decrease and cellular membrane damage under high pressure CO(2). After exposure to 150 psi CO(2) for 5 h, no viable cells survived, the cellular contents were released, and microscopy images confirmed significant cell structure deformation. However, after a relatively short exposure (25 min) to 150 psi CO(2), MR-1 could fully recover their growth within 24 h after the stress was removed, and the reduction of MnO(2) by MR-1 was observed right after the stress was removed. Furthermore, MR-1 survived better if the cells were aggregated rather than suspended, or if pH buffering minerals, such as calcite, were present. To predict the cell viability under different CO(2) pressures and exposure times, a two-parameter mathematical model was developed.

Multi-heme Cytochromes in Shewanella oneidensis MR-1: Structures, functions and opportunities

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

Breuer, Marian; Rosso, Kevin M.; Blumberger, Jochen

Multi-heme cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometers. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-heme cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-heme cytochromes have attracted much interest and contributed to advances inmore » bioenergy applications and bioremediation of contaminated soils. Looking forward there are opportunities to engage multi-heme cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-heme cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-heme cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.« less

Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

PubMed Central

Breuer, Marian; Rosso, Kevin M.; Blumberger, Jochen; Butt, Julea N.

2015-01-01

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies. PMID:25411412

Survival of Shewanella Oneidensis MR-1 to GPa pressures

NASA Astrophysics Data System (ADS)

Hazael, Rachael; Foglia, Fabrizia; Leighs, James; Appleby-Thomas, Gareth; Daniel, Isabelle; Eakins, Daniel; Meersman, Filip; McMillian, Paul

2013-06-01

Most life on Earth is thought to occupy near-surface environments under relatively mild conditions of temperature, pressure, pH, salinity etc. That view is changing following discovery of extremophile organisms that prefer environments based on high or low T, extreme chemistries, or very high pressures. Over the past three decades, geomicrobiologists have discovered an extensive subsurface biosphere, that may account for between 1/10 to 1/3 of Earth's living biomass. We subjected samples of Shewanella oneidensis to several pressure cycles to examine its survival to static high pressures to above 1.5 GPa. Shewanella forms part of a genus that contains several piezophile species like S. violacea and S. benthica. We have obtained growth curves for populations recovered from high P conditions and cultured in the laboratory, before being subjected to even higher pressures. We have also carried out dynamic shock experiments using a specially designed cell to maintain high-P, low-T conditions during shock-recovery experiments and observe colony formation among the survivors. Colony counts, shape and growth curves allow us to compare the static vs dynamic pressure resistance of wild type vs pressure-adapted strains. Leverhulme

Promotion of Iron Oxide Reduction and Extracellular Electron Transfer in Shewanella oneidensis by DMSO

PubMed Central

Cheng, Yuan-Yuan; Li, Bing-Bing; Li, Dao-Bo; Chen, Jie-Jie; Li, Wen-Wei; Tong, Zhong-Hua; Wu, Chao; Yu, Han-Qing

2013-01-01

The dissimilatory metal reducing bacterium Shewanella oneidensis MR-1, known for its capacity of reducing iron and manganese oxides, has great environmental impacts. The iron oxides reducing process is affected by the coexistence of alternative electron acceptors in the environment, while investigation into it is limited so far. In this work, the impact of dimethyl sulphoxide (DMSO), a ubiquitous chemical in marine environment, on the reduction of hydrous ferric oxide (HFO) by S. oneidensis MR-1 was investigated. Results show that DMSO promoted HFO reduction by both wild type and ΔdmsE, but had no effect on the HFO reduction by ΔdmsB, indicating that such a promotion was dependent on the DMSO respiration. With the DMSO dosing, the levels of extracellular flavins and omcA expression were significantly increased in WT and further increased in ΔdmsE. Bioelectrochemical analysis show that DMSO also promoted the extracellular electron transfer of WT and ΔdmsE. These results demonstrate that DMSO could stimulate the HFO reduction through metabolic and genetic regulation in S. oneidensis MR-1, rather than compete for electrons with HFO. This may provide a potential respiratory pathway to enhance the microbial electron flows for environmental and engineering applications. PMID:24244312

Fluxomics - connecting 'omics analysis and phenotypes.

PubMed

Winter, Gal; Krömer, Jens O

2013-07-01

In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies. © 2012 John Wiley & Sons Ltd and Society for Applied Microbiology.

Trace Element Speciation and Distribution Study at Shewanella oneidensis MR-1 Biofilm/Mineral/Water Interfaces

NASA Astrophysics Data System (ADS)

Gelabert, A.; Wang, Y.; Gescher, J.; Ha, J.; Cordova, C. D.; Singer, D. M.; Spormann, A. M.; Trainor, T. P.; Eng, P. J.; Brown, G. E.

2006-12-01

Fe- and Al-(oxyhydr)oxides are among the most reactive mineral surfaces contacted by surface and ground waters, and thus they constitute important sorbents for heavy metal and metalloid ions. As microbial biofilms may be present as coatings on these minerals, they are likely to induce major changes in surface charges and sorption capacities for metal(loid) ions compared to biofilm-free mineral surfaces. In addition, the micro- environments in biofilms can be quite different from those in bulk solutions, which can enhance (or inhibit) metal adsorption on mineral surfaces and produce biominerals that are not predicted by equilibrium thermodynamics based on the bulk solution values. In order to provide a more quantitative understanding of these effects, we have carried out a study of the interaction of Zn(II), Pb(II), and As(V) with Shewanella oneidensis (wild type, EPS-deficient mutant, and ppx- and ppk-deficient mutants) grown on highly polished and oriented single crystal surfaces of α-Al2O3 (1-102) and α-Fe2O3 (0001). This gram-negative bacterium commonly found in soil and sediments can use a wide range of electron donors and terminal electron acceptors including Fe(III) and Mn(IV) oxides under anaerobic conditions. In-situ ATR-FTIR analyses and potentiometric titrations of S. oneidensis biofilm collected from a glass bead-filled column inoculated with S. oneidensis were conducted in order to determine the nature of functional groups present on the bacterial surfaces, to quantify the site densities and protonation constants for these groups, and to determine the electrostatic parameters for S. oneidensis surfaces. GI-XAFS analyses performed on BL 11-2 at SSRL, together with macroscopic metal adsorption experiments as a function of pH (2 to 6.5), metal concentration (10-3 to 10-7 M), and ionic strength (10-1 to 10-3 M), were used to determine ion speciation and local coordination environments in the biofilm and to develop a surface complexation model describing

ArcS, the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1.

PubMed

Lassak, Jürgen; Henche, Anna-Lena; Binnenkade, Lucas; Thormann, Kai M

2010-05-01

The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria such as Shewanella species, which thrive in redox-stratified environments. One of the best-studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in Escherichia coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in Shewanella oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction, and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analyses suggest that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organizations. Thus, we speculate that ArcS might have adopted the role of ArcB after a loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment.

Identifying the role of cytochromes upon the attachment, growth and detachment of Shewanella oneidensis MR-1 on hematite during dissimilatory iron reduction under natural- flow conditions

NASA Astrophysics Data System (ADS)

Mitchell, A. C.; Geesey, G. G.

2006-12-01

Current understanding of bacterial respiration by dissimilatory iron (Fe) reduction is based primarily on studies of closed systems using soluble Fe(III). However, natural environments likely to support Fe reduction are typically open systems and contain Fe(III) primarily in the form of crystalline (hydr)oxides. Mechanisms by which electrons are transported between bacteria and mineral terminal electron acceptors (TEAs) under open system conditions are still poorly understood. However, a number of cytochromes have been identified as potentially playing a critical role in the electron transport system of some Fe reducing bacteria. Experiments were performed using (i) omcA, (ii) mtrC, or (iii) omcA and mtrC cytochrome deficient mutants of the Fe-reducing bacteria, Shewanella oneidensis MR-1, in transparent-window flow- reactors containing hematite as the only TEA. These were operated under defined hydrodynamic and anaerobic conditions. Cells expressed green fluorescent protein (gfp), allowing real time measurement of cells at the mineral surface by epifluorescence microscopy. Cytochromes which play a critical role in the anaerobic growth of S. Oneidensis by Fe reduction under open system natural-flow conditions could then be identified. Differences in the accumulation, maximum density, detachment and total production of surface-associated cells growing on hematite surfaces were apparent between the mutants, and between the mutants and the wild-type. Mutants deficient in cytochromes grew to a lower max density by up to 2 orders of magnitude than the wild-type, and exhibited no reduced Fe in the reactor effluent or at the surface of the hematite at the conclusion of the experiment, as revealed by X-Ray photoelectron spectroscopy (XPS). Therefore omcA and / or mtrC cytochromes appear critical for electron shuttling and anaerobic growth of S. Oneidensis on hematite under natural-flow conditions.

Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell.

PubMed

Li, Feng; Li, Yuanxiu; Sun, Liming; Li, Xiaofei; Yin, Changji; An, Xingjuan; Chen, Xiaoli; Tian, Yao; Song, Hao

2017-01-01

The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications. Herein, to enable S. oneidensis to directly utilize xylose as the sole carbon source for bioelectricity production in MFCs, we used synthetic biology strategies to successfully construct four genetically engineered S. oneidensis (namely XE, GE, XS, and GS) by assembling one of the xylose transporters (from Candida intermedia and Clostridium acetobutylicum ) with one of intracellular xylose metabolic pathways (the isomerase pathway from Escherichia coli and the oxidoreductase pathway from Scheffersomyces stipites ), respectively. We found that among these engineered S. oneidensis strains, the strain GS (i.e. harbouring Gxf1 gene encoding the xylose facilitator from C. intermedi , and XYL1 , XYL2 , and XKS1 genes encoding the xylose oxidoreductase pathway from S. stipites ) was able to generate the highest power density, enabling a maximum electricity power density of 2.1 ± 0.1 mW/m 2 . To the best of our knowledge, this was the first report on the rationally designed Shewanella that could use xylose as the sole carbon source and electron donor to produce electricity. The synthetic biology strategies developed in this study could be further extended to rationally engineer other exoelectrogens for lignocellulosic biomass utilization to generate electricity power.

Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.

The surface properties of Shewanella putrefaciens 200 and S. oneidensis MR-1: the effect of pH and terminal electron acceptors.

PubMed

Furukawa, Yoko; Dale, Jason R

2013-04-08

We investigated the surface characteristics of two strains of Shewanella sp., S. oneidensis MR-1 and S. putrefaciens 200, that were grown under aerobic conditions as well as under anaerobic conditions with trimethylamine oxide (TMAO) as the electron acceptor. The investigation focused on the experimental determination of electrophoretic mobility (EPM) under a range of pH and ionic strength, as well as by subsequent modeling in which Shewanella cells were considered to be soft particles with water- and ion-permeable outermost layers. The soft layer of p200 is significantly more highly charged (i.e., more negative) than that of MR-1. The effect of electron acceptor on the soft particle characteristics of Shewanella sp. is complex. The fixed charge density, which is a measure of the deionized and deprotonated functional groups in the soft layer polymers, is slightly greater (i.e., more negative) for aerobically grown p200 than for p200 grown with TMAO. On the other hand, the fixed charge density of aerobically grown MR1 is slightly less than that of p200 grown with TMAO. The effect of pH on the soft particle characteristics is also complex, and does not exhibit a clear pH-dependent trend. The Shewanella surface characteristics were attributed to the nature of the outermost soft layer, the extracellular polymeric substances (EPS) in case of p200 and lypopolysaccharides (LPS) in case of MR1 which generally lacks EPS. The growth conditions (i.e., aerobic vs. anaerobic TMAO) have an influence on the soft layer characteristics of Shewanella sp. cells. Meanwhile, the clear pH dependency of the mechanical and morphological characteristics of EPS and LPS layers, observed in previous studies through atomic force microscopy, adhesion tests and spectroscopies, cannot be corroborated by the electrohydrodynamics-based soft particle characteristics which does not exhibited a clear pH dependency in this study. While the electrohydrodynamics-based soft-particle model is a useful tool

Biogeochemical modification of Nontronite by Shewanella oneidensis MR-1: Evidence of Microbially induced Smectite-to-Illite reaction

NASA Astrophysics Data System (ADS)

Koo, T. H.; Kogure, T.; Kim, J. W.

2017-12-01

The biogeochemical modification of chemistry/structure of smectite associated with microbial Fe(III) respiration is a major process of promoting smectite-to-illite reaction (S-I reaction). Direct evidence of illitization including K-fixation and changes in Al/Si, formation of K-nontronite/illite-like structure has not been suggested systematically. Nontronite (NAu-1) was inoculated with Fe-reducing bacteria (FeRB), Shewanella oneidensis MR-1 at 30 ° with pH buffered (7.0 and 8.0) M1 medium in the anaerobic chamber, and the evidence of illitization was suggested by microscopic/spectroscopic measurements as well as aqueous chemistry in the supernatant with various incubation time. A progressive morphological change in bio-reduced notnronite (altered nontronite → K-nontronite → illite) corresponded to chemical modification in solid phase (Al/Si 0.16 to 0.28). Fe and Al contents in the supernatant increased continuously up to 70 days of incubation (3.4 to 20 and 1.7 to 13 20 mmol/mg of NAu-1, respectively) then decreased in 120 days of incubation (20 to 8 and 13 to 3 mmol/mg of NAu-1, respectively) indicating new mineral phase precipitated. Si contents showed slightly decreased in 7 days (133 to 100 mmol/mg of NAu-1) then showed fluctuated pattern (increased to 183 mmol/mg of NAu-1 in 70 days, then decreased to 102 mmol/mg of NAu-1 in 120 days of incubation). Formation of biotic silica globule within 120-day incubation supported the dissolution of bio-reduced notnronite. Indeed, modification in structure (appearance of 10-Å shoulder in X-ray diffraction profile) and formation of discrete illite-like packet (d001=1.0 nm) in the wavy bio-reduced nontronite matrix (d001=1.2-1.3 nm) strongly suggest that bio-reduced nontronite underwent the reductive dissolution and precipitated the newly formed illite

Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1

PubMed Central

Alves, Mónica N.; Neto, Sónia E.; Alves, Alexandra S.; Fonseca, Bruno M.; Carrêlo, Afonso; Pacheco, Isabel; Paquete, Catarina M.; Soares, Cláudio M.; Louro, Ricardo O.

2015-01-01

The versatile anaerobic metabolism of the Gram-negative bacterium Shewanella oneidensis MR-1 (SOMR-1) relies on a multitude of redox proteins found in its periplasm. Most are multiheme cytochromes that carry electrons to terminal reductases of insoluble electron acceptors located at the cell surface, or bona fide terminal reductases of soluble electron acceptors. In this study, the interaction network of several multiheme cytochromes was explored by a combination of NMR spectroscopy, activity assays followed by UV-visible spectroscopy and comparison of surface electrostatic potentials. From these data the small tetraheme cytochrome (STC) emerges as the main periplasmic redox shuttle in SOMR-1. It accepts electrons from CymA and distributes them to a number of terminal oxidoreductases involved in the respiration of various compounds. STC is also involved in the electron transfer pathway to reduce nitrite by interaction with the octaheme tetrathionate reductase (OTR), but not with cytochrome c nitrite reductase (ccNiR). In the main pathway leading the metal respiration STC pairs with flavocytochrome c (FccA), the other major periplasmic cytochrome, which provides redundancy in this important pathway. The data reveals that the two proteins compete for the binding site at the surface of MtrA, the decaheme cytochrome inserted on the periplasmic side of the MtrCAB–OmcA outer-membrane complex. However, this is not observed for the MtrA homologues. Indeed, neither STC nor FccA interact with MtrD, the best replacement for MtrA, and only STC is able to interact with the decaheme cytochrome DmsE of the outer-membrane complex DmsEFABGH. Overall, these results shown that STC plays a central role in the anaerobic respiratory metabolism of SOMR-1. Nonetheless, the trans-periplasmic electron transfer chain is functionally resilient as a consequence of redundancies that arise from the presence of alternative pathways that bypass/compete with STC. PMID:26175726

Reduced Heme Levels Underlie the Exponential Growth Defect of the Shewanella oneidensis hfq Mutant

PubMed Central

Mezoian, Taylor; Hunt, Taylor M.; Keane, Meaghan L.; Leonard, Jessica N.; Scola, Shelby E.; Beer, Emma N.; Perdue, Sarah; Pellock, Brett J.

2014-01-01

The RNA chaperone Hfq fulfills important roles in small regulatory RNA (sRNA) function in many bacteria. Loss of Hfq in the dissimilatory metal reducing bacterium Shewanella oneidensis strain MR-1 results in slow exponential phase growth and a reduced terminal cell density at stationary phase. We have found that the exponential phase growth defect of the hfq mutant in LB is the result of reduced heme levels. Both heme levels and exponential phase growth of the hfq mutant can be completely restored by supplementing LB medium with 5-aminolevulinic acid (5-ALA), the first committed intermediate synthesized during heme synthesis. Increasing expression of gtrA, which encodes the enzyme that catalyzes the first step in heme biosynthesis, also restores heme levels and exponential phase growth of the hfq mutant. Taken together, our data indicate that reduced heme levels are responsible for the exponential growth defect of the S. oneidensis hfq mutant in LB medium and suggest that the S. oneidensis hfq mutant is deficient in heme production at the 5-ALA synthesis step. PMID:25356668

Programming the quorum sensing-based AND gate in Shewanella oneidensis for logic gated-microbial fuel cells.

PubMed

Hu, Yidan; Yang, Yun; Katz, Evgeny; Song, Hao

2015-03-11

An AND logic gate based on a synthetic quorum-sensing (QS) module was constructed in a Shewanella oneidensis MR-1 mtrA knockout mutant. The presence of two input signals activated the expression of a periplasmic decaheme cytochrome MtrA to regenerate the extracellular electron transfer conduit, enabling the construction of AND-gated microbial fuel cells.

Probing electron transfer mechanisms in Shewanella oneidensis MR-1 using a nanoelectrode platform and single-cell imaging

PubMed Central

Jiang, Xiaocheng; Hu, Jinsong; Fitzgerald, Lisa A.; Biffinger, Justin C.; Xie, Ping; Ringeisen, Bradley R.; Lieber, Charles M.

2010-01-01

Microbial fuel cells (MFCs) represent a promising approach for sustainable energy production as they generate electricity directly from metabolism of organic substrates without the need for catalysts. However, the mechanisms of electron transfer between microbes and electrodes, which could ultimately limit power extraction, remain controversial. Here we demonstrate optically transparent nanoelectrodes as a platform to investigate extracellular electron transfer in Shewanella oneidensis MR-1, where an array of nanoholes precludes or single window allows for direct microbe-electrode contacts. Following addition of cells, short-circuit current measurements showed similar amplitude and temporal response for both electrode configurations, while in situ optical imaging demonstrates that the measured currents were uncorrelated with the cell number on the electrodes. High-resolution imaging showed the presence of thin, 4- to 5-nm diameter filaments emanating from cell bodies, although these filaments do not appear correlated with current generation. Both types of electrodes yielded similar currents at longer times in dense cell layers and exhibited a rapid drop in current upon removal of diffusible mediators. Reintroduction of the original cell-free media yielded a rapid increase in current to ∼80% of original level, whereas imaging showed that the positions of > 70% of cells remained unchanged during solution exchange. Together, these measurements show that electron transfer occurs predominantly by mediated mechanism in this model system. Last, simultaneous measurements of current and cell positions showed that cell motility and electron transfer were inversely correlated. The ability to control and image cell/electrode interactions down to the single-cell level provide a powerful approach for advancing our fundamental understanding of MFCs. PMID:20837546

Use of an Electrochemical Split Cell Technique to Evaluate the Influence of Shewanella oneidensis Activities on Corrosion of Carbon Steel

PubMed Central

Miller, Robert Bertram; Sadek, Anwar; Rodriguez, Alvaro; Iannuzzi, Mariano; Giai, Carla; Senko, John M.; Monty, Chelsea N.

2016-01-01

Microbially induced corrosion (MIC) is a complex problem that affects various industries. Several techniques have been developed to monitor corrosion and elucidate corrosion mechanisms, including microbiological processes that induce metal deterioration. We used zero resistance ammetry (ZRA) in a split chamber configuration to evaluate the effects of the facultatively anaerobic Fe(III) reducing bacterium Shewanella oneidensis MR-1 on the corrosion of UNS G10180 carbon steel. We show that activities of S. oneidensis inhibit corrosion of steel with which that organism has direct contact. However, when a carbon steel coupon in contact with S. oneidensis was electrically connected to a second coupon that was free of biofilm (in separate chambers of the split chamber assembly), ZRA-based measurements indicated that current moved from the S. oneidensis-containing chamber to the cell-free chamber. This electron transfer enhanced the O2 reduction reaction on the coupon deployed in the cell free chamber, and consequently, enhanced oxidation and corrosion of that electrode. Our results illustrate a novel mechanism for MIC in cases where metal surfaces are heterogeneously covered by biofilms. PMID:26824529

Use of an Electrochemical Split Cell Technique to Evaluate the Influence of Shewanella oneidensis Activities on Corrosion of Carbon Steel.

PubMed

Miller, Robert Bertram; Sadek, Anwar; Rodriguez, Alvaro; Iannuzzi, Mariano; Giai, Carla; Senko, John M; Monty, Chelsea N

2016-01-01

Microbially induced corrosion (MIC) is a complex problem that affects various industries. Several techniques have been developed to monitor corrosion and elucidate corrosion mechanisms, including microbiological processes that induce metal deterioration. We used zero resistance ammetry (ZRA) in a split chamber configuration to evaluate the effects of the facultatively anaerobic Fe(III) reducing bacterium Shewanella oneidensis MR-1 on the corrosion of UNS G10180 carbon steel. We show that activities of S. oneidensis inhibit corrosion of steel with which that organism has direct contact. However, when a carbon steel coupon in contact with S. oneidensis was electrically connected to a second coupon that was free of biofilm (in separate chambers of the split chamber assembly), ZRA-based measurements indicated that current moved from the S. oneidensis-containing chamber to the cell-free chamber. This electron transfer enhanced the O2 reduction reaction on the coupon deployed in the cell free chamber, and consequently, enhanced oxidation and corrosion of that electrode. Our results illustrate a novel mechanism for MIC in cases where metal surfaces are heterogeneously covered by biofilms.

Targeted Protein Degradation of Outer Membrane Decaheme Cytochrome MtrC Metal Reductase in Shewanella oneidensis MR-1 Measured Using Biarsenical Probe CrAsH-EDT2

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

Xiong, Yijia; Chen, Baowei; Shi, Liang

2011-10-14

Development of efficient microbial biofuel cells requires an ability to exploit interfacial electron transfer reactions to external electron acceptors, such as metal oxides; such reactions occur in the facultative anaerobic gram-negative bacterium Shewanella oneidensis MR-1 through the catalytic activity of the outer membrane decaheme c-type cytochrome MtrC. Central to the utility of this pathway to synthetic biology is an understanding of cellular mechanisms that maintain optimal MtrC function, cellular localization, and renewal by degradation and resynthesis. In order to monitor trafficking to the outer membrane, and the environmental sensitivity of MtrC, we have engineered a tetracysteine tag (i.e., CCPGCC) atmore » its C-terminus that permits labeling by the cell impermeable biarsenical fluorophore, carboxy-FlAsH (CrAsH) of MtrC at the surface of living Shewanella oneidensis MR-1 cells. In comparison, the cell permeable reagent FlAsH permits labeling of the entire population of MtrC, including proteolytic fragments resulting from incorrect maturation. We demonstrate specific labeling by CrAsH of engineered MtrC which is dependent on the presence of a functional type-2 secretion system (T2S), as evidenced by T2S system gspD or gspG deletion mutants which are incapable of CrAsH labeling. Under these latter conditions, MtrC undergoes proteolytic degradation to form a large 35-38 kDa fragment; this degradation product is also resolved during normal turnover of the CrAsH-labeled MtrC protein. No MtrC protein is released into the medium during turnover, suggesting the presence of cellular turnover systems involving MtrC reuptake and degradation. The mature MtrC localized on the outer membrane is a long-lived protein, with a turnover rate of 0.043 hr-1 that is insensitive to O2 concentration. Maturation of MtrC is relatively inefficient, with substantial rates of turnover of the immature protein prior to export to the outer membrane (i.e., 0.028 hr-1) that are

Iron triggers λSo prophage induction and release of extracellular DNA in Shewanella oneidensis MR-1 biofilms.

PubMed

Binnenkade, Lucas; Teichmann, Laura; Thormann, Kai M

2014-09-01

Prophages are ubiquitous elements within bacterial chromosomes and affect host physiology and ecology in multiple ways. We have previously demonstrated that phage-induced lysis is required for extracellular DNA (eDNA) release and normal biofilm formation in Shewanella oneidensis MR-1. Here, we investigated the regulatory mechanisms of prophage λSo spatiotemporal induction in biofilms. To this end, we used a functional fluorescence fusion to monitor λSo activation in various mutant backgrounds and in response to different physiological conditions. λSo induction occurred mainly in a subpopulation of filamentous cells in a strictly RecA-dependent manner, implicating oxidative stress-induced DNA damage as the major trigger. Accordingly, mutants affected in the oxidative stress response (ΔoxyR) or iron homeostasis (Δfur) displayed drastically increased levels of phage induction and abnormal biofilm formation, while planktonic cells were not or only marginally affected. To further investigate the role of oxidative stress, we performed a mutant screen and identified two independent amino acid substitutions in OxyR (T104N and L197P) that suppress induction of λSo by hydrogen peroxide (H2O2). However, λSo induction was not suppressed in biofilms formed by both mutants, suggesting a minor role of intracellular H2O2 in this process. In contrast, addition of iron to biofilms strongly enhanced λSo induction and eDNA release, while both processes were significantly suppressed at low iron levels, strongly indicating that iron is the limiting factor. We conclude that uptake of iron during biofilm formation triggers λSo-mediated lysis of a subpopulation of cells, likely by an increase in iron-mediated DNA damage sensed by RecA. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

A method adapting microarray technology for signature tagged mutagenesis of Dusulfovibrio dusulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments

USGS Publications Warehouse

Groh, Jennifer L.; Luo, Qingwei; Ballard , Jimmy D.; Krumholz, Lee R.

2005-01-01

Signature-tagged mutagenesis (STM) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. To date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. We used a mini-Tn10 transposon-bearing plasmid, pBSL180, that efficiently and randomly mutagenized Desulfovibrio desulfuricans G20 in addition to Shewanella oneidensis MR-1. Using these organisms as model sediment-dwelling anaerobic bacteria, we developed a new screening system, modified from former STM procedures, to identify genes that are critical for sediment survival. The screening system uses microarray technology to visualize tags from input and output pools, allowing us to identify those lost during sediment incubations. While the majority of data on survival genes identified will be presented in future papers, we report here on chemotaxis-related genes identified by our STM method in both bacteria in order to validate our method. This system may be applicable to the study of numerous environmental bacteria, allowing us to identify functions and roles of survival genes in various habitats.

Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1.

PubMed

Ding, Dewu; Sun, Xiao

2018-01-16

Shewanella oneidensis MR-1 can transfer electrons from the intracellular environment to the extracellular space of the cells to reduce the extracellular insoluble electron acceptors (Extracellular Electron Transfer, EET). Benefiting from this EET capability, Shewanella has been widely used in different areas, such as energy production, wastewater treatment, and bioremediation. Genome-wide proteomics data was used to determine the active proteins involved in activating the EET process. We identified 1012 proteins with decreased expression and 811 proteins with increased expression when the EET process changed from inactivation to activation. We then networked these proteins to construct the active protein networks, and identified the top 20 key active proteins by network centralization analysis, including metabolism- and energy-related proteins, signal and transcriptional regulatory proteins, translation-related proteins, and the EET-related proteins. We also constructed the integrated protein interaction and transcriptional regulatory networks for the active proteins, then found three exclusive active network motifs involved in activating the EET process-Bi-feedforward Loop, Regulatory Cascade with a Feedback, and Feedback with a Protein-Protein Interaction (PPI)-and identified the active proteins involved in these motifs. Both enrichment analysis and comparative analysis to the whole-genome data implicated the multiheme c -type cytochromes and multiple signal processing proteins involved in the process. Furthermore, the interactions of these motif-guided active proteins and the involved functional modules were discussed. Collectively, by using network-based methods, this work reported a proteome-wide search for the key active proteins that potentially activate the EET process.

Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor.

PubMed

Kane, Aunica L; Brutinel, Evan D; Joo, Heena; Maysonet, Rebecca; VanDrisse, Chelsey M; Kotloski, Nicholas J; Gralnick, Jeffrey A

2016-04-01

Shewanella oneidensis strain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized by S. oneidensis are more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms inS. oneidensis have been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced by S. oneidensis through pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield of S. oneidensis through the generation of proton motive force. Exogenous formate also greatly accelerated growth on N-acetylglucosamine, a carbon source normally utilized very slowly by S. oneidensis under anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth of S. oneidensis using pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation inS. oneidensis. Shewanella species have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the proteins for

Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor

PubMed Central

Kane, Aunica L.; Brutinel, Evan D.; Joo, Heena; Maysonet, Rebecca; VanDrisse, Chelsey M.; Kotloski, Nicholas J.

2016-01-01

ABSTRACT Shewanella oneidensis strain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized by S. oneidensis are more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms in S. oneidensis have been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced by S. oneidensis through pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield of S. oneidensis through the generation of proton motive force. Exogenous formate also greatly accelerated growth on N-acetylglucosamine, a carbon source normally utilized very slowly by S. oneidensis under anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth of S. oneidensis using pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation in S. oneidensis. IMPORTANCE Shewanella species have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the

Cellular Response of Shewanella oneidensis to Strontium Stress†

PubMed Central

Brown, Steven D.; Martin, Madhavi; Deshpande, Sameer; Seal, Sudipta; Huang, Katherine; Alm, Eric; Yang, Yunfeng; Wu, Liyou; Yan, Tingfen; Liu, Xueduan; Arkin, Adam; Chourey, Karuna; Zhou, Jizhong; Thompson, Dorothea K.

2006-01-01

The physiology and transcriptome dynamics of the metal ion-reducing bacterium Shewanella oneidensis strain MR-1 in response to nonradioactive strontium (Sr) exposure were investigated. Studies indicated that MR-1 was able to grow aerobically in complex medium in the presence of 180 mM SrCl2 but showed severe growth inhibition at levels above that concentration. Temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase MR-1 cells shocked with 180 mM SrCl2 and analyzed for significant differences in mRNA abundance with reference to data for nonstressed MR-1 cells. Genes with annotated functions in siderophore biosynthesis and iron transport were among the most highly induced (>100-fold [P < 0.05]) open reading frames in response to acute Sr stress, and a mutant (SO3032::pKNOCK) defective in siderophore production was found to be hypersensitive to SrCl2 exposure, compared to parental and wild-type strains. Transcripts encoding multidrug and heavy metal efflux pumps, proteins involved in osmotic adaptation, sulfate ABC transporters, and assimilative sulfur metabolism enzymes also were differentially expressed following Sr exposure but at levels that were several orders of magnitude lower than those for iron transport genes. Precipitate formation was observed during aerobic growth of MR-1 in broth cultures amended with 50, 100, or 150 mM SrCl2 but not in cultures of the SO3032::pKNOCK mutant or in the abiotic control. Chemical analysis of this precipitate using laser-induced breakdown spectroscopy and static secondary ion mass spectrometry indicated extracellular solid-phase sequestration of Sr, with at least a portion of the heavy metal associated with carbonate phases. PMID:16391131

Disruption of Putrescine Biosynthesis in Shewanella oneidensis Enhances Biofilm Cohesiveness and Performance in Cr(VI) Immobilization

PubMed Central

Ding, Yuanzhao; Peng, Ni; Du, Yonghua; Ji, Lianghui

2014-01-01

Although biofilm-based bioprocesses have been increasingly used in various applications, the long-term robust and efficient biofilm performance remains one of the main bottlenecks. In this study, we demonstrated that biofilm cohesiveness and performance of Shewanella oneidensis can be enhanced through disrupting putrescine biosynthesis. Through random transposon mutagenesis library screening, one hyperadherent mutant strain, CP2-1-S1, exhibiting an enhanced capability in biofilm formation, was obtained. Comparative analysis of the performance of biofilms formed by S. oneidensis MR-1 wild type (WT) and CP2-1-S1 in removing dichromate (Cr2O72−), i.e., Cr(VI), from the aqueous phase showed that, compared with the WT biofilms, CP2-1-S1 biofilms displayed a substantially lower rate of cell detachment upon exposure to Cr(VI), suggesting a higher cohesiveness of the mutant biofilms. In addition, the amount of Cr(III) immobilized by CP2-1-S1 biofilms was much larger, indicating an enhanced performance in Cr(VI) bioremediation. We further showed that speF, a putrescine biosynthesis gene, was disrupted in CP2-1-S1 and that the biofilm phenotypes could be restored by both genetic and chemical complementations. Our results also demonstrated an important role of putrescine in mediating matrix disassembly in S. oneidensis biofilms. PMID:24362428

Iron Reduction and Carbonate Precipitation by Shewanella oneidensis

NASA Astrophysics Data System (ADS)

Zeng, Z.; Tice, M. M.

2011-12-01

This study is to contribute to better understanding of how Archean microbes induced carbonate diagenesis in mats and stromatolites. Previous studies showed sulfate reduction, a common promoter of carbonate precipitation in modern mats[1], is likely to have been less effective in Archean mats in marine fluids lower in sulfate[2]. Alternatively, iron reduction produces far more alkalinity per unit carbon respired than sulfate reduction. Therefore, we hypothesize iron reduction can promote much more carbonate precipitation than sulfate reduction. Our study might also have some relevance to banded iron formation on which microbial iron reduction played a potential role[3]. To test our hypothesis, Shewanella oneidensis MR-1, a dissimilatory iron reducing bacterium will be cultured anaerobically (79%N2, 20%CO2 and 1%H2) in basal medium to trigger iron reduction. Lactate will be used as electron donor, and the electron acceptor will be fresh ferrihydrite. Culture medium will be added with various metal ions, such as Ca2+ and Mg2+, to obtain potential carbonate precipitate. Escherichia coli (with fumarate added as an electron acceptor) will be used to provide a comparison to live but non-iron- reduction cells. After 20 days incubation, precipitate will be collected, washed and identified by X-ray diffraction (XRD). Besides, iron reduction rate (ferrozine assay)[4], PH and amount of precipitate (carbonate and oxidize fractions)[5] will be measured over time to well understand how S. oneidensis drives carbonate precipitation.

Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor

USDA-ARS?s Scientific Manuscript database

Background. Shewanella oneidensis is a target of extensive research efforts in the fields of bioelectrochemical systems and bioremediation because of its versatile metabolic capabilities, especially in regards to the respiration with extracellular electron acceptors. Here, we took a global approach ...

Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1

DOE PAGES

Chubiz, Lon M.; Marx, Christopher J.

2017-03-13

Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved whenShewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism ofN-acetylglucosamine are the common basis for evolved glucose metabolism across populations.more » The loss ofnagRresults in the constitutive expression of genes for anN-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK toward glucose allow for the transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent inS. oneidensis. 13C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and preexisting enzymatic promiscuity, and not gain-of-function mutations, were the drivers of increased metabolic capacity. However, we observed a significant decrease in the growth rate on lactate after adaptation to glucose catabolism, suggesting that trade-offs may explain why glycolytic function may not be readily observed inS. oneidensisin natural environments despite it being readily accessible through just a single mutational event.Gains in metabolic capacity are frequently associated with the acquisition of novel genetic material via natural or engineered horizontal gene transfer events. Here, we explored how a bacterium that typically consumes small organic acids and amino acids expands its metabolic capacity to include

Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1

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

Chubiz, Lon M.; Marx, Christopher J.

Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved whenShewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism ofN-acetylglucosamine are the common basis for evolved glucose metabolism across populations.more » The loss ofnagRresults in the constitutive expression of genes for anN-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK toward glucose allow for the transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent inS. oneidensis. 13C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and preexisting enzymatic promiscuity, and not gain-of-function mutations, were the drivers of increased metabolic capacity. However, we observed a significant decrease in the growth rate on lactate after adaptation to glucose catabolism, suggesting that trade-offs may explain why glycolytic function may not be readily observed inS. oneidensisin natural environments despite it being readily accessible through just a single mutational event.Gains in metabolic capacity are frequently associated with the acquisition of novel genetic material via natural or engineered horizontal gene transfer events. Here, we explored how a bacterium that typically consumes small organic acids and amino acids expands its metabolic capacity to include

In vitro enzymatic reduction kinetics of mineral oxides by membrane fractions from Shewanella oneidensis MR-1

NASA Astrophysics Data System (ADS)

Ruebush, Shane S.; Icopini, Gary A.; Brantley, Susan L.; Tien, Ming

2006-01-01

This study documents the first example of in vitro solid-phase mineral oxide reduction by enzyme-containing membrane fractions. Previous in vitro studies have only reported the reduction of aqueous ions. Total membrane (TM) fractions from iron-grown cultures of Shewanella oneidensis MR-1 were isolated and shown to catalyze the reduction of goethite, hematite, birnessite, and ramsdellite/pyrolusite using formate. In contrast, nicotinamide adenine dinucleotide (NADH) and succinate cannot function as electron donors. The significant implications of observations related to this cell-free system are: (i) both iron and manganese mineral oxides are reduced by the TM fraction, but aqueous U(VI) is not; (ii) TM fractions from anaerobically grown, but not aerobically grown, cells can reduce the mineral oxides; (iii) electron shuttles and iron chelators are not needed for this in vitro reduction, documenting conclusively that reduction can occur by direct contact with the mineral oxide; (iv) electron shuttles and EDTA stimulate the in vitro Fe(III) reduction, documenting that exogenous molecules can enhance rates of enzymatic mineral reduction; and (v) multiple membrane components are involved in solid-phase oxide reduction. The membrane fractions, consisting of liposomes of cytoplasmic and outer membrane segments, contain at least 100 proteins including the enzyme that oxidizes formate, formate dehydrogenase. Mineral oxide reduction was inhibited by the addition of detergent Triton X-100, which solubilizes membranes and their associated proteins, consistent with the involvement of multiple electron carriers that are disrupted by detergent addition. In contrast, formate dehydrogenase activity was not inhibited by Triton X-100. The addition of anthraquinone-2,6-disulfonate (AQDS) and menaquinone-4 was unable to restore activity; however, menadione (MD) restored 33% of the activity. The addition of AQDS and MD to reactions without added detergent increased the rate of goethite

Transcriptome Profiling of Shewanella oneidensis Gene Expression following Exposure to Acidic and Alkaline pH†

PubMed Central

Leaphart, Adam B.; Thompson, Dorothea K.; Huang, Katherine; Alm, Eric; Wan, Xiu-Feng; Arkin, Adam; Brown, Steven D.; Wu, Liyou; Yan, Tingfen; Liu, Xueduan; Wickham, Gene S.; Zhou, Jizhong

2006-01-01

The molecular response of Shewanella oneidensis MR-1 to variations in extracellular pH was investigated based on genomewide gene expression profiling. Microarray analysis revealed that cells elicited both general and specific transcriptome responses when challenged with environmental acid (pH 4) or base (pH 10) conditions over a 60-min period. Global responses included the differential expression of genes functionally linked to amino acid metabolism, transcriptional regulation and signal transduction, transport, cell membrane structure, and oxidative stress protection. Response to acid stress included the elevated expression of genes encoding glycogen biosynthetic enzymes, phosphate transporters, and the RNA polymerase sigma-38 factor (rpoS), whereas the molecular response to alkaline pH was characterized by upregulation of nhaA and nhaR, which are predicted to encode an Na+/H+ antiporter and transcriptional activator, respectively, as well as sulfate transport and sulfur metabolism genes. Collectively, these results suggest that S. oneidensis modulates multiple transporters, cell envelope components, and pathways of amino acid consumption and central intermediary metabolism as part of its transcriptome response to changing external pH conditions. PMID:16452448

Contributions of the [NiFe]- and [FeFe]-hydrogenase to H2 production in Shewanella oneidensis MR-1 as revealed by isotope ratio analysis of evolved H2

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

Kreuzer, Helen W.; Hill, Eric A.; Moran, James J.

2014-03-01

Shewanella oneidensis MR-1 encodes both a [NiFe]- and an [FeFe]-hydrogenase. While the output of these proteins has been characterized in mutant strains expressing only one of the enzymes, the contribution of each to H2 synthesis in the wild-type organism is not clear. Here we use stable isotope analysis of H2 in the culture headspace, along with transcription data and measurements of the concentrations of gases in the headspace, to characterize H2 production in the wild-type strain. After most of the O2 in the headspace had been consumed, H2 was produced and then consumed by the bidirectional [NiFe]-hydrogenase. Once the culturesmore » were completely anaerobic, a new burst of H2 synthesis catalyzed by both enzymes took place. Our data is consistent with the hypothesis that at this point in the culture cycle, a pool of electrons is shunted toward both hydrogenases in the wild-type organism, but that in the absence of one of the hydrogenases, the flux is redirected to the available enzyme. To our knowledge, this is the first use of stable isotope analysis of a metabolic product to elucidate substrate flux through two alternative enzymes in the same cellular system.« less

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.

PubMed

Wu, Stephen Gang; Wang, Yuxuan; Jiang, Wu; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie J; Bao, Forrest Sheng

2016-04-01

13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species.

The utilization of Eschericia coli and Shewanella oneidensis for microbial fuel cell

NASA Astrophysics Data System (ADS)

Juliastuti, S. R.; Darmawan, R.; Ayuningtyas, A.; Ellyza, N.

2018-03-01

Microbial Fuel Cell (MFC) is a technology that convert chemical energy into electrical energy with catalytic reaction from microorganism. The research method using bacteria in organic waste on anode compartment and ferricyanide solution on cathode compartment. Wastewater from sugar factory was used as organic waste with bacterial concentration of 10%, 12.5%, 15%, 17.5% (v/v) and with bacteria mixture ratio 1:1, 1:2, 2:1. The result of the research showed that the best voltage of bacteria concentration was 12.5% for Eschericia coli and Shewanella oneidensis bacteria, which were 847 mV and 988 mV, and for the mixed bacteria variable was 1:2 ratio with the voltage was 1261 mV. For 12 days, the largest percentage of the decrease of BOD5 was 12.5% Eschericia coli bacteria concentration variable reached 84.531% and 17.5% Shewanella oneidensis was 73.779%. The best Fe3+ reduction was 53.52% for Escherichia coli at 10% concentration (v/v), and for Shewanella oneidensis bacteria reached out of 62.22% at 15% concentration (v/v). In the variable with mixed bacteria was obtained the best reduction result on the ratio of Eschericia coli : Shewanella oneidensis 1:2 was 77,44%.

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

PubMed Central

Wu, Stephen Gang; Wang, Yuxuan; Jiang, Wu; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie J.; Bao, Forrest Sheng

2016-01-01

13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species. PMID:27092947

Role of Outer Membrane C-Type Cytochromes MtrC and OmcA in Shewanella Oneidensis MR-1 Cell Production, Accumulation, and Detachment During Respiration on Hematite

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

Mitchell, Andrew C.; Peterson, L.; Reardon, Catherine L.

2012-07-01

Solid phase iron oxides are considered to be important terminal electron acceptors for microbial respiration in many anoxic environments. Besides the knowledge that cells attach to and reduce these substrates, other aspects of surface-associated cell behavior and the related cell surface components that influence cell-mineral interactions are not well understood. In the present study, wild-type cells of the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1 formed thin biofilms one-to-two cell layers in thickness when respiring on natural specular hematite under flow conditions similar to those which exist in aquatic sediments and subsurface environments. The distribution of cells within the biofilm indicatedmore » that direct contact was not required for electron transfer from cells to the mineral surface. Detached biomass in the form of single cells represented >99% of the surface-associated wild-type cell production from respiration on hematite over the biofilm life cycle. A mutant deficient in the outer membrane c35 type cytochrome OmcA, while still able to respire and replicate on hematite, established a lower steady-state cell density on the mineral surface than that of the wild-type strain. A mutant deficient in MtrC, another outer membrane c-type cytochrome, and a mutant deficient in both cytochromes were unable to reduce sufficient amounts of hematite to support detectable growth on the mineral surface. When considered in the context of previous work, the results support a growing body of evidence that the relative importance of OmcA and MtrC to cell respiration and replication depends on the form of iron oxide available as terminal electron acceptor.« less

Natural isotope correction of MS/MS measurements for metabolomics and (13)C fluxomics.

PubMed

Niedenführ, Sebastian; ten Pierick, Angela; van Dam, Patricia T N; Suarez-Mendez, Camilo A; Nöh, Katharina; Wahl, S Aljoscha

2016-05-01

Fluxomics and metabolomics are crucial tools for metabolic engineering and biomedical analysis to determine the in vivo cellular state. Especially, the application of (13)C isotopes allows comprehensive insights into the functional operation of cellular metabolism. Compared to single MS, tandem mass spectrometry (MS/MS) provides more detailed and accurate measurements of the metabolite enrichment patterns (tandem mass isotopomers), increasing the accuracy of metabolite concentration measurements and metabolic flux estimation. MS-type data from isotope labeling experiments is biased by naturally occurring stable isotopes (C, H, N, O, etc.). In particular, GC-MS(/MS) requires derivatization for the usually non-volatile intracellular metabolites introducing additional natural isotopes leading to measurements that do not directly represent the carbon labeling distribution. To make full use of LC- and GC-MS/MS mass isotopomer measurements, the influence of natural isotopes has to be eliminated (corrected). Our correction approach is analyzed for the two most common applications; (13)C fluxomics and isotope dilution mass spectrometry (IDMS) based metabolomics. Natural isotopes can have an impact on the calculated flux distribution which strongly depends on the substrate labeling and the actual flux distribution. Second, we show that in IDMS based metabolomics natural isotopes lead to underestimated concentrations that can and should be corrected with a nonlinear calibration. Our simulations indicate that the correction for natural abundance in isotope based fluxomics and quantitative metabolomics is essential for correct data interpretation. © 2015 Wiley Periodicals, Inc.

Iodate Reduction by Shewanella oneidensis Does Not Involve Nitrate Reductase

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

Mok, Jung Kee; Toporek, Yael J.; Shin, Hyun-Dong

Microbial iodate (IO 3 -) reduction is a major component of the iodine biogeochemical reaction network and is the basis of alternative strategies for remediation of iodine-contaminated environments. The molecular mechanism of microbial IO 3 - reduction, however, is not well understood. In microorganisms displaying IO 3 - and nitrate (NO 3 -) reduction activities, NO 3 - reductase is postulated to reduce IO 3 - as alternate electron acceptor. In the present study, whole genome analyses of 25 NO 3 --reducing Shewanella strains identified various combinations of genes encoding one assimilatory (cytoplasmic Nas) and three dissimilatory (membrane-associated Nar andmore » periplasmic Napα and Napβ) NO 3 - reductases. S. oneidensis was the only Shewanella strain whose genome encoded a single NO 3 - reductase (Napβ). Terminal electron acceptor competition experiments in S. oneidensis batch cultures amended with both NO 3 - and IO 3 - demonstrated that neither NO 3 - nor IO 3 - reduction activities were competitively inhibited by the presence of the competing electron acceptor. The lack of involvement of S. oneidensis Napβ in IO 3 - reduction was confirmed via phenotypic analysis of an in-frame gene deletion mutant lacking napβΑ (encoding the NO 3 --reducing NapβA catalytic subunit). S. oneidensis ΔnapβA was unable to reduce NO 3 -, yet reduced IO 3 - at rates higher than the wild-type strain. Thus, NapβA is required for dissimilatory NO 3 - reduction by S. oneidensis, while neither the assimilatory (Nas) nor dissimilatory (Napα, Napβ, and Nar) NO 3 - reductases are required for IO 3 - reduction. These findings oppose the traditional view that NO 3 - reductase reduces IO 3 - as alternate electron acceptor and indicate that S. oneidensis reduces IO 3 - via an as yet undiscovered enzymatic mechanism.« less

Effect of biofilm coatings at metal-oxide/water interfaces I: Pb(II) and Zn(II) partitioning and speciation at Shewanella oneidensis/metal-oxide/water interfaces

NASA Astrophysics Data System (ADS)

Wang, Yingge; Gélabert, Alexandre; Michel, F. Marc; Choi, Yongseong; Gescher, Johannes; Ona-Nguema, Georges; Eng, Peter J.; Bargar, John R.; Farges, Francois; Spormann, Alfred M.; Brown, Gordon E.

2016-09-01

Microbial biofilms are often present as coatings on metal-oxide surfaces in natural and industrial environments and may induce significant changes in the partitioning behavior and speciation of aqueous metal ions, which in turn can impact their transport and fate. In this study, long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy was used to measure under in situ conditions the partitioning of aqueous Pb(II) and Zn(II) between multilayer Shewanella oneidensis MR-1 biofilms and highly polished, oriented single-crystal surfaces of α-Al2O3 and α-Fe2O3 as a function of metal-ion concentration and time at pH 6.0. We show that after 3-h exposure time, Pb(II) binds preferentially to the α-Al2O3 (1-102) and α-Fe2O3 (0 0 0 1) surfaces at low Pb concentration ([Pb] = 10-7 M) and then increasingly partitions into the biofilm coatings at higher concentrations (10-6 to 10-4 M). In contrast, Zn(II) partitions preferentially into the biofilm coating for both surfaces at all Zn concentrations studied (10-7 to 10-4 M). In comparison, the α-Al2O3 (0 0 0 1) surface has a low affinity for both Pb(II) and Zn(II), and the biofilm coatings are the dominant sink for both ions. These findings suggest that in the presence of S. oneidensis biofilm coatings, α-Al2O3 (0 0 0 1) is the least reactive surface for Pb(II) and Zn(II) compared to α-Al2O3 (1-102) and α-Fe2O3 (0 0 0 1). They also show that Zn(II) has a lower affinity than Pb(II) for reactive sites on α-Al2O3 (1-102) and α-Fe2O3 (0 0 0 1) at [Me(II)] of 10-7 M; at 10-5 M, the bulk of the metal ions partition into the biofilm coatings. At longer exposure times (20-24 h), both Pb(II) and Zn(II) increasingly partition to the metal-oxide surfaces at [Me(II)] = 10-5 M and pH 6.0, indicating possible reaction/diffusion-controlled sorption processes. Pb LIII-edge and Zn K-edge grazing-incidence extended X-ray absorption fine structure (GI-EXAFS) measurements suggest that both Pb(II) and Zn(II) ions may be

Aerated Shewanella oneidensis in Continuously-fed Bioelectrochemical Systems for Power and Hydrogen Production

USDA-ARS?s Scientific Manuscript database

We studied the effects of aeration of Shewanella oneidensis on potentiostatic current production, iron(III) reduction, hydrogen production in a microbial electrolysis cell, and electric power generation in a microbial fuel cell. The potentiostatic performance of aerated S. oneidensis was considerab...

Effect of biofilm coatings at metal-oxide/water interfaces I: Pb(II) and Zn(II) partitioning and speciation at Shewanella oneidensis/metal-oxide/water interfaces

DOE PAGES

Wang, Yingge; Gelabert, Alexandre; Michel, F. Marc; ...

2016-05-30

Microbial biofilms are often present as coatings on metal-oxide surfaces in natural and industrial environments and may induce significant changes in the partitioning behavior and speciation of aqueous metal ions, which in turn can impact their transport and fate. In this study, long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy was used to measure under in situ conditions the partitioning of aqueous Pb(II) and Zn(II) between multilayer Shewanella oneidensis MR-1 biofilms and highly polished, oriented single-crystal surfaces of α-Al 2O 3 and α-Fe 2O 3 as a function of metal-ion concentration and time at pH 6.0. We show that after 3-hmore » exposure time, Pb(II) binds preferentially to the alpha-Al 2O 3 (1-102) and α-Fe 2O 3 (0001) surfaces at low Pb concentration ([Pb] = 10 –7 M) and then increasingly partitions into the biofilm coatings at higher concentrations (10 –6 to 10 –4 M). In contrast, Zn(II) partitions preferentially into the biofilm coating for both surfaces at all Zn concentrations studied (10 –7 to 10 –4 M). In comparison, the α-Al 2O 3 (0001) surface has a low affinity for both Pb(II) and Zn(II), and the biofilm coatings are the dominant sink for both ions. These findings suggest that in the presence of S. oneidensis biofilm coatings, α-Al 2O 3 (0001) is the least reactive surface for Pb(II) and Zn(II) compared to α-Al 2O 3 (1-102) and α-Fe 2O 3 (0001). They also show that Zn(II) has a lower affinity than Pb(II) for reactive sites on α-Al 2O 3 (1-102) and α-Fe 2O 3 (0001) at [Me(II)] of 10 –7 M; at 10 –5 M, the bulk of the metal ions partition into the biofilm coatings. At longer exposure times (20-24 h), both Pb(II) and Zn(II) increasingly partition to the metal-oxide surfaces at [Me(II)] = 10 –5 M and pH 6.0, indicating possible reaction/diffusion-controlled sorption processes. Pb L-III-edge and Zn K-edge grazing-incidence extended X-ray absorption fine structure (GI-EXAFS) measurements suggest

Effect of oxygen on the per‐cell extracellular electron transfer rate of Shewanella oneidensis MR‐1 explored in bioelectrochemical systems

PubMed Central

Lu, Mengqian; Chan, Shirley; Babanova, Sofia

2016-01-01

ABSTRACT Extracellular electron transfer (EET) is a mechanism that enables microbes to respire solid‐phase electron acceptors. These EET reactions most often occur in the absence of oxygen, since oxygen can act as a competitive electron acceptor for many facultative microbes. However, for Shewanella oneidensis MR‐1, oxygen may increase biomass development, which could result in an overall increase in EET activity. Here, we studied the effect of oxygen on S. oneidensis MR‐1 EET rates using bioelectrochemical systems (BESs). We utilized optically accessible BESs to monitor real‐time biomass growth, and studied the per‐cell EET rate as a function of oxygen and riboflavin concentrations in BESs of different design and operational conditions. Our results show that oxygen exposure promotes biomass development on the electrode, but significantly impairs per‐cell EET rates even though current production does not always decrease with oxygen exposure. Additionally, our results indicated that oxygen can affect the role of riboflavin in EET. Under anaerobic conditions, both current density and per‐cell EET rate increase with the riboflavin concentration. However, as the dissolved oxygen (DO) value increased to 0.42 mg/L, riboflavin showed very limited enhancement on per‐cell EET rate and current generation. Since it is known that oxygen can promote flavins secretion in S. oneidensis, the role of riboflavin may change under anaerobic and aerobic conditions. Biotechnol. Bioeng. 2017;114: 96–105. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:27399911

Evolution of Cell Size Homeostasis and Growth Rate Diversity during Initial Surface Colonization of Shewanella oneidensis.

PubMed

Lee, Calvin K; Kim, Alexander J; Santos, Giancarlo S; Lai, Peter Y; Lee, Stella Y; Qiao, David F; Anda, Jaime De; Young, Thomas D; Chen, Yujie; Rowe, Annette R; Nealson, Kenneth H; Weiss, Paul S; Wong, Gerard C L

2016-09-06

Cell size control and homeostasis are fundamental features of bacterial metabolism. Recent work suggests that cells add a constant size between birth and division ("adder" model). However, it is not known how cell size homeostasis is influenced by the existence of heterogeneous microenvironments, such as those during biofilm formation. Shewanella oneidensis MR-1 can use diverse energy sources on a range of surfaces via extracellular electron transport (EET), which can impact growth, metabolism, and size diversity. Here, we track bacterial surface communities at single-cell resolution to show that not only do bacterial motility appendages influence the transition from two- to three-dimensional biofilm growth and control postdivisional cell fates, they strongly impact cell size homeostasis. For every generation, we find that the average growth rate for cells that stay on the surface and continue to divide (nondetaching population) and that for cells that detach before their next division (detaching population) are roughly constant. However, the growth rate distribution is narrow for the nondetaching population, but broad for the detaching population in each generation. Interestingly, the appendage deletion mutants (ΔpilA, ΔmshA-D, Δflg) have significantly broader growth rate distributions than that of the wild type for both detaching and nondetaching populations, which suggests that Shewanella appendages are important for sensing and integrating environmental inputs that contribute to size homeostasis. Moreover, our results suggest multiplexing of appendages for sensing and motility functions contributes to cell size dysregulation. These results can potentially provide a framework for generating metabolic diversity in S. oneidensis populations to optimize EET in heterogeneous environments.

Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.

PubMed

Baym, Michael; Shaket, Lev; Anzai, Isao A; Adesina, Oluwakemi; Barstow, Buz

2016-11-10

Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction and purification of a curated whole-genome collection of single-gene transposon disruption mutants termed Knockout Sudoku. Using simple combinatorial pooling, a highly oversampled collection of mutants is condensed into a next-generation sequencing library in a single day, a 30- to 100-fold improvement over prior methods. The identities of the mutants in the collection are then solved by a probabilistic algorithm that uses internal self-consistency within the sequencing data set, followed by rapid algorithmically guided condensation to a minimal representative set of mutants, validation, and curation. Starting from a progenitor collection of 39,918 mutants, we compile a quality-controlled knockout collection of the electroactive microbe Shewanella oneidensis MR-1 containing representatives for 3,667 genes that is functionally validated by high-throughput kinetic measurements of quinone reduction.

Oxygen exposure promotes fuel diversity for Shewanella oneidensis microbial fuel cells.

PubMed

Biffinger, Justin C; Byrd, Jacqueline N; Dudley, Breanna L; Ringeisen, Bradley R

2008-01-18

Miniature microbial fuel cells (mini-MFCs) were used to monitor the current generated by Shewanella oneidensis DSP10 under both anaerobic and aerobic conditions when exposed to glucose as a potential electron donor. In addition to glucose, other carbon fuels including fructose, sucrose, acetate, and ascorbic acid were also tested. When the anolyte containing S. oneidensis was grown in the presence of oxygen, power densities of 270+/-10, 350+/-20, and 120+/-10 W/m(3) were recorded from the mini-MFC for glucose, fructose, and ascorbic acid electron donors, respectively, while sucrose and acetate produced no response. The power produced from glucose decreased considerably (oneidensis, this reduction in power output is most likely due to the differential expression of proteins by these bacteria when grown under oxygen-rich or anoxic conditions. The power densities generated from the mini-MFC exposed to oxygen led to significant changes in current production over time with repeated feedings of these carbon nutrients. This work expands the breadth of potential electron donors for S. oneidensis MFCs and demonstrates the importance of studying microbial anolytes under diverse environmental conditions.

Synthetic Klebsiella pneumoniae-Shewanella oneidensis Consortium Enables Glycerol-Fed High-Performance Microbial Fuel Cells.

PubMed

Li, Feng; Yin, Changji; Sun, Liming; Li, Yuanxiu; Guo, Xuewu; Song, Hao

2018-05-01

Microbial fuel cell (MFC) is an eco-friendly bio-electrochemical sys-tem that uses microorganism as biocatalyst to convert biomass into electricity. Glycerol, as a waste in the biodiesel refinery processes, is an appealing substrate for MFC. Nevertheless, glycerol cannot be utilized as carbon source by well-known exoelectrogens such as Shewanella oneidensis. Herein, to generate electricity by rapidly harnessing glycerol, the authors rationally constructed a Klebsiella pneumoniae-Shewanella oneidensis microbial consortium to efficiently harvest electricity from glyc-erol, in which K. pneumoniae converted glycerol into lactate, fed to S. oneidensis as carbon source and electron donor. To improve electricity output, the authors systematically engineered the consortium in terms of carbon flux distribution and efficiency of extracellular electron transfer (EET). To direct more carbon flux to lactate biosynthesis in K. pneumoniae, the authors eliminated the ethanol pathway by knocking out the alcohol dehydrogenase gene (adhE), and enhanced lactate biosynthesis by heterologously expressing a lactate dehydrogen-ase gene (ldhD) from Lactobacillus bulgaricus and a lactate transporter gene (lldP) from Escherichia coli. To facilitate EET between S. oneidensis and anode surfaces, a biosynthetic flavins pathway from Bacillus subtilis is introduced into S. oneidensis. The author further optimized the glycerol concentration, thus S. oneidensis could be continuously fed with lactate synthesized from K. pneumoniae at a constant rate. Our glycerol-fed MFC generated a maximum power density of 19.9 mW/m 2 , significantly higher than that of the wild-type consor-tium. This work suggested that engineering microbial consortia is an effi-cient strategy to expand the spectrum of usable carbon sources and promote electricity power production in MFCs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deletion of degQ gene enhances outer membrane vesicle production of Shewanella oneidensis cells.

PubMed

Ojima, Yoshihiro; Mohanadas, Thivagaran; Kitamura, Kosei; Nunogami, Shota; Yajima, Reiki; Taya, Masahito

2017-04-01

Shewanella oneidensis is a Gram-negative facultative anaerobe that can use a wide variety of terminal electron acceptors for anaerobic respiration. In this study, S. oneidensis degQ gene, encoding a putative periplasmic serine protease, was cloned and expressed. The activity of purified DegQ was inhibited by diisopropyl fluorophosphate, a typical serine protease-specific inhibitor, indicating that DegQ is a serine protease. In-frame deletion and subsequent complementation of the degQ were carried out to examine the effect of envelope stress on the production of outer membrane vesicles (OMVs). Analysis of periplasmic proteins from the resulting S. oneidensis strain showed that deletion of degQ induced protein accumulation and resulted in a significant decrease in protease activity within the periplasmic space. OMVs from the wild-type and mutant strains were purified and observed by transmission electron microscopy. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the OMVs showed a prominent band at ~37 kDa. Nanoliquid chromatography-tandem mass spectrometry analysis identified three outer membrane porins (SO3896, SO1821, and SO3545) as dominant components of the band, suggesting that these proteins could be used as indices for comparing OMV production by S. oneidensis strains. Quantitative evaluation showed that degQ-deficient cells had a fivefold increase in OMV production compared with wild-type cells. Thus, the increased OMV production following the deletion of DegQ in S. oneidensis may be responsible for the increase in envelope stress.

c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis

PubMed Central

Marshall, Matthew J; Dohnalkova, Alice C; Kennedy, David W; Shi, Liang; Wang, Zheming; Boyanov, Maxim I; Lai, Barry; Kemner, Kenneth M; McLean, Jeffrey S; Reed, Samantha B; Culley, David E; Bailey, Vanessa L; Simonson, Cody J; Saffarini, Daad A; Romine, Margaret F; Zachara, John M

2006-01-01

Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, are essential for the reduction of U(VI) and formation of extracelluar UO 2 nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC (metal reduction), previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild-type MR-1. Similar to the wild-type, the mutants accumulated UO 2 nanoparticles extracellularly to high densities in association with an extracellular polymeric substance (EPS). In wild-type cells, this UO 2-EPS matrix exhibited glycocalyx-like properties and contained multiple elements of the OM, polysaccharide, and heme-containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high-resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO 2 nanoparticles with MtrC and OmcA (outer membrane cytochrome). This is the first study to our knowledge to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO 2 nanoparticles. In the environment, such association of UO 2 nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O 2 or transport in soils and sediments. PMID:16875436

Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes

PubMed Central

Shi, Liang; Squier, Thomas C; Zachara, John M; Fredrickson, James K

2007-01-01

Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram-negative bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c-type cytochromes (c-Cyts). In S. oneidensis MR-1, multihaem c-Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR-1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c-Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c-Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c-Cyts play critical roles in S. oneidensis MR-1- and G. sulfurreducens-mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope. PMID:17581116

Laue Crystal Structure of Shewanella oneidensis Cytochrome c Nitrite Reductase from a High-yield Expression System

PubMed Central

Youngblut, Matthew; Judd, Evan T.; Srajer, Vukica; Sayyed, Bilal; Goelzer, Tyler; Elliott, Sean J.; Schmidt, Marius; Pacheco, A. Andrew

2012-01-01

The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR), and its characterization by a variety of methods, notably Laue crystallography, is reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein “Small Tetra-heme c” replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated ~20 mg crude ccNiR/L culture, compared with 0.5–1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for E. coli ccNiR, and is stable for over two weeks in pH 7 solution at 4° C. UV/Vis spectropotentiometric titrations and protein film voltammetry identified 5 independent 1-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the 5 reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed amongst the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good quality crystals, with which the 2.59 Å resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein). PMID:22382353

Microbial Reduction and Precipitation of Vanadium by Shewanella oneidensis

PubMed Central

Carpentier, W.; Sandra, K.; De Smet, I.; Brigé, A.; De Smet, L.; Van Beeumen, J.

2003-01-01

Shewanella oneidensis couples anaerobic oxidation of lactate, formate, and pyruvate to the reduction of vanadium pentoxide (VV). The bacterium reduces VV (vanadate ion) to VIV (vanadyl ion) in an anaerobic atmosphere. The resulting vanadyl ion precipitates as a VIV-containing solid. PMID:12788772

Contribution of direct electron transfer mechanisms to overall electron transfer in microbial fuel cells utilising Shewanella oneidensis as biocatalyst.

PubMed

Fapetu, Segun; Keshavarz, Taj; Clements, Mark; Kyazze, Godfrey

2016-09-01

To investigate the contribution of direct electron transfer mechanisms to electricity production in microbial fuel cells by physically retaining Shewanella oneidensis cells close to or away from the anode electrode. A maximum power output of 114 ± 6 mWm(-2) was obtained when cells were retained close to the anode using a dialysis membrane. This was 3.5 times more than when the cells were separated away from the anode. Without the membrane the maximum power output was 129 ± 6 mWm(-2). The direct mechanisms of electron transfer contributed significantly to overall electron transfer from S. oneidensis to electrodes, a result that was corroborated by another experiment where S. oneidensis cells were entrapped in alginate gels. S. oneidensis transfers electrons primarily by direct electron transfer as opposed to mediated electron transfer.

Particle size effect and the mechanism of hematite reduction by the outer membrane cytochrome OmcA of Shewanella oneidensis MR-1

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

Liu, Juan; Pearce, Carolyn I.; Shi, Liang

The cycling of iron at the Earth’s near surface is profoundly influenced by dissimilatory metal reducing microorganisms, and many studies have focused on unraveling electron transfer mechanisms between these bacteria and Fe(III)-(oxyhydr)oxides. However, these efforts have been complicated by the fact that these minerals often occur in the micro- to nanosize regime, and in relevant natural environments as well as in the laboratory are subject to aggregation. The nature of the physical interface between the cellular envelope, the outer-membrane cytochromes responsible for facilitating the interfacial electron transfer step, and these complex mineral particulates is thus difficult to probe. Previous studiesmore » using whole cells have reported reduction rates that do not correlate with particle size. In the present study we isolate the interaction between the decaheme outer-membrane cytochrome OmcA of Shewanella oneidensis and nanoparticulate hematite, examining the reduction rate as a function of particle size and reaction products through detailed characterization of the electron balance and the structure and valence of iron at particle surfaces. By comparison with abiotic reduction via the smaller molecule ascorbic acid, we show that the reduction rate is systematically controlled by the sterically accessible interfacial contact area between OmcA and hematite in particle aggregates; rates increase once pore throat sizes in aggregates become as large as OmcA. Simultaneous measure of OmcA oxidation against Fe(II) release shows a ratio of 1:10, consistent with a cascade OmcA oxidation mechanism heme by heme. X-ray absorption spectroscopies reveal incipient magnetite on the reacted surfaces of the hematite nanoparticles after reaction. The collective findings establish the importance of accessibility of physical contact between the terminal reductases and iron oxide surfaces, and through apparent consistency of observations help reconcile behavior reported at the

Particle size effect and the mechanism of hematite reduction by the outer membrane cytochrome OmcA of Shewanella oneidensis MR-1

NASA Astrophysics Data System (ADS)

Liu, Juan; Pearce, Carolyn I.; Shi, Liang; Wang, Zheming; Shi, Zhi; Arenholz, Elke; Rosso, Kevin M.

2016-11-01

The cycling of iron at the Earth's near surface is profoundly influenced by dissimilatory metal reducing microorganisms, and many studies have focused on unraveling electron transfer mechanisms between these bacteria and Fe(III)-(oxyhydr)oxides. However, these efforts have been complicated by the fact that these minerals often occur in the micro- to nanosize regime, and in relevant natural environments as well as in the laboratory are subject to aggregation. The nature of the physical interface between the cellular envelope, the outer-membrane cytochromes responsible for facilitating the interfacial electron transfer step, and these complex mineral particulates is thus difficult to probe. Previous studies using whole cells have reported reduction rates that do not correlate with particle size. In the present study we isolate the interaction between the decaheme outer-membrane cytochrome OmcA of Shewanella oneidensis and nanoparticulate hematite, examining the reduction rate as a function of particle size and reaction products through detailed characterization of the electron balance and the structure and valence of iron at particle surfaces. By comparison with abiotic reduction via the smaller molecule ascorbic acid, we show that the reduction rate is systematically controlled by the sterically accessible interfacial contact area between OmcA and hematite in particle aggregates; rates increase once pore throat sizes in aggregates become as large as OmcA. Simultaneous measure of OmcA oxidation against Fe(II) release shows a ratio of 1:10, consistent with a cascade OmcA oxidation mechanism heme by heme. X-ray absorption spectroscopies reveal incipient magnetite on the reacted surfaces of the hematite nanoparticles after reaction. The collective findings establish the importance of accessibility of physical contact between the terminal reductases and iron oxide surfaces, and through apparent consistency of observations help reconcile behavior reported at the larger

PBP1a/LpoA but Not PBP1b/LpoB Are Involved in Regulation of the Major β-Lactamase Gene blaA in Shewanella oneidensis

PubMed Central

Yin, Jianhua; Sun, Yiyang; Mao, Yinting; Jin, Miao

2015-01-01

β-Lactamase production is one of the most important strategies for Gram-negative bacteria to combat β-lactam antibiotics. Studies of the regulation of β-lactamase expression have largely been focused on the class C β-lactamase AmpC, whose induction by β-lactams requires LysR-type regulator AmpR and permease AmpG-dependent peptidoglycan recycling intermediates. In Shewanella, which is ubiquitous in aquatic environments and is a reservoir for antibiotic resistance, production of the class D β-lactamase BlaA confers bacteria with natural resistance to many β-lactams. Expression of the blaA gene in the genus representative Shewanella oneidensis is distinct from the AmpC paradigm because of the lack of an AmpR homologue and the presence of an additional AmpG-independent regulatory pathway. In this study, using transposon mutagenesis, we identify proteins that are involved in blaA regulation. Inactivation of mrcA and lpoA, which encode penicillin binding protein 1a (PBP1a) and its lipoprotein cofactor, LpoA, respectively, drastically enhances blaA expression in the absence of β-lactams. Although PBP1b and its cognate, LpoB, also exist in S. oneidensis, their roles in blaA induction are dispensable. We further show that the mrcA-mediated blaA expression is independent of AmpG. PMID:25824223

Metabolic Profiling Directly from the Petri Dish Using Nanospray Desorption Electrospray Ionization Imaging Mass Spectrometry

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

Watrous, Jeramie D.; Roach, Patrick J.; Heath, Brandi S.

2013-11-05

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1,more » Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.« less

Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle.

PubMed

Ahn, Eunyong; Kumar, Praveen; Mukha, Dzmitry; Tzur, Amit; Shlomi, Tomer

2017-11-06

Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal-fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse-chase LC-MS-based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling. We find that TCA cycle fluxes are rewired as cells progress through the cell cycle with complementary oscillations of glucose versus glutamine-derived fluxes: Oxidation of glucose-derived flux peaks in late G1 phase, while oxidative and reductive glutamine metabolism dominates S phase. These complementary flux oscillations maintain a constant production rate of reducing equivalents and oxidative phosphorylation flux throughout the cell cycle. The shift from glucose to glutamine oxidation in S phase plays an important role in cell cycle progression and cell proliferation. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Myofibrillogenesis regulator 1 (MR-1): a potential therapeutic target for cancer and PNKD.

PubMed

Wang, Junxia; Zhao, Wuli; Liu, Hong; He, Hongwei; Shao, Rongguang

2017-11-15

Human myofibrillogenesis regulator 1 (MR-1) is a functional gene also known as paroxysmal nonkinesigenic dyskinesia (PNKD). It is localised on human chromosome 2q35 and three different isomers, MR-1L, MR-1M and MR-1S, are formed by alternative splicing. MR-1S promotes cardiac hypertrophy and is closely related to cancer. MR-1S is overexpressed in haematologic and solid malignancies, such as hepatoma, breast cancer and chronic myelogenous leukaemia. MR-1S causes disordered cell differentiation, initiates malignant transformation and accelerates metastasis. MR-1S directly phosphorylates and activates the MEK-ERK-RSK pathway to accelerate cancer growth and facilitates metastasis by activating the MLC2-FAK-AKT pathway. Silencing MR-1 inhibits cancer cell proliferation and metastasis. MR-1S causes disordered cell differentiation, initiates malignant transformation and accelerates metastasis. MR-1 interacts with eukaryotic translation initiation factors and MRIP-1, which contains Ras GTPase, PH and zinc-containing ArfGap domains, as well as three ankyrin repeats. Mutations in the N-terminal region of MR-1L and MR-1S are the main causes of PNKD (a hereditary disease characterised by paroxysmal dystonic choreoathetosis) and targeting the mutated protein could provide symptomatic relief. These findings provide compelling evidence that MR-1 might be a diagnostic marker and therapeutic target for solid tumours, myelogenous leukaemia and PNKD.

Surface display of roGFP for monitoring redox status of extracellular microenvironments in Shewanella oneidensis biofilms.

PubMed

Sivakumar, Krishnakumar; Mukherjee, Manisha; Cheng, Hsin-I; Zhang, Yingdan; Ji, Lianghui; Cao, Bin

2015-03-01

Biofilms are the most ubiquitous and resilient form of microbial life on earth. One most important feature of a biofilm is the presence of a self-produced matrix, which creates highly heterogeneous and dynamic microenvironments within biofilms. Redox status in biofilm microenvironments plays a critical role in biofilm development and function. However, there is a lack of non-intrusive tools to quantify extracellular redox status of microenvironments within a biofilm matrix. In this study, using Shewanella oneidensis as a model organism, we demonstrated a novel approach to monitor extracellular redox status in biofilm microenvironments. Specifically, we displayed a redox sensitive fluorescence protein roGFP onto the cell surface of S. oneidensis by fusing it to the C-terminus of BpfA, a large surface protein, and used the surface displayed roGFP as a sensor to quantify the extracellular redox status in the matrix of S. oneidensis biofilms. The fusion of roGFP into BpfA has no negative impacts on cell growth and biofilm formation. Upon exposure to oxidizing agents such as H2 O2 , Ag(+) , and SeO3 (2-) , S. oneidensis BpfA-roGFP cells exhibited a characteristic fluorescence of roGFP. Proteinase treatment assay and super-resolution structured illumination microscopy confirmed the surface localization of BpfA-roGFP. We further used the surface displayed roGFP monitored the extracellular redox status in the matrix at different depths of a biofilm exposed to H2 O2 . This study provides a novel approach to non-invasively monitor extracellular redox status in microenvironments within biofilms, which can be used to understand redox responses of biofilms to environmental perturbations. © 2014 Wiley Periodicals, Inc.

Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms: Characterization by Infrared Spectroscopy and Proteomics

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

Cao, Bin; Shi, Liang; Brown, Roslyn N.

This study characterizes the composition of extracellular polymeric substances (EPS) from Shewanella sp. HRCR-1 biofilms to provide insight into potential interactions of EPS with redox-active metals and radionuclides. Both bound and loosely associated EPS were extracted from Shewanella sp. HRCR-1 biofilms prepared using a hollow-fiber membrane biofilm reactor (HfMBR). FTIR spectra revealed the presence of proteins, polysaccharides, nucleic acids, membrane lipids, and fatty acids in both bound and loosely associated EPS. Using a global proteomic approach, a total of 58 extracellular and outer membrane proteins were identified in the EPS. These included homologues of multiple S. oneidensis MR-1 proteins thatmore » potentially contribute to key physiological biofilm processes, such as biofilm-promoting protein BpfA, surface-associated serine protease, nucleotidases (CpdB and UshA), an extracellular lipase, and oligopeptidases (PtrB and a M13 family oligopeptidase lipoprotein). In addition, 20 redox proteins were found in extracted EPS. Among the detected redox proteins were the homologues of two S. oneidensis MR-1 c-type cytochromes, MtrC and OmcA, which have been implicated in extracellular electron transfer. Given their detection in the EPS of Shewanella sp. HRCR 1 biofilms, c-type cytochromes may contribute to the possible redox activity of the biofilm matrix and play important roles in extracellular electron transfer reactions.« less

Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation

PubMed Central

Li, Xiaoping; Schilkey, Faye; Smith, Geoffrey B.

2018-01-01

Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72.1 to 0.9 nGy h-1 from control to treatment, respectively. RNASeq transcriptome analysis showed the differential expression of 4.6 and 7.6% of the S. oneidensis genome during early- and late-exponential phases of growth, respectively. The greatest change observed in the treatment was the downregulation of ribosomal proteins (21% of all annotated ribosomal protein genes during early- and 14% during late-exponential) and tRNA genes (14% of all annotated tRNA genes in early-exponential), indicating a marked decrease in protein translation. Other significant changes were the upregulation of membrane transporters, implying an increase in the traffic of substrates across the cell membrane, as well as the up and downregulation of genes related to respiration, which could be interpreted as a response to insufficient oxidants in the cells. In other reports, there is evidence in multiple species that some ROS not just lead to oxidative stress, but act as signaling molecules to control cellular metabolism at the transcriptional level. Consistent with these reports, several genes involved in the metabolism of carbon and biosynthesis of amino acids were also regulated, lending support to the idea of a wide metabolic response. Our results indicate that S. oneidensis is sensitive to the withdrawal of background levels of ionizing radiation and suggest that a transcriptional response is required to maintain homeostasis and retain normal growth. PMID:29768440

Dehydrochlorination of 1,1,1-trichloroethane and pentachloroethane by microbially reduced ferruginous smectite.

PubMed

Cervini-Silva, Javiera; Kostka, Joel E; Larson, Richard A; Stucki, Joseph W; Wu, Jun

2003-05-01

Reduction of structural Fe(III) in smectite clay minerals has been identified as a means to promote dechlorination of polychlorinated ethanes, but its environmental significance has yet to be fully assessed because Fe reduction has normally been achieved by agents uncommon in the environment (e.g., dithionite). This study reports the dehydrochlorination of pentachloroethane and 1,1,1-trichloroethane in the presence of ferruginous smectite reduced by two cultures of microorganisms, Shewanella oneidensis strain MR-1 (MR-R) and an enrichment culture from rice paddy soils (PS-R), in aqueous suspension under anoxic conditions. Microbially reduced ferruginous smectite facilitated dehydrochlorination of 1,1,1-trichloroethane to 1,1-dichloroethene with up to 60% conversion within 3 h of incubation time. In contrast, no formation of 1,1-dichloroethene was observed after incubation of 1,1,1-trichloroethane with chemically reduced ferruginous smectite for 24 h. Microbially reduced ferruginous smectite by MR-R and PS-R promoted the dehydrochlorination of pentachloroethane to tetrachloroethene by 80 and 15%, respectively, after 3 h of incubation time. The conversion of pentachloroethane to tetrachloroethene in the presence of chemically reduced ferruginous smectite after 24 h was 65%. These results indicate that structural Fe(II) in clay minerals has the potential to be an important reductant controlling the fate of organic chemicals in contaminated sediments.

Effect of biofilm coatings at metal-oxide/water interfaces II: Competitive sorption between Pb(II) and Zn(II) at Shewanella oneidensis/metal-oxide/water interfaces

DOE PAGES

Wang, Yingge; Gelabert, Alexandre; Michel, F. Marc; ...

2016-05-07

Competitive sorption of Pb(II) and Zn(II) on Shewanella oneidensis MR-1 biofilm-coated single-crystal α-Al 2O 3 (1 –1 0 2) and α-Fe 2O 3 (0 0 0 1) surfaces was investigated using long-period X-ray standing wave-florescence yield (LP-XSW-FY) spectroscopy. In situ partitioning of aqueous Pb(II) and Zn(II) between the biofilms and underlying metal-oxide substrates was probed following exposure of these complex interfaces to equi-molar Pb and Zn solutions (0.01 M NaNO 3 as background electrolyte, pH = 6.0, and 3-h equilibration time). At higher Pb and Zn concentrations (≥10 –5 M), more than 99% of these ions partitioned into the biofilmsmore » at S. oneidensis/α-Al 2O 3 (1 –1 0 2)/water interfaces, which is consistent with the partitioning behavior of both Pb(II) or Zn(II) in single-metal-ion experiments. Furthermore, no apparent competitive effects were found in this system at these relatively high metal-ion concentrations. However, at lower equi-molar concentrations (≤10 –6 M), Pb(II) and Zn(II) partitioning in the same system changed significantly compared to the single-metal-ion systems. The presence of Zn(II) decreased Pb(II) partitioning onto α-Al 2O 3 (1 –1 0 2) substantially (~52% to ~13% at 10 –7 M, and ~23% to ~5% at 10–6 M), whereas the presence of Pb(II) caused more Zn(II) to partition onto α-Al 2O 3 (1 –1 0 2) surfaces (~15% to ~28% at 10 –7 M, and ~1% to ~7% at 10 –6 M) .The higher observed partitioning of Zn(II) (~28%) at the α-Al 2O 3 (1 –1 0 2) surfaces compared to Pb(II) (~13%) in the mixed-metal-ion systems at the lowest concentration (10 –7 M) suggests that Zn(II) is slightly favored over Pb(II) for sorption sites on α-Al 2O 3 (1 –1 0 2) surfaces under our experimental conditions.« less

Probing Single- to Multi-Cell Level Charge Transport in Geobacter sulfurreducens DL-1

DTIC Science & Technology

2013-11-08

nanoelectrodes in which an array of nanoholes (200 400 nm2) precludes or single window (6 10 mm2) allows for direct microbe/electrode contacts (Supplementary...previous measurement with S. oneidensis MR-1 cells, which gave almost identical current output between window and nanohole electrodes30. At longer times, it...is interesting to note that the nanohole electrode was also able to yield a current, albeit at a much smaller magnitude, which could be attributed to

Rapid two-dimensional ALSOFAST-HSQC experiment for metabolomics and fluxomics studies: application to a 13C-enriched cancer cell model treated with gold nanoparticles.

PubMed

Schätzlein, Martina Palomino; Becker, Johanna; Schulze-Sünninghausen, David; Pineda-Lucena, Antonio; Herance, José Raul; Luy, Burkhard

2018-04-01

Isotope labeling enables the use of 13 C-based metabolomics techniques with strongly improved resolution for a better identification of relevant metabolites and tracing of metabolic fluxes in cell and animal models, as required in fluxomics studies. However, even at high NMR-active isotope abundance, the acquisition of one-dimensional 13 C and classical two-dimensional 1 H, 13 C-HSQC experiments remains time consuming. With the aim to provide a shorter, more efficient alternative, herein we explored the ALSOFAST-HSQC experiment with its rapid acquisition scheme for the analysis of 13 C-labeled metabolites in complex biological mixtures. As an initial step, the parameters of the pulse sequence were optimized to take into account the specific characteristics of the complex samples. We then applied the fast two-dimensional experiment to study the effect of different kinds of antioxidant gold nanoparticles on a HeLa cancer cell model grown on 13 C glucose-enriched medium. As a result, 1 H, 13 C-2D correlations could be obtained in a couple of seconds to few minutes, allowing a simple and reliable identification of various 13 C-enriched metabolites and the determination of specific variations between the different sample groups. Thus, it was possible to monitor glucose metabolism in the cell model and study the antioxidant effect of the coated gold nanoparticles in detail. Finally, with an experiment time of only half an hour, highly resolved 1 H, 13 C-HSQC spectra using the ALSOFAST-HSQC pulse sequence were acquired, revealing the isotope-position-patterns of the corresponding 13 C-nuclei from carbon multiplets. Graphical abstract Fast NMR applied to metabolomics and fluxomics studies with gold nanoparticles.

Microbial-enzymatic-hybrid biological fuel cell with optimized growth conditions for Shewanella oneidensis DSP-10.

PubMed

Roy, Jared N; Luckarift, Heather R; Sizemore, Susan R; Farrington, Karen E; Lau, Carolin; Johnson, Glenn R; Atanassov, Plamen

2013-07-10

In this work we present a biological fuel cell fabricated by combining a Shewanella oneidensis microbial anode and a laccase-modified air-breathing cathode. This concept is devised as an extension to traditional biochemical methods by incorporating diverse biological catalysts with the aim of powering small devices. In preparing the biological fuel cell anode, novel hierarchical-structured architectures and biofilm configurations were investigated. A method for creating an artificial biofilm based on encapsulating microorganisms in a porous, thin film of silica was compared with S. oneidensis biofilms that were allowed to colonize naturally. Results indicate comparable current and power densities for artificial and natural biofilm formations, based on growth characteristics. As a result, this work describes methods for creating controllable and reproducible bio-anodes and demonstrates the versatility of hybrid biological fuel cells. Copyright © 2013 Elsevier Inc. All rights reserved.

An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis

DOE PAGES

Dai, Jingcheng; Wei, Hehong; Tian, Chunyuan; ...

2015-01-01

Background: Bacteria use alternative sigma factors (σs) to regulate condition-specific gene expression for survival and Shewanella harbors multiple ECF (extracytoplasmic function) σ genes and cognate anti-sigma factor genes. Here we comparatively analyzed two of the rpoE-like operons in the strain MR-1: rpoE-rseA-rseB-rseC and rpoE2-chrR. Results: RpoE was important for bacterial growth at low and high temperatures, in the minimal medium, and high salinity. The degP/htrA orthologue, required for growth of Escherichia coli and Pseudomonas aeruginosa at high temperature, is absent in Shewanella, while the degQ gene is RpoE-regulated and is required for bacterial growth at high temperature. RpoE2 was essentialmore » for the optimal growth in oxidative stress conditions because the rpoE2 mutant was sensitive to hydrogen peroxide and paraquat. The operon encoding a ferrochelatase paralogue (HemH2) and a periplasmic glutathione peroxidase (PgpD) was identified as RpoE2-dependent. PgpD exhibited higher activities and played a more important role in the oxidative stress responses than the cytoplasmic glutathione peroxidase CgpD under tested conditions. The rpoE2-chrR operon and the identified regulon genes, including pgpD and hemH2, are coincidently absent in several psychrophilic and/or deep-sea Shewanella strains. Conclusion: In S. oneidensis MR-1, the RpoE-dependent degQ gene is required for optimal growth under high temperature. The rpoE2 and RpoE2-dependent pgpD gene encoding a periplasmic glutathione peroxidase are involved in oxidative stress responses. But rpoE2 is not required for bacterial growth at low temperature and it even affected bacterial growth under salt stress, indicating that there is a tradeoff between the salt resistance and RpoE2-mediated oxidative stress responses.« less

An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis

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

Dai, Jingcheng; Wei, Hehong; Tian, Chunyuan

Background: Bacteria use alternative sigma factors (σs) to regulate condition-specific gene expression for survival and Shewanella harbors multiple ECF (extracytoplasmic function) σ genes and cognate anti-sigma factor genes. Here we comparatively analyzed two of the rpoE-like operons in the strain MR-1: rpoE-rseA-rseB-rseC and rpoE2-chrR. Results: RpoE was important for bacterial growth at low and high temperatures, in the minimal medium, and high salinity. The degP/htrA orthologue, required for growth of Escherichia coli and Pseudomonas aeruginosa at high temperature, is absent in Shewanella, while the degQ gene is RpoE-regulated and is required for bacterial growth at high temperature. RpoE2 was essentialmore » for the optimal growth in oxidative stress conditions because the rpoE2 mutant was sensitive to hydrogen peroxide and paraquat. The operon encoding a ferrochelatase paralogue (HemH2) and a periplasmic glutathione peroxidase (PgpD) was identified as RpoE2-dependent. PgpD exhibited higher activities and played a more important role in the oxidative stress responses than the cytoplasmic glutathione peroxidase CgpD under tested conditions. The rpoE2-chrR operon and the identified regulon genes, including pgpD and hemH2, are coincidently absent in several psychrophilic and/or deep-sea Shewanella strains. Conclusion: In S. oneidensis MR-1, the RpoE-dependent degQ gene is required for optimal growth under high temperature. The rpoE2 and RpoE2-dependent pgpD gene encoding a periplasmic glutathione peroxidase are involved in oxidative stress responses. But rpoE2 is not required for bacterial growth at low temperature and it even affected bacterial growth under salt stress, indicating that there is a tradeoff between the salt resistance and RpoE2-mediated oxidative stress responses.« less

Bion M1. Peculiarities of life activities of microbes in 30-day spaceflight

NASA Astrophysics Data System (ADS)

Viacheslav, Ilyin; Korshunov, Denis; Morozova, Julia; Voeikova, Tatiana; Tyaglov, Boris; Novikova, Liudmila; Krestyanova, Irina; Emelyanova, Lydia

The aim of this work was to analyze the influence of space flight factors ( SFF) to microorganism strains , exposed inside unmanned spacecraft Bion M-1 during the 30- day space flight. Objectives of the work - the study of the influence of the SFF exchange chromosomal DNA in crosses microorganisms of the genus Streptomyces; the level of spontaneous phage induction of lysogenic strains fS31 from Streptomyces lividans 66 and Streptomyces coelicolor A3 ( 2 ) on the biosynthesis of the antibiotic tylosin strain of Streptomyces fradiae; survival electrogenic bacteria Shewanella oneidensis MR- 1 is used in the microbial fuel cell As a result of this work it was found that the SFF affect the exchange of chromosomal DNA by crossing strains of Streptomyces. Was detected polarity crossing , expressed in an advantageous contribution chromosome fragment of one of the parent strains in recombinant offspring. This fact may indicate a more prolonged exposure of cells in microgravity and , as a consequence, the transfer of longer fragments of chromosomal DNA This feature is the transfer of genetic material in microgravity could lead to wider dissemination and horizontal transfer of chromosomal and plasmid DNA of symbiotic microflora astronauts and other strains present in the spacecraft. It was shown no effect on the frequency of recombination PCF and the level of mutation model reversion of auxotrophic markers to prototrophy It was demonstrated that PCF increase the level of induction of cell actinophage fS31 lysogenic strain of S. lividans 66, but did not affect the level of induction of this phage cells S. coelicolor A3 ( 2). It is shown that the lower the level of synthesis PCF antibiotic aktinorodina (actinorhodin) in lysogenic strain S. coelicolor A3 ( 2). 66 Strains of S. lividans and S. coelicolor A3 ( 2 ) can be used as a biosensor for studying the effect on microorganisms PCF It is shown that the effect of the PCF reduces synthesis of tylosin and desmicosyn S. fradiae at

Effect of Thiols, Zinc, and Redox Conditions on Hg Uptake in Shewanella oneidensis

DOE PAGES

Szczuka, Aleksandra; Morel, Francois M. M.; Schaefer, Jeffra K.

2015-05-18

Mercury uptake in bacteria represents a key first step in the production and accumulation Of methylmercury in biota. Previous experiments with mercury methylating bacteria have shown that Hg uptake is enhanced by some thiols, in particular cysteine, and that it is an energy-dependent process through heavy Metal TA transporters. In this study, we examine Hg uptake in the nonmethylating facultative aerobe, Shewanella oneidensis, under both anaerobic and aerobic conditions. Our results demonstrate similar characteristics of the Hg uptake system to those of the Hg methylating strains: uptake is enhanced in the presence of some thiols but not others; uptake ismore » energy dependent as evidenced by inhibition by a protonophore; and uptake is inhibited by high Zn(II) concentrations. Initial cellular uptake rates in S. oneidensis were remarkably similar under aerobic and fumarate-reducing conditions. In conclusion, these data support a similar Hg(II) uptake mechanism within the proteobacteria of accidental Hg(II) transport through heavy metal transporters with similar rates of uptake but differences in the ability to take up Hg bound to different thiols.« less

Comparative Genomics Analysis and Phenotypic Characterization of Shewanella putrefaciens W3-18-1: Anaerobic Respiration, Bacterial Microcompartments, and Lateral Flagella

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

Qiu, D.; Tu, Q.; He, Zhili

2010-05-17

Respiratory versatility and psychrophily are the hallmarks of Shewanella. The ability to utilize a wide range of electron acceptors for respiration is due to the large number of c-type cytochrome genes present in the genome of Shewanella strains. More recently the dissimilatory metal reduction of Shewanella species has been extensively and intensively studied for potential applications in the bioremediation of radioactive wastes of groundwater and subsurface environments. Multiple Shewanella genome sequences are now available in the public databases (Fredrickson et al., 2008). Most of the sequenced Shewanella strains were isolated from marine environments and this genus was believed to bemore » of marine origin (Hau and Gralnick, 2007). However, the well-characterized model strain, S. oneidensis MR-1, was isolated from the freshwater lake sediment of Lake Oneida, New York (Myers and Nealson, 1988) and similar bacteria have also been isolated from other freshwater environments (Venkateswaran et al., 1999). Here we comparatively analyzed the genome sequence and physiological characteristics of S. putrefaciens W3-18-1 and S. oneidensis MR-1, isolated from the marine and freshwater lake sediments, respectively. The anaerobic respirations, carbon source utilization, and cell motility have been experimentally investigated. Large scale horizontal gene transfers have been revealed and the genetic divergence between these two strains was considered to be critical to the bacterial adaptation to specific habitats, freshwater or marine sediments.« less

High power density from a miniature microbial fuel cell using Shewanella oneidensis DSP10.

PubMed

Ringeisen, Bradley R; Henderson, Emily; Wu, Peter K; Pietron, Jeremy; Ray, Ricky; Little, Brenda; Biffinger, Justin C; Jones-Meehan, Joanne M

2006-04-15

A miniature microbial fuel cell (mini-MFC) is described that demonstrates high output power per device cross-section (2.0 cm2) and volume (1.2 cm3). Shewanella oneidensis DSP10 in growth medium with lactate and buffered ferricyanide solutions were used as the anolyte and catholyte, respectively. Maximum power densities of 24 and 10 mW/m2 were measured using the true surface areas of reticulated vitreous carbon (RVC) and graphite felt (GF) electrodes without the addition of exogenous mediators in the anolyte. Current densities at maximum power were measured as 44 and 20 mA/m2 for RVC and GF, while short circuit current densities reached 32 mA/m2 for GF anodes and 100 mA/m2 for RVC. When the power density for GF was calculated using the cross sectional area of the device or the volume of the anode chamber, we found values (3 W/m2, 500 W/m3) similar to the maxima reported in the literature. The addition of electron mediators resulted in current and power increases of 30-100%. These power densities were surprisingly high considering a pure S. oneidensis culture was used. We found that the short diffusion lengths and high surface-area-to-chamber volume ratio utilized in the mini-MFC enhanced power density when compared to output from similar macroscopic MFCs.

Charge-associated effects of fullerene derivatives on microbialstructural integrity and central metabolism

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

Tang, Yinjie J.; Ashcroft, Jared M.; Chen, Ding

2007-01-23

The effects of four types of fullerene compounds (C60,C60-OH, C60-COOH, C60-NH2) were examined on two model microorganisms(Escherichia coli W3110 and Shewanella oneidensis MR-1). Positivelycharged C60-NH2 at concentrations as low as 10 mg/L inhibited growth andreduced substrate uptake for both microorganisms. Scanning ElectronMicroscopy (SEM) revealed damage to cellular structures.Neutrally-charged C60 and C60-OH had mild negative effects on S.oneidensis MR-1, whereas the negatively-charged C60-COOH did not affecteither microorganism s growth. The effect of fullerene compounds onglobal metabolism was further investigated using [3-13C]L-lactateisotopic labeling, which tracks perturbations to metabolic reaction ratesin bacteria by examining the change in the isotopic labeling pattern inthe resultingmore » metabolites (often amino acids).1-3 The 13C isotopomeranalysis from all fullerene-exposed cultures revealed no significantdifferences in isotopomer distributions from unstressed cells. Thisresult indicates that microbial central metabolism is robust toenvironmental stress inflicted by fullerene nanoparticles. In addition,although C60-NH2 compounds caused mechanical stress on the cell wall ormembrane, both S. oneidensis MR-1 and E. coli W3110 can efficientlyalleviate such stress by cell aggregation and precipitation of the toxicnanoparticles. The results presented here favor the hypothesis thatfullerenes cause more membrane stress4, 5, 6 than perturbation to energymetabolism7« less

From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

2015-12-01

Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations

GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data.

PubMed

Pang, Shuai; Stones, Rebecca J; Ren, Ming-Ming; Liu, Xiao-Guang; Wang, Gang; Xia, Hong-ju; Wu, Hao-Yang; Liu, Yang; Xie, Qiang

2015-09-01

We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC)(3) (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC)(3) to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The effect of metal loading on Cd adsorption onto Shewanella oneidensis bacterial cell envelopes: The role of sulfhydryl sites

NASA Astrophysics Data System (ADS)

Yu, Qiang; Fein, Jeremy B.

2015-10-01

The adsorption and desorption of Cd onto Shewanella oneidensis bacterial cells with and without blocking of sulfhydryl sites was measured in order to determine the effect of metal loading and to understand the role of sulfhydryl sites in the adsorption reactions. The observed adsorption/desorption behaviors display strong dependence on metal loading. Under a high loading of 40 μmol Cd/g bacterial cells, blocking the sulfhydryl sites within the cell envelope by exposure of the biomass to monobromo(trimethylammonio)bimane bromide (qBBr) does not significantly affect the extent of Cd adsorption, and we observed fully reversible adsorption under this condition. In contrast, under a low metal loading of 1.3 μmol Cd/g bacterial cells, the extent of Cd adsorption onto sulfhydryl-blocked S. oneidensis cells was significantly lower than that onto untreated cells, and only approximately 50-60% of the adsorbed Cd desorbed from the cells upon acidification. In conjunction with previous EXAFS results, our findings demonstrate that Cd adsorption onto S. oneidensis under low metal loading conditions is dominated by sulfhydryl binding, and thus is controlled by a distinct adsorption mechanism from the non-sulfhydryl site binding which controls Cd adsorption under high metal loading conditions. We use the data to develop a surface complexation model that constrains the values of the stability constants for individual Cd-sulfhydryl and Cd-non-sulfhydryl bacterial complexes, and we use this approach to account for the Cd adsorption behavior as a function of both pH and metal loading. This approach is crucial in order to predict metal adsorption onto bacteria under environmentally relevant metal loading conditions where sulfhydryl binding sites can dominate the adsorption reaction.

Enhanced Shewanella biofilm promotes bioelectricity generation.

PubMed

Liu, Ting; Yu, Yang-Yang; Deng, Xiao-Peng; Ng, Chun Kiat; Cao, Bin; Wang, Jing-Yuan; Rice, Scott A; Kjelleberg, Staffan; Song, Hao

2015-10-01

Electroactive biofilms play essential roles in determining the power output of microbial fuel cells (MFCs). To engineer the electroactive biofilm formation of Shewanella oneidensis MR-1, a model exoelectrogen, we herein heterologously overexpressed a c-di-GMP biosynthesis gene ydeH in S. oneidensis MR-1, constructing a mutant strain in which the expression of ydeH is under the control of IPTG-inducible promoter, and a strain in which ydeH is under the control of a constitutive promoter. Such engineered Shewanella strains had significantly enhanced biofilm formation and bioelectricity generation. The MFCs inoculated with these engineered strains accomplished a maximum power density of 167.6 ± 3.6 mW/m(2) , which was ∼ 2.8 times of that achieved by the wild-type MR-1 (61.0 ± 1.9 mW/m(2) ). In addition, the engineered strains in the bioelectrochemical system at poised potential of 0.2 V vs. saturated calomel electrode (SCE) generated a stable current density of 1100 mA/m(2) , ∼ 3.4 times of that by wild-type MR-1 (320 mA/m(2) ). © 2015 Wiley Periodicals, Inc.

T1ρ MR Imaging of Human Musculoskeletal System

PubMed Central

Wang, Ligong; Regatte, Ravinder R.

2014-01-01

Magnetic resonance imaging (MRI) offers the direct visualization of human musculoskeletal (MSK) system, especially all diarthrodial tissues including cartilage, bone, menisci, ligaments, tendon, hip, synovium etc. Conventional MR imaging techniques based on T1- and T2-weighted, proton density (PD) contrast are inconclusive in quantifying early biochemically degenerative changes in MSK system in general and articular cartilage in particular. In recent years, quantitative MR parameter mapping techniques have been used to quantify the biochemical changes in articular cartilage with a special emphasis on evaluating joint injury, cartilage degeneration, and soft tissue repair. In this article, we will focus on cartilage biochemical composition, basic principles of T1ρ MR imaging, implementation of T1ρ pulse sequences, biochemical validation, and summarize the potential applications of T1ρ MR imaging technique in MSK diseases including osteoarthritis (OA), anterior cruciate ligament (ACL) injury, and knee joint repair. Finally, we will also review the potential advantages, challenges, and future prospects of T1ρ MR imaging for widespread clinical translation. PMID:24935818

Characterization of a prototype MR-compatible Delta4 QA system in a 1.5 tesla MR-linac

NASA Astrophysics Data System (ADS)

de Vries, J. H. W.; Seravalli, E.; Houweling, A. C.; Woodings, S. J.; van Rooij, R.; Wolthaus, J. W. H.; Lagendijk, J. J. W.; Raaymakers, B. W.

2018-01-01

To perform patient plan quality assurance (QA) on a newly installed MR-linac (MRL) it is necessary to have an MR-compatible QA device. An MR compatible device (MR-Delta4) has been developed together with Scandidos AB (Uppsala, Sweden). The basic characteristics of the detector response, such as short-term reproducibility, dose linearity, field size dependency, dose rate dependency, dose-per-pulse dependency and angular dependency, were investigated for the clinical Delta4-PT as well as for the MR compatible version. All tests were performed with both devices on a conventional linac and the MR compatible device was tested on the MRL as well. No statistically significant differences were found in the short-term reproducibility (<0.1%), dose linearity (⩽0.5%), field size dependency (<2.0% for field sizes larger than 5  ×  5 cm2), dose rate dependency (<1.0%) or angular dependency for any phantom/linac combination. The dose-per-pulse dependency (<0.8%) was found to be significantly different between the two devices. This difference can be explained by the fact that the diodes in the clinical Delta4-PT were irradiated with a much larger dose than the MR-Delta4-PT ones. The absolute difference between the devices (<0.5%) was found to be small, so no clinical impact is expected. For both devices, the results were consistent with the characteristics of the Delta4-PT device reported in the literature (Bedford et al 2009 Phys. Med. Biol. 54 N167-76 Sadagopan et al 2009 J. Appl. Clin. Med. Phys. 10 2928). We found that the characteristics of the MR compatible Delta4 phantom were found to be comparable to the clinically used one. Also, the found characteristics do not differ from the previously reported characteristics of the commercially available non-MR compatible Delta4-PT phantom. Therefore, the MR compatible Delta4 prototype was found to be safe and effective for use in the 1.5 tesla magnetic field of the Elekta MR-linac

A near-infrared light responsive c-di-GMP module-based AND logic gate in Shewanella oneidensis.

PubMed

Hu, Yidan; Wu, Yichao; Mukherjee, Manisha; Cao, Bin

2017-01-31

A novel, biofilm-based AND logic gate was constructed in Shewanella oneidensis through a near-infrared (NIR) light responsive c-di-GMP module. The logic gate was demonstrated in microbial fuel cells with isopropyl β-d-thiogalactoside (IPTG) and NIR light as the inputs and electrical signals as the output.

Stress induction in the bacteria Shewanella oneidensis and Deinococcus radiodurans in response to below-background ionizing radiation.

PubMed

Castillo, Hugo; Schoderbek, Donald; Dulal, Santosh; Escobar, Gabriela; Wood, Jeffrey; Nelson, Roger; Smith, Geoffrey

2015-01-01

The 'Linear no-threshold' (LNT) model predicts that any amount of radiation increases the risk of organisms to accumulate negative effects. Several studies at below background radiation levels (4.5-11.4 nGy h(-1)) show decreased growth rates and an increased susceptibility to oxidative stress. The purpose of our study is to obtain molecular evidence of a stress response in Shewanella oneidensis and Deinococcus radiodurans grown at a gamma dose rate of 0.16 nGy h(-1), about 400 times less than normal background radiation. Bacteria cultures were grown at a dose rate of 0.16 or 71.3 nGy h(-1) gamma irradiation. Total RNA was extracted from samples at early-exponential and stationary phases for the rt-PCR relative quantification (radiation-deprived treatment/background radiation control) of the stress-related genes katB (catalase), recA (recombinase), oxyR (oxidative stress transcriptional regulator), lexA (SOS regulon transcriptional repressor), dnaK (heat shock protein 70) and SOA0154 (putative heavy metal efflux pump). Deprivation of normal levels of radiation caused a reduction in growth of both bacterial species, accompanied by the upregulation of katB, recA, SOA0154 genes in S. oneidensis and the upregulation of dnaK in D. radiodurans. When cells were returned to background radiation levels, growth rates recovered and the stress response dissipated. Our results indicate that below-background levels of radiation inhibited growth and elicited a stress response in two species of bacteria, contrary to the LNT model prediction.

Microbial mediated iron redox cycling in Fe (hydr)oxides for nitrite removal.

PubMed

Lu, Yongsheng; Xu, Lu; Shu, Weikang; Zhou, Jizhi; Chen, Xueping; Xu, Yunfeng; Qian, Guangren

2017-01-01

Nitrite, at an environmentally relevant concentration, was significantly reduced with iron (hydr)oxides mediated by Shewanella oneidensis MR-1. The average nitrite removal rates of 1.28±0.08 and 0.65±0.02(mgL -1 )h -1 were achieved with ferrihydrite and magnetite, respectively. The results showed that nitrite removal was able to undergo multiple redox cycles with iron (hydr)oxides mediated by Shewanella oneidensis MR-1. During the bioreduction of the following cycles, biogenic Fe(II) was subsequently chemically oxidized to Fe(III), which is associated with nitrite reduction. There was 11.18±1.26mgL -1 of NH 4 + -N generated in the process of redox cycling of ferrihydrite. Additionally, results obtained by using X-ray diffraction showed that ferrihydrite and magnetite remained mainly stable in the system. This study indicated that redox cycling of Fe in iron (hydr)oxides was a potential process associated with NO 2 - -N removal from solution, and reduced most nitrite abiotically to gaseous nitrogen species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

NASA Technical Reports Server (NTRS)

Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B. J.; Ringelberg, D. B.; White, D. C.; Nishijima, M.; Sano, H.;

Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex

PubMed Central

Okamoto, Akihiro; Tokunou, Yoshihide; Saito, Junki

2016-01-01

Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of anaerobic respiration. The kinetics of this electron transport has implications for controlling the rate of microbial electron transport during bioenergy or biochemical production, iron corrosion, and natural mineral cycling. Herein, we review the findings from in-vivo and in-vitro studies examining electron transport kinetics through single OM c-Cyt complexes in Shewanella oneidensis MR-1. In-vitro electron flux via a purified OM c-Cyt complex, comprised of MtrA, B, and C proteins from S. oneidensis MR-1, embedded in a proteoliposome system is reported to be 10- to 100-fold faster compared with in-vivo estimates based on measurements of electron flux per cell and OM c-Cyts density. As the proteoliposome system is estimated to have 10-fold higher cation flux via potassium channels than electrons, we speculate that the slower rate of electron-coupled cation transport across the OM is responsible for the significantly lower electron transport rate that is observed in-vivo. As most studies to date have primarily focused on the energetics or kinetics of interheme electron hopping in OM c-Cyts in this microbial electron transport mechanism, the proposed model involving cation transport provides new insight into the rate detemining step of EET, as well as the role of self-secreted flavin molecules bound to OM c-Cyt and proton management for energy conservation and production in S. oneidensis MR-1. PMID:27924259

Quantification of hepatic steatosis with T1-independent, T2-corrected MR imaging with spectral modeling of fat: blinded comparison with MR spectroscopy.

PubMed

Meisamy, Sina; Hines, Catherine D G; Hamilton, Gavin; Sirlin, Claude B; McKenzie, Charles A; Yu, Huanzhou; Brittain, Jean H; Reeder, Scott B

2011-03-01

To prospectively compare an investigational version of a complex-based chemical shift-based fat fraction magnetic resonance (MR) imaging method with MR spectroscopy for the quantification of hepatic steatosis. This study was approved by the institutional review board and was HIPAA compliant. Written informed consent was obtained before all studies. Fifty-five patients (31 women, 24 men; age range, 24-71 years) were prospectively imaged at 1.5 T with quantitative MR imaging and single-voxel MR spectroscopy, each within a single breath hold. The effects of T2 correction, spectral modeling of fat, and magnitude fitting for eddy current correction on fat quantification with MR imaging were investigated by reconstructing fat fraction images from the same source data with different combinations of error correction. Single-voxel T2-corrected MR spectroscopy was used to measure fat fraction and served as the reference standard. All MR spectroscopy data were postprocessed at a separate institution by an MR physicist who was blinded to MR imaging results. Fat fractions measured with MR imaging and MR spectroscopy were compared statistically to determine the correlation (r(2)), and the slope and intercept as measures of agreement between MR imaging and MR spectroscopy fat fraction measurements, to determine whether MR imaging can help quantify fat, and examine the importance of T2 correction, spectral modeling of fat, and eddy current correction. Two-sided t tests (significance level, P = .05) were used to determine whether estimated slopes and intercepts were significantly different from 1.0 and 0.0, respectively. Sensitivity and specificity for the classification of clinically significant steatosis were evaluated. Overall, there was excellent correlation between MR imaging and MR spectroscopy for all reconstruction combinations. However, agreement was only achieved when T2 correction, spectral modeling of fat, and magnitude fitting for eddy current correction were used (r(2

Intramyocellular lipid quantification: repeatability with 1H MR spectroscopy.

PubMed

Torriani, Martin; Thomas, Bijoy J; Halpern, Elkan F; Jensen, Megan E; Rosenthal, Daniel I; Palmer, William E

2005-08-01

To prospectively determine the repeatability and variability of tibialis anterior intramyocellular lipid (IMCL) quantifications performed by using 1.5-T hydrogen 1 (1H) magnetic resonance (MR) spectroscopy in healthy subjects. Institutional review board approval and written informed consent were obtained for this Health Insurance Portability and Accountability Act-compliant study. The authors examined the anterior tibial muscles of 27 healthy subjects aged 19-48 years (12 men, 15 women; mean age, 25 years) by using single-voxel short-echo-time point-resolved 1H MR spectroscopy. During a first visit, the subjects underwent 1H MR spectroscopy before and after being repositioned in the magnet bore, with voxels carefully placed on the basis of osseous landmarks. Measurements were repeated after a mean interval of 12 days. All spectra were fitted by using Java-based MR user interface (jMRUI) and LCModel software, and lipid peaks were scaled to the unsuppressed water peak (at 4.7 ppm) and the total creatine peak (at approximately 3.0 ppm). A one-way random-effects variance components model was used to determine intraday and intervisit coefficients of variation (CVs). A power analysis was performed to determine the detectable percentage change in lipid measurements for two subject sample sizes. Measurements of the IMCL methylene protons peak at a resonance of 1.3 ppm scaled to the unsuppressed water peak (IMCL(W)) that were obtained by using jMRUI software yielded the lowest CVs overall (intraday and intervisit CVs, 13.4% and 14.4%, respectively). The random-effects variance components model revealed that nonbiologic factors (equipment and repositioning) accounted for 50% of the total variability in IMCL quantifications. Power analysis for a sample size of 20 subjects revealed that changes in IMCL(W) of greater than 15% could be confidently detected between 1H MR spectroscopic measurements obtained on different days. 1H MR spectroscopy is feasible for repeatable

High-and low-affinity binding sites for Cd on the bacterial cell walls of Bacillus subtilis and Shewanella oneidensis.

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

Mishra, B.; Boyanov, M.; Bunker, B. A.

2010-08-01

Bulk Cd adsorption isotherm experiments, thermodynamic equilibrium modeling, and Cd K edge EXAFS were used to constrain the mechanisms of proton and Cd adsorption to bacterial cells of the commonly occurring Gram-positive and Gram-negative bacteria, Bacillus subtilis and Shewanella oneidensis, respectively. Potentiometric titrations were used to characterize the functional group reactivity of the S. oneidensis cells, and we model the titration data using the same type of non-electrostatic surface complexation approach as was applied to titrations of B. subtilis suspensions by Fein et al. (2005). Similar to the results for B. subtilis, the S. oneidensis cells exhibit buffering behavior frommore » approximately pH 3-9 that requires the presence of four distinct sites, with pK{sub a} values of 3.3 {+-} 0.2, 4.8 {+-} 0.2, 6.7 {+-} 0.4, and 9.4 {+-} 0.5, and site concentrations of 8.9({+-}2.6) x 10{sup -5}, 1.3({+-}0.2) x 10{sup -4}, 5.9({+-}3.3) x 10{sup -5}, and 1.1({+-}0.6) x 10{sup -4} moles/g bacteria (wet mass), respectively. The bulk Cd isotherm adsorption data for both species, conducted at pH 5.9 as a function of Cd concentration at a fixed biomass concentration, were best modeled by reactions with a Cd:site stoichiometry of 1:1. EXAFS data were collected for both bacterial species as a function of Cd concentration at pH 5.9 and 10 g/L bacteria. The EXAFS results show that the same types of binding sites are responsible for Cd sorption to both bacterial species at all Cd loadings tested (1-200 ppm). Carboxyl sites are responsible for the binding at intermediate Cd loadings. Phosphoryl ligands are more important than carboxyl ligands for Cd binding at high Cd loadings. For the lowest Cd loadings studied here, a sulfhydryl site was found to dominate the bound Cd budgets for both species, in addition to the carboxyl and phosphoryl sites that dominate the higher loadings. The EXAFS results suggest that both Gram-positive and Gram-negative bacterial cell walls

Quantification of Hepatic Steatosis with T1-independent, T2*-corrected MR Imaging with Spectral Modeling of Fat: Blinded Comparison with MR Spectroscopy

PubMed Central

Hines, Catherine D. G.; Hamilton, Gavin; Sirlin, Claude B.; McKenzie, Charles A.; Yu, Huanzhou; Brittain, Jean H.; Reeder, Scott B.

2011-01-01

Purpose: To prospectively compare an investigational version of a complex-based chemical shift–based fat fraction magnetic resonance (MR) imaging method with MR spectroscopy for the quantification of hepatic steatosis. Materials and Methods: This study was approved by the institutional review board and was HIPAA compliant. Written informed consent was obtained before all studies. Fifty-five patients (31 women, 24 men; age range, 24–71 years) were prospectively imaged at 1.5 T with quantitative MR imaging and single-voxel MR spectroscopy, each within a single breath hold. The effects of T2* correction, spectral modeling of fat, and magnitude fitting for eddy current correction on fat quantification with MR imaging were investigated by reconstructing fat fraction images from the same source data with different combinations of error correction. Single-voxel T2-corrected MR spectroscopy was used to measure fat fraction and served as the reference standard. All MR spectroscopy data were postprocessed at a separate institution by an MR physicist who was blinded to MR imaging results. Fat fractions measured with MR imaging and MR spectroscopy were compared statistically to determine the correlation (r2), and the slope and intercept as measures of agreement between MR imaging and MR spectroscopy fat fraction measurements, to determine whether MR imaging can help quantify fat, and examine the importance of T2* correction, spectral modeling of fat, and eddy current correction. Two-sided t tests (significance level, P = .05) were used to determine whether estimated slopes and intercepts were significantly different from 1.0 and 0.0, respectively. Sensitivity and specificity for the classification of clinically significant steatosis were evaluated. Results: Overall, there was excellent correlation between MR imaging and MR spectroscopy for all reconstruction combinations. However, agreement was only achieved when T2* correction, spectral modeling of fat, and magnitude

Microfabricated Microbial Fuel Cell Arrays Reveal Electrochemically Active Microbes

PubMed Central

Cho, Younghak; de Figueiredo, Paul; Han, Arum

2009-01-01

Microbial fuel cells (MFCs) are remarkable “green energy” devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated. PMID:19668333

Combining position-specific 13C labeling with compound-specific isotope analysis: first steps towards soil fluxomics

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Kuzyakov, Yakov

2015-04-01

Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino

Parallel determination of gut permeability in man with M(r) 400, M(r) 1500, M(r) 4000 and M(r) 10,000 polyethylene glycol.

PubMed

Parlesak, A; Bode, J C; Bode, C

1994-11-01

Polyethylene glycol has been in use for a number of years for the assessment of gut permeability. The methods so far employed are usually limited to polyethylene glycols in the low relative molecular mass range (up to M(r) 1300). We developed a method for the simultaneous determination of gut permeability to M(r) 400, M(r) 1500, M(r) 4000 and M(r) 10,000 polyethylene glycol, by applying a single oral dose of an appropriate mixture of these polyethylene glycols. After extraction from 24 h-urine, M(r) 1500, M(r) 4000 and M(r) 10,000 polyethylene glycol were quantified by size exclusion chromatography, while M(r) 400 polyethylene glycol was determined by reversed phase chromatography. The detection limit of polyethylene glycol in the relative molecular mass range between M(r) 1500 and M(r) 10,000 was found to be 0.2 mg/l urine, and the detection limit of M(r) 400 polyethylene glycol 5 mg/l urine. Recovery of the polyethylene glycols (N = 6) were 86.6% (CV: 4.8%) for M(r) 400, 94.1% (CV: 7.2%) for M(r) 1500, 97.1% (CV: 5.5%) for M(r) 4000 and 97.4% (CV: 5.6%) for M(r) 10,000. No significant difference was found between the excretion rates in 24 h-urine of M(r) 400 and M(r) 1500 polyethylene glycols in patients with Crohn's disease (M(r) 400: 34.4 +/- 5.5%; M(r) 1500: 5.22 +/- 2.27%; mean +/- SEM, N = 10) and healthy controls (M(r) 400: 33.6 +/- 3.2%, M(r) 1500: 1.09 +/- 0.26%; N = 21). The excretion rate of M(r) 4000 polyethylene glycol was markedly higher in patients with Crohn's disease (0.462 +/- 0.177%) than in healthy controls (0.049 +/- 0.012%, p < 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Silver nanocrystallites: Facile biofabrication using Shewanella oneidensis, and an evaluation of their comparative toxicity on Gram-negative and Gram-positive bacteria

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

Suresh, Anil K; Wang, Wei; Pelletier, Dale A

Microorganisms have long been known to develop resistance to metal ions either by sequestering metals inside the cell or by effluxing them into the extracellular media. Here we report the biosynthesis of extracellular silver based single nanocrystallites of well-defined composition and homogeneous morphology utilizing the -proteobacterium, Shewanella oneidensis strain MR-1, upon incubation with an aqueous solution of silver nitrate. Further characterization of these particles revealed that the crystals consist of small, reasonably monodispersed spheres in the size range 2 11 nm (with an average of 4 1.5 nm). The bactericidal effect of these biologically synthesized silver nanoparticles (biogenic-Ag) are comparedmore » to similar chemically synthesized nanoparticles (colloidal silver [colloidal-Ag] and oleate capped silver [oleate-Ag]). The determination of the bactericidal effect of these different silver nanoparticles was assessed using both Gram-negative (E. coli) and Gram-positive (B. subtilis) bacteria and based on the diameter of the inhibition zone in disc diffusion tests, minimum inhibitory concentrations, Live/Dead staining assays, and atomic force microscopy. From a toxicity perspective, a clear synthesis procedure, and a surface coat- and strain-dependent inhibition were observed for silver nanoparticles. Biogenic-Ag was found to be of higher toxicity when compared to colloidal-Ag for both E. coli and B. subtilis. E. coli was found to be more resistant to either of these nanoparticles than B. subtilis. In contrast, Oleate-Ag was not toxic to either of the bacteria. These findings have important implications for the potential uses of Ag nanomaterials and for their fate in biological and environmental systems.« less

In Folio Respiratory Fluxomics Revealed by 13C Isotopic Labeling and H/D Isotope Effects Highlight the Noncyclic Nature of the Tricarboxylic Acid “Cycle” in Illuminated Leaves1[W

PubMed Central

Tcherkez, Guillaume; Mahé, Aline; Gauthier, Paul; Mauve, Caroline; Gout, Elizabeth; Bligny, Richard; Cornic, Gabriel; Hodges, Michael

2009-01-01

While the possible importance of the tricarboxylic acid (TCA) cycle reactions for leaf photosynthesis operation has been recognized, many uncertainties remain on whether TCA cycle biochemistry is similar in the light compared with the dark. It is widely accepted that leaf day respiration and the metabolic commitment to TCA decarboxylation are down-regulated in illuminated leaves. However, the metabolic basis (i.e. the limiting steps involved in such a down-regulation) is not well known. Here, we investigated the in vivo metabolic fluxes of individual reactions of the TCA cycle by developing two isotopic methods, 13C tracing and fluxomics and the use of H/D isotope effects, with Xanthium strumarium leaves. We provide evidence that the TCA “cycle” does not work in the forward direction like a proper cycle but, rather, operates in both the reverse and forward directions to produce fumarate and glutamate, respectively. Such a functional division of the cycle plausibly reflects the compromise between two contrasted forces: (1) the feedback inhibition by NADH and ATP on TCA enzymes in the light, and (2) the need to provide pH-buffering organic acids and carbon skeletons for nitrate absorption and assimilation. PMID:19675152

Shewanella frigidimarina microbial fuel cells and the influence of divalent cations on current output.

PubMed

Fitzgerald, Lisa A; Petersen, Emily R; Leary, Dagmar H; Nadeau, Lloyd J; Soto, Carissa M; Ray, Richard I; Little, Brenda J; Ringeisen, Bradley R; Johnson, Glenn R; Vora, Gary J; Biffinger, Justin C

2013-02-15

The genes involved in the proposed pathway for Shewanella extracellular electron transfer (EET) are highly conserved. While extensive studies involving EET from a fresh water Shewanella microbe (S. oneidensis MR-1) to soluble and insoluble electron acceptors have been published, only a few reports have examined EET from marine strains of Shewanella. Thus, Shewanella frigidimarina (an isolate from Antarctic Sea ice) was used within miniature microbial fuel cells (mini-MFC) to evaluate potential power output. During the course of this study several distinct differences were observed between S. oneidensis MR-1 and S. frigidimarina under comparable conditions. The maximum power density with S. frigidimarina was observed when the anolyte was half-strength marine broth (1/2 MB) (0.28 μW/cm(2)) compared to Luria-Bertani (LB) (0.07 μW/cm(2)) or a defined growth minimal medium (MM) (0.02 μW/cm(2)). The systematic modification of S. frigidimarina cultured in 1/2 MB and LB with divalent cations shows that a maximum current output can be generated independent of internal ionic ohmic losses and the presence of external mediators. Published by Elsevier B.V.

MR-based motion correction for PET imaging using wired active MR microcoils in simultaneous PET-MR: Phantom study1

PubMed Central

Huang, Chuan; Ackerman, Jerome L.; Petibon, Yoann; Brady, Thomas J.; El Fakhri, Georges; Ouyang, Jinsong

2014-01-01

Purpose: Artifacts caused by head motion present a major challenge in brain positron emission tomography (PET) imaging. The authors investigated the feasibility of using wired active MR microcoils to track head motion and incorporate the measured rigid motion fields into iterative PET reconstruction. Methods: Several wired active MR microcoils and a dedicated MR coil-tracking sequence were developed. The microcoils were attached to the outer surface of an anthropomorphic 18F-filled Hoffman phantom to mimic a brain PET scan. Complex rotation/translation motion of the phantom was induced by a balloon, which was connected to a ventilator. PET list-mode and MR tracking data were acquired simultaneously on a PET-MR scanner. The acquired dynamic PET data were reconstructed iteratively with and without motion correction. Additionally, static phantom data were acquired and used as the gold standard. Results: Motion artifacts in PET images were effectively removed by wired active MR microcoil based motion correction. Motion correction yielded an activity concentration bias ranging from −0.6% to 3.4% as compared to a bias ranging from −25.0% to 16.6% if no motion correction was applied. The contrast recovery values were improved by 37%–156% with motion correction as compared to no motion correction. The image correlation (mean ± standard deviation) between the motion corrected (uncorrected) images of 20 independent noise realizations and static reference was R2 = 0.978 ± 0.007 (0.588 ± 0.010, respectively). Conclusions: Wired active MR microcoil based motion correction significantly improves brain PET quantitative accuracy and image contrast. PMID:24694141

Core Fluxome and Metafluxome of Lactic Acid Bacteria under Simulated Cocoa Pulp Fermentation Conditions

PubMed Central

Adler, Philipp; Bolten, Christoph Josef; Dohnt, Katrin; Hansen, Carl Erik

2013-01-01

In the present work, simulated cocoa fermentation was investigated at the level of metabolic pathway fluxes (fluxome) of lactic acid bacteria (LAB), which are typically found in the microbial consortium known to convert nutrients from the cocoa pulp into organic acids. A comprehensive 13C labeling approach allowed to quantify carbon fluxes during simulated cocoa fermentation by (i) parallel 13C studies with [13C6]glucose, [1,2-13C2]glucose, and [13C6]fructose, respectively, (ii) gas chromatography-mass spectrometry (GC/MS) analysis of secreted acetate and lactate, (iii) stoichiometric profiling, and (iv) isotopomer modeling for flux calculation. The study of several strains of L. fermentum and L. plantarum revealed major differences in their fluxes. The L. fermentum strains channeled only a small amount (4 to 6%) of fructose into central metabolism, i.e., the phosphoketolase pathway, whereas only L. fermentum NCC 575 used fructose to form mannitol. In contrast, L. plantarum strains exhibited a high glycolytic flux. All strains differed in acetate flux, which originated from fractions of citrate (25 to 80%) and corresponding amounts of glucose and fructose. Subsequent, metafluxome studies with consortia of different L. fermentum and L. plantarum strains indicated a dominant (96%) contribution of L. fermentum NCC 575 to the overall flux in the microbial community, a scenario that was not observed for the other strains. This highlights the idea that individual LAB strains vary in their metabolic contribution to the overall fermentation process and opens up new routes toward streamlined starter cultures. L. fermentum NCC 575 might be one candidate due to its superior performance in flux activity. PMID:23851099

Biotic-Abiotic Nanoscale Interactions in Biological Fuel Cells

DTIC Science & Technology

2014-03-28

oneidensis MR-1 bacterial nanowires are lipid-based extensions of the outer- membrane and periplasmic electron transport proteins, Science Magazine ...Minnesota Biotechnology Institute Seminar 2013 California State University, Long Beach Physics Colloquium 2014 Okayama University, Japan. Mini...Investigator Program Award 2012 Selected by Popular Science Magazine as one of the “Brilliant 10” of 2012 2013 USC Dornsife Raubenheimer award for

Bioremediation of nanomaterials

DOEpatents

Chen, Frank Fanqing; Keasling, Jay D; Tang, Yinjie J

2013-05-14

The present invention provides a method comprising the use of microorganisms for nanotoxicity study and bioremediation. In some embodiment, the microorganisms are bacterial organisms such as Gram negative bacteria, which are used as model organisms to study the nanotoxicity of the fullerene compounds: E. coli W3110, a human related enterobacterium and Shewanella oneidensis MR-1, an environmentally important bacterium with versatile metabolism.

MR1 antigen presentation to mucosal-associated invariant T cells was highly conserved in evolution

PubMed Central

Huang, Shouxiong; Martin, Emmanuel; Kim, Sojung; Yu, Lawrence; Soudais, Claire; Fremont, Daved H.; Lantz, Olivier; Hansen, Ted H.

2009-01-01

Several nonclassical major histocompatibilty antigens (class Ib molecules) have emerged as key players in the early immune response to pathogens or stress. Class Ib molecules activate subsets of T cells that mount effector responses before the adaptive immune system, and thus are called innate T cells. MR1 is a novel class Ib molecule with properties highly suggestive of its regulation of mucosal immunity. The Mr1 gene is evolutionarily conserved, is non-Mhc linked, and controls the development of mucosal-associated invariant T (MAIT) cells. MAIT cells preferentially reside in the gut, and their development is dependent on commensal microbiota. Although these properties suggest that MAIT cells function as innate T cells in the mucosa, this has been difficult to test, due to the (i) paucity of MAIT cells that display MR1-specific activation in vitro and (ii) lack of knowledge of whether or not MR1 presents antigen. Here we show that both mouse and human MAIT cells display a high level of cross-reactivity on mammalian MR1 orthologs, but with differences consistent with limited ligand discrimination. Furthermore, acid eluates from recombinant or cellular MR1 proteins enhance MAIT cell activation in an MR1-specific and cross-species manner. Our findings demonstrate that the presentation pathway of MR1 to MAIT cells is highly evolutionarily conserved. PMID:19416870

SU-G-IeP1-08: MR Geometric Distortion Dependency On Imaging Sequence, Acquisition Orientation and Receiver Bandwidth of a Dedicated 1.5T MR-Simulator

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

Law, M; Yuan, J; Wong, O

Purpose: To investigate the 3D geometric distortion of four potential MR sequences for radiotheraptic applications, and its dependency on sequence-type, acquisition-orientation and receiver-bandwidth from a dedicated 1.5T 700mm-wide bore MR-simulator (Magnetom-Aera, Sienmens Healthcare, Erlangen, Germany), using a large customized geometric accuracy phantom. Methods: This work studied 3D gradient-echo (VIBE) and spin-echo (SPACE) sequences for anatomical imaging; a specific ultra-short-TE sequence (PETRA) potentially for bone imaging and MR-based dosimetry; and a motion-insensitive sequence (BLADE) for dynamic applications like 4D-MRI. Integrated geometric-correction was employed, three orthogonal acquisition-orientations and up to three receiver-bandwidths were used, yielding 27 acquisitions for testing (Table 1a).A customizedmore » geometric accuracy phantom (polyurethane, MR/CT invisible, W×L×H:55×55×32.5cm3) was constructed and filled with 3892 spherical markers (6mm diameter, MR/CT visible) arranged on a 25mm-interval 3D isotropic-grid (Fig.1). The marker positions in MR images were quantitatively calculated and compared against those in the CT-reference using customized MatLab scripts. Results: The average distortion within various diameter-of-spherical-volumes (DSVs) and the usable DSVs under various distortion limits were measured (Tables 1b-c). It was observed that distortions fluctuated when sequence-type, acquisition-orientation or receiver-bandwidth changed (e.g. within 300mm-DSV, the lowest/highest average distortions of VIBE were 0.40mm/0.59mm, a 47.5% difference). According to AAPM-TG66 (<1mm distortion, left-most column of Table 1c), PETRA (Largest-DSV:253.9mm) has the potential on brain treatment, while BLADE (Largest-DSV:207.2mm) may need improvement for thoracic/abdominal applications. The results of VIBE (Largest-DSVs:294.3mm, the best among tested acquisitions) and SPACE (Largest-DSVs:267.7mm) suggests their potentials on head and neck

Photoreduction of Shewanella oneidensis Extracellular Cytochromes by Organic Chromophores and Dye‐Sensitized TiO2

PubMed Central

Ainsworth, Emma V.; Lockwood, Colin W. J.; White, Gaye F.; Hwang, Ee Taek; Sakai, Tsubasa; Gross, Manuela A.; Richardson, David J.; Clarke, Thomas A.

2016-01-01

Abstract The transfer of photoenergized electrons from extracellular photosensitizers across a bacterial cell envelope to drive intracellular chemical transformations represents an attractive way to harness nature's catalytic machinery for solar‐assisted chemical synthesis. In Shewanella oneidensis MR‐1 (MR‐1), trans‐outer‐membrane electron transfer is performed by the extracellular cytochromes MtrC and OmcA acting together with the outer‐membrane‐spanning porin⋅cytochrome complex (MtrAB). Here we demonstrate photoreduction of solutions of MtrC, OmcA, and the MtrCAB complex by soluble photosensitizers: namely, eosin Y, fluorescein, proflavine, flavin, and adenine dinucleotide, as well as by riboflavin and flavin mononucleotide, two compounds secreted by MR‐1. We show photoreduction of MtrC and OmcA adsorbed on RuII‐dye‐sensitized TiO2 nanoparticles and that these protein‐coated particles perform photocatalytic reduction of solutions of MtrC, OmcA, and MtrCAB. These findings provide a framework for informed development of strategies for using the outer‐membrane‐associated cytochromes of MR‐1 for solar‐driven microbial synthesis in natural and engineered bacteria. PMID:27685371

The knee: Surface-coil MR imaging at 1. 5 T

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

Beltran, J.; Noto, A.M.; Mosure, J.C.

1986-06-01

Seven normal knees (in five volunteers) and seven injured knees (in seven patients) were examined by high-resolution magnetic resonance (MR) imaging at 1.5 T with a surface coil. Seven medial meniscal tears, three anterior cruciate ligament tears, one posterior cruciate ligament avulsion, an old osteochondral fracture, femoral condylar chondro-malacia, and one case of semimembranous tendon reinsertion were identified. MR images correlated well with recent double-contrast arthrograms or results of surgery. All tears were identified in both the sagittal and coronal planes. Because of its ability to demonstrate small meniscal lesions and ligamentous injuries readily, MR imaging with a surface coilmore » may eventually replace the more invasive arthrography.« less

MR-guided radiofrequency ablation of hepatic malignancies at 1.5 T: initial results.

PubMed

Mahnken, Andreas H; Buecker, Arno; Spuentrup, Elmar; Krombach, Gabriele A; Henzler, Dietrich; Günther, Rolf W; Tacke, Josef

2004-03-01

To assess the feasibility of magnetic resonance (MR)-guided radiofrequency ablation (RFA) of hepatic malignancies using a high-field MR scanner. A total of 10 patients with 14 primary (N = 1) or secondary (N = 13) hepatic malignancies underwent MR-guided RFA using a closed-bore 1.5 T MR scanner. Lesion diameters ranged from 2.0 cm to 4.7 cm. RFA was performed using a 200-W generator in combination with a 3.5-cm LeVeen electrode applying a standardized energy protocol. RFA was technically feasible in all patients. Necrosis diameter ranged from 2.5 cm to 6.8 cm. The mean follow-up period is 12.2 (1-18) months. In nine out of 10 patients, local tumor control was achieved. For this purpose, a second CT-guided RFA was required in two patients. In four patients, multifocal hepatic tumor progression occurred, with the treated lesion remaining tumor-free in three of these patients. Two patients showed extrahepatic tumor progression. Four patients remained tumor-free. No major complications occurred. MR-guided RFA of hepatic malignancies in a closed-bore high-field MR scanner is technically feasible and safe. It can be advantageous in locations considered unfavorable for CT-guided puncture or in patients in which iodinated contrast material is contraindicated. Copyright 2004 Wiley-Liss, Inc.

The Influence of Acidity on Microbial Fuel Cells Containing Shewanella Oneidensis (PREPRINT)

DTIC Science & Technology

2008-09-01

d a fi b i s a h t s p t o m d C H p F 8 ig. 4. Cyclic voltammetry of filter sterilized media after 4 days of growth of S. neidensis MR-1 or S...of autologous mediators in the rowthmedium changeswith pH.We analyzed filter sterilized cul- ure supernatants by cyclic voltammetry (Fig. 4), and HPLC...Marsili et al., 2008). Cyclic voltammetrywas used to detect redox-active compounds n growthmedia supernatants fromMR-1 andDSP10 cultures. Fig. 4 hows

Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering.

PubMed

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F

2016-01-07

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth's deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å(-1) corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.

MR-based source localization for MR-guided HDR brachytherapy

NASA Astrophysics Data System (ADS)

Beld, E.; Moerland, M. A.; Zijlstra, F.; Viergever, M. A.; Lagendijk, J. J. W.; Seevinck, P. R.

2018-04-01

For the purpose of MR-guided high-dose-rate (HDR) brachytherapy, a method for real-time localization of an HDR brachytherapy source was developed, which requires high spatial and temporal resolutions. MR-based localization of an HDR source serves two main aims. First, it enables real-time treatment verification by determination of the HDR source positions during treatment. Second, when using a dummy source, MR-based source localization provides an automatic detection of the source dwell positions after catheter insertion, allowing elimination of the catheter reconstruction procedure. Localization of the HDR source was conducted by simulation of the MR artifacts, followed by a phase correlation localization algorithm applied to the MR images and the simulated images, to determine the position of the HDR source in the MR images. To increase the temporal resolution of the MR acquisition, the spatial resolution was decreased, and a subpixel localization operation was introduced. Furthermore, parallel imaging (sensitivity encoding) was applied to further decrease the MR scan time. The localization method was validated by a comparison with CT, and the accuracy and precision were investigated. The results demonstrated that the described method could be used to determine the HDR source position with a high accuracy (0.4–0.6 mm) and a high precision (⩽0.1 mm), at high temporal resolutions (0.15–1.2 s per slice). This would enable real-time treatment verification as well as an automatic detection of the source dwell positions.

Deep Learning MR Imaging-based Attenuation Correction for PET/MR Imaging.

PubMed

Liu, Fang; Jang, Hyungseok; Kijowski, Richard; Bradshaw, Tyler; McMillan, Alan B

2018-02-01

Purpose To develop and evaluate the feasibility of deep learning approaches for magnetic resonance (MR) imaging-based attenuation correction (AC) (termed deep MRAC) in brain positron emission tomography (PET)/MR imaging. Materials and Methods A PET/MR imaging AC pipeline was built by using a deep learning approach to generate pseudo computed tomographic (CT) scans from MR images. A deep convolutional auto-encoder network was trained to identify air, bone, and soft tissue in volumetric head MR images coregistered to CT data for training. A set of 30 retrospective three-dimensional T1-weighted head images was used to train the model, which was then evaluated in 10 patients by comparing the generated pseudo CT scan to an acquired CT scan. A prospective study was carried out for utilizing simultaneous PET/MR imaging for five subjects by using the proposed approach. Analysis of covariance and paired-sample t tests were used for statistical analysis to compare PET reconstruction error with deep MRAC and two existing MR imaging-based AC approaches with CT-based AC. Results Deep MRAC provides an accurate pseudo CT scan with a mean Dice coefficient of 0.971 ± 0.005 for air, 0.936 ± 0.011 for soft tissue, and 0.803 ± 0.021 for bone. Furthermore, deep MRAC provides good PET results, with average errors of less than 1% in most brain regions. Significantly lower PET reconstruction errors were realized with deep MRAC (-0.7% ± 1.1) compared with Dixon-based soft-tissue and air segmentation (-5.8% ± 3.1) and anatomic CT-based template registration (-4.8% ± 2.2). Conclusion The authors developed an automated approach that allows generation of discrete-valued pseudo CT scans (soft tissue, bone, and air) from a single high-spatial-resolution diagnostic-quality three-dimensional MR image and evaluated it in brain PET/MR imaging. This deep learning approach for MR imaging-based AC provided reduced PET reconstruction error relative to a CT-based standard within the brain compared

Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

PubMed Central

Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

2018-01-01

Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

Characterisation and Expression Analysis of MrLip1, a Class 3 Family Lipase of Malassezia restricta.

PubMed

Park, Minji; Jung, Won Hee; Han, Song Hee; Lee, Young Hoon; Lee, Yang Won

2015-11-01

The genus Malassezia is associated with a wide range of skin diseases and is the predominant fungal genus isolated from human skin. Of the 14 Malassezia species identified, M. restricta is the most abundant fungal species found from both healthy and diseased skin. Emerging evidences have suggested that extracellular lipases of Malassezia play a critical role in its survival on the host skin surface. This study aimed to characterise the lipase 1 homologue (MrLip1) in M. restricta and to analyse its expression under different environmental conditions. The full sequence of the gene encoding MrLip1 was determined by rapid amplification of cDNA ends, and it was then heterologously expressed in Pichia pastoris. MrLip1 protein was successfully purified and used for lipase assay and specific antibody generation for use in expression analysis. The optimum pH and temperature for the activity of purified MrLip1 were pH 5.0 and 34 °C respectively. Furthermore, the expression of MrLip1 peaked at a similar pH and temperature, suggesting that the optimal conditions for MrLip1 protein activity and expression are similar to that found on the human skin surface. This study provides data to improve our understanding of the role and characteristics of lipase 1 in M. restricta. © 2015 Blackwell Verlag GmbH.

Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering

NASA Astrophysics Data System (ADS)

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G.; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V.; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F.

2016-01-01

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth’s deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å-1 corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.

SU-E-J-217: Multiparametric MR Imaging of Cranial Tumors On a Dedicated 1.0T MR Simulator Prior to Stereotactic Radiosurgery

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

Wen, N; Glide-Hurst, C; Liu, M

Purpose: Quantitative magnetic resonance imaging (MRI) of cranial lesions prior to stereotactic radiosurgery (SRS) may improve treatment planning and provide potential prognostic value. The practicality and logistics of acquiring advanced multiparametric MRI sequences to measure vascular and cellular properties of cerebral tumors are explored on a 1.0 Tesla MR Simulator. Methods: MR simulation was performed immediately following routine CT simulation on a 1T MR Simulator. MR sequences used were in the order they were performed: T2-Weighted Turbo Spin Echo (T2W-TSE), T2 FLAIR, Diffusion-weighted (DWI, b = 0, 800 to generate an apparent diffusion coefficient (ADC) map), 3D T1-Weighted Fast Fieldmore » Echo (T1W-FFE), Dynamic Contrast Enhanced (DCE) and Post Gadolinium Contrast Enhanced 3D T1W-FFE images. T1 pre-contrast values was generated by acquiring six different flip angles. The arterial input function was derived from arterial pixels in the perfusion images selected manually. The extended Tofts model was used to generate the permeability maps. Routine MRI scans took about 30 minutes to complete; the additional scans added 12 minutes. Results: To date, seven patients with cerebral tumors have been imaged and tumor physiology characterized. For example, on a glioblastoma patient, the volume contoured on T1 Gd images, ADC map and the pharmacokinetic map (Ktrans) were 1.9, 1.4, and 1.5 cc respectively with strong spatial correlation. The mean ADC value of the entire volume was 1141 μm2/s while the value in the white matter was 811 μm2/s. The mean value of Ktrans was 0.02 min-1 in the tumor volume and 0.00 in the normal white matter. Conclusion: Our initial results suggest that multiparametric MRI sequences may provide a more quantitative evaluation of vascular and tumor properties. Implementing functional imaging during MR-SIM may be particularly beneficial in assessing tumor extent, differentiating radiation necrosis from tumor recurrence, and establishing

Mr Tompkins in Paperback

NASA Astrophysics Data System (ADS)

Gamow, George; Penrose, Foreword by Roger

2012-03-01

Foreword Roger Penrose; 1. City speed limit; 2. The Professor's lecture on relativity which caused Mr Tompkins's dream; 3. Mr Tompkins takes a holiday; 4. The Professor's lecture on curved space, gravity and the universe; 5. The pulsating universe; 6. Cosmic opera; 7. Quantum billiards; 8. Quantum jungles; 9. Maxwell's demon; 10. The gay tribe of electrons; 10 1/2. A part of the previous lecture which Mr Tompkins slept through; 12. Inside the nucleus; 13. The wood carver; 14. Holes in nothing; 15. Mr Tompkins tastes a Japanese meal.

Design of a multimodal (1H/23Na MR/CT) anthropomorphic thorax phantom.

PubMed

Neumann, Wiebke; Lietzmann, Florian; Schad, Lothar R; Zöllner, Frank G

2017-06-01

This work proposes a modular, anthropomorphic MR and CT thorax phantom that enables the comparison of experimental studies for quantitative evaluation of deformable, multimodal image registration algorithms and realistic multi-nuclear MR imaging techniques. A human thorax phantom was developed with insertable modules representing lung, liver, ribs and additional tracking spheres. The quality of human tissue mimicking characteristics was evaluated for 1 H and 23 Na MR as well as CT imaging. The position of landmarks in the lung lobes was tracked during CT image acquisition at several positions during breathing cycles. 1 H MR measurements of the liver were repeated after seven months to determine long term stability. The modules possess HU, T 1 and T 2 values comparable to human tissues (lung module: -756±148HU, artificial ribs: 218±56HU (low CaCO 3 concentration) and 339±121 (high CaCO 3 concentration), liver module: T 1 =790±28ms, T 2 =65±1ms). Motion analysis showed that the landmarks in the lung lobes follow a 3D trajectory similar to human breathing motion. The tracking spheres are well detectable in both CT and MRI. The parameters of the tracking spheres can be adjusted in the following ranges to result in a distinct signal: HU values from 150 to 900HU, T 1 relaxation time from 550ms to 2000ms, T 2 relaxation time from 40ms to 200ms. The presented anthropomorphic multimodal thorax phantom fulfills the demands of a simple, inexpensive system with interchangeable components. In future, the modular design allows for complementing the present set up with additional modules focusing on specific research targets such as perfusion studies, 23 Na MR quantification experiments and an increasing level of complexity for motion studies. Copyright © 2016. Published by Elsevier GmbH.

XAFS and X-Ray and Electron Microscopy Investigations of Radionuclide Transformations at the Mineral-Microbe Interface

NASA Astrophysics Data System (ADS)

Kemner, Ken; O'Loughlin, Ed; Kelly, Shelly; Ravel, Bruce; Boyanov, Maxim; Sholto-Douglas, Deirdre; Lai, Barry; Cook, Russ; Carpenter, Everett; Harris, Vince; Nealson, Ken

2007-02-01

The microenvironment at and adjacent to surfaces of actively metabolizing cells, whether in a planktonic state or adhered to mineral surfaces, can be significantly different from the bulk environment. Microbial polymers (polysaccharides, DNA, RNA, and proteins), whether attached to or released from the cell, can contribute to the development of steep chemical gradients over very short distances. It is currently difficult to predict the behavior of contaminant radionuclides and metals in such microenvironments, because the chemistry there has been difficult or impossible to define. The behavior of contaminants in such microenvironments can ultimately affect their macroscopic fates. We have successfully performed a series of U LIII edge x-ray absorption fine structure (XAFS) spectroscopy, hard x-ray fluorescence (XRF) microprobe (150 nm resolution), and electron microscopy (EM) measurements on lepidocrocite thin films (˜1 micron thickness) deposited on kapton films that have been inoculated with the dissimilatory metal reducing bacterium Shewanella oneidensis MR-1 and exposed to 0.05 mM uranyl acetate under anoxic conditions. Similarly, we have performed a series of U LIII edge EXAFS measurements on lepidocrocite powders exposed to 0.05 mM uranyl acetate and exopolymeric components harvested from S. oneidensis MR-1 grown under aerobic conditions. These results demonstrate the utility of combining bulk XAFS with x-ray and electron microscopies.

High signal intensity of intervertebral calcified disks on T1-weighted MR images resulting from fat content.

PubMed

Malghem, Jacques; Lecouvet, Frédéric E; François, Robert; Vande Berg, Bruno C; Duprez, Thierry; Cosnard, Guy; Maldague, Baudouin E

2005-02-01

To explain a cause of high signal intensity on T1-weighted MR images in calcified intervertebral disks associated with spinal fusion. Magnetic resonance and radiological examinations of 13 patients were reviewed, presenting one or several intervertebral disks showing a high signal intensity on T1-weighted MR images, associated both with the presence of calcifications in the disks and with peripheral fusion of the corresponding spinal segments. Fusion was due to ligament ossifications (n=8), ankylosing spondylitis (n=4), or posterior arthrodesis (n=1). Imaging files included X-rays and T1-weighted MR images in all cases, T2-weighted MR images in 12 cases, MR images with fat signal suppression in 7 cases, and a CT scan in 1 case. Histological study of a calcified disk from an anatomical specimen of an ankylosed lumbar spine resulting from ankylosing spondylitis was examined. The signal intensity of the disks was similar to that of the bone marrow or of perivertebral fat both on T1-weighted MR images and on all sequences, including those with fat signal suppression. In one of these disks, a strongly negative absorption coefficient was focally measured by CT scan, suggesting a fatty content. The histological examination of the ankylosed calcified disk revealed the presence of well-differentiated bone tissue and fatty marrow within the disk. The high signal intensity of some calcified intervertebral disks on T1-weighted MR images can result from the presence of fatty marrow, probably related to a disk ossification process in ankylosed spines.

MR/PET quantification tools: Registration, segmentation, classification, and MR-based attenuation correction

PubMed Central

Fei, Baowei; Yang, Xiaofeng; Nye, Jonathon A.; Aarsvold, John N.; Raghunath, Nivedita; Cervo, Morgan; Stark, Rebecca; Meltzer, Carolyn C.; Votaw, John R.

2012-01-01

Purpose: Combined MR/PET is a relatively new, hybrid imaging modality. A human MR/PET prototype system consisting of a Siemens 3T Trio MR and brain PET insert was installed and tested at our institution. Its present design does not offer measured attenuation correction (AC) using traditional transmission imaging. This study is the development of quantification tools including MR-based AC for quantification in combined MR/PET for brain imaging. Methods: The developed quantification tools include image registration, segmentation, classification, and MR-based AC. These components were integrated into a single scheme for processing MR/PET data. The segmentation method is multiscale and based on the Radon transform of brain MR images. It was developed to segment the skull on T1-weighted MR images. A modified fuzzy C-means classification scheme was developed to classify brain tissue into gray matter, white matter, and cerebrospinal fluid. Classified tissue is assigned an attenuation coefficient so that AC factors can be generated. PET emission data are then reconstructed using a three-dimensional ordered sets expectation maximization method with the MR-based AC map. Ten subjects had separate MR and PET scans. The PET with [11C]PIB was acquired using a high-resolution research tomography (HRRT) PET. MR-based AC was compared with transmission (TX)-based AC on the HRRT. Seventeen volumes of interest were drawn manually on each subject image to compare the PET activities between the MR-based and TX-based AC methods. Results: For skull segmentation, the overlap ratio between our segmented results and the ground truth is 85.2 ± 2.6%. Attenuation correction results from the ten subjects show that the difference between the MR and TX-based methods was <6.5%. Conclusions: MR-based AC compared favorably with conventional transmission-based AC. Quantitative tools including registration, segmentation, classification, and MR-based AC have been developed for use in combined MR

Liver Metabolite Concentrations Measured with 1H MR Spectroscopy

PubMed Central

Pettigrew, Roderic I.; Gharib, Ahmed M.

2012-01-01

Purpose: To determine the feasibility of measuring choline and glycogen concentrations in normal human liver in vivo with proton (hydrogen 1 [1H]) magnetic resonance (MR) spectroscopy. Materials and Methods: Signed consent to participate in an institutional review board–approved and HIPAA-compliant study was obtained from 46 subjects (mean age, 46 years ± 17 [standard deviation]; 24 women) consecutively recruited during 285 days. Navigator-gated MR images were used to select 8-mL volumes for point-resolved spectroscopy (PRESS) with a 35-msec echo time. Line widths were minimized with fast breath-hold B0 field mapping and further manual shimming. Navigator-gated spectra were recorded with and without water suppression to determine metabolite concentrations with water signals as an internal reference. In three subjects, echo time was varied to determine the glycogen and choline T2. Linear regression analysis was used to examine relations between choline, hepatic lipid content, body mass index, glycogen content, and age. Results: Choline concentrations could be determined in 46 of 48 studies and was found to be 8.6 mmol per kilogram of wet weight ± 3.1 (range, 3.8–17.6; n = 44). Twenty-seven spectra in 25 individuals with narrow line widths and low lipid content were adequate for quantitation of glycogen. The glycogen (glucosyl unit) concentration was 38.1 mmol/kg wet weight ± 14.4. The T2 of combined glycogen peaks in the liver of three subjects was 36 msec ± 8. Choline levels showed a weak but significant correlation with glycogen (r2 = 0.15; P < .05) but not with lipid content. Conclusion: Navigator-gated and gradient-echo shimmed PRESS 1H MR spectroscopy may allow quantification of liver metabolites that are important for understanding and identifying disorders of glucose and lipid metabolism. © RSNA, 2012 Supplemental material: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.12112344/-/DC1 PMID:22891360

MR fingerprinting with simultaneous B1 estimation.

PubMed

Buonincontri, Guido; Sawiak, Stephen J

2016-10-01

MR fingerprinting (MRF) can be used for quantitative estimation of physical parameters in MRI. Here, we extend the method to incorporate B1 estimation. The acquisition is based on steady state free precession MR fingerprinting with a Cartesian trajectory. To increase the sensitivity to the B1 profile, abrupt changes in flip angle were introduced in the sequence. Slice profile and B1 effects were included in the dictionary and the results from two- and three-dimensional (3D) acquisitions were compared. Acceleration was demonstrated using retrospective undersampling in the phase encode directions of 3D data exploiting redundancy between MRF frames at the edges of k-space. Without B1 estimation, T2 and B1 were inaccurate by more than 20%. Abrupt changes in flip angle improved B1 maps. T1 and T2 values obtained with the new MRF methods agree with classical spin echo measurements and are independent of the B1 field profile. When using view sharing reconstruction, results remained accurate (error <10%) when sampling under 10% of k-space from the 3D data. The methods demonstrated here can successfully measure T1, T2, and B1. Errors due to slice profile can be substantially reduced by including its effect in the dictionary or acquiring data in 3D. Magn Reson Med 76:1127-1135, 2016. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3.

PubMed

Aigle, Axel; Bonin, Patricia; Iobbi-Nivol, Chantal; Méjean, Vincent; Michotey, Valérie

2017-03-20

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

NASA Astrophysics Data System (ADS)

Aigle, Axel; Bonin, Patricia; Iobbi-Nivol, Chantal; Méjean, Vincent; Michotey, Valérie

2017-03-01

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

Bioelectrochemical biosensor for water toxicity detection: generation of dual signals for electrochemical assay confirmation.

PubMed

Yang, Yuan; Wang, Yan-Zhai; Fang, Zhen; Yu, Yang-Yang; Yong, Yang-Chun

2018-02-01

Toxicity assessment of water is of great important to the safety of human health and to social security because of more and more toxic compounds that are spilled into the aquatic environment. Therefore, the development of fast and reliable toxicity assessment methods is of great interest and attracts much attention. In this study, by using the electrochemical activity of Shewanella oneidensis MR-1 cells as the toxicity indicator, 3,5-dichlorophenol (DCP) as the model toxic compound, a new biosensor for water toxicity assessment was developed. Strikingly, the presence of DCP in the water significantly inhibited the maximum current output of the S. oneidensis MR-1 in a three-electrode system and also retarded the current evolution by the cells. Under the optimized conditions, the maximum current output of the biosensor was proportional to the concentration of DCP up to 30 mg/L. The half maximal inhibitory concentration of DCP determined by this biosensor is about 14.5 mg/L. Furthermore, simultaneous monitoring of the retarded time (Δt) for current generation allowed the identification of another biosensor signal in response to DCP which could be employed to verify the electrochemical result by dual confirmation. Thus, the present study has provided a reliable and promising approach for water quality assessment and risk warning of water toxicity.

SU-F-J-172: Hybrid MR/CT Compatible Phantom for MR-Only Based Radiotherapy

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

Kim, M; Lee, S; Song, K

2016-06-15

Purpose: Development of hybrid MR/CT compatible phantom was introduced to fully establish MR image only radiation treatment and this suggested technique using in-house developed hybrid MR/CT compatible phantom image would utilize to generate radiation treatment planning and perform dose calculation without multi-modal registration process or generation of pseudo CT. Methods: Fundamental characteristics for “hybrid MR/CT compatible phantom” was established: Relaxation times equivalent to human tissue, dielectric properties, homogeneous relaxation times, sufficient strength to fabricate a torso, ease of handling, a wide variety of density material for calibration, chemical and physical stability over an extended time. For this requirements, chemical componentmore » in each tested plug which would be tissue equivalent to human tissue on MR and CT image and production of phantom body and plug was performed. Chemical component has described below: Agaros, GdCl{sub 3}, NaN{sub 3}, NaCl, K{sub 2}Co{sub 3}, deionized-distilled water. Various mixture of chemical component to simulate human tissue on both MR and CT image was tested by measuring T1, T2 relaxation time and signal intensity (SI) on MR image and Hounsfield unit (HU) on CT and each value was compared. The hybrid MR/CT compatible phantom with 14 plugs was designed and has made. Total height and external diameter was decided by internal size of 32 channel MR head-coil. Results: Tissue-equivalent chemical component materials and hybrid MR/CT compatible phantom was developed. The range of T1, T2 relaxation time and SI on MR image, HU on CT was acquired and could be adjusted to correspond to simulated human tissue. Conclusion: Current result shows its possibility for MR-only based radiotherapy and the best mixing rate of chemical component for tissue-equivalent image on MR and CT was founded. However, additional technical issues remain to be overcome. Conversion of SI on MR image into HU and dose calculation

Radiofrequency power deposition near metallic wires during MR imaging: feasibility study using T1-weighted thermal imaging.

PubMed

Oulmane, F; Detti, V; Grenier, D; Perrin, E; Saint-Jalmes, H

2007-01-01

The presence of metallic conductors (implants, wires or catheters) is prohibited in MR imaging for safety purpose with respect to radiofrequency (RF) power deposition caused by RF excitation B1 field. This work describes the use of T1-weigthed MR imaging for estimating a thermal map around a metallic (copper) wire located in the center of a MR imaging unit during an imaging sequence. The experimental set up and the methodology used for capturing the elevation of temperature created by radiofrequency power deposition around the wire is presented. A proof of its efficiency to followup temperature elevation about 0,5 degrees C in a milimetric region of interest (pixel size: 1 x 1 mm2, slice thickness 5 mm) located around the wire is given, leading to further developments of MR imaging in presence of metallic implants, coils or catheters.

Diffusion in biofilms respiring on electrodes

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

Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.

2012-11-15

The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed for noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensionalmore » De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that (1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; (2) Drs at a given location decreases with G. sulfurreducens biofilm age; (3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and (4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.« less

Detection and staging of chondromalacia patellae: relative efficacies of conventional MR imaging, MR arthrography, and CT arthrography.

PubMed

Gagliardi, J A; Chung, E M; Chandnani, V P; Kesling, K L; Christensen, K P; Null, R N; Radvany, M G; Hansen, M F

1994-09-01

Chondromalacia patellae is a condition characterized by softening, fraying, and ulceration of patellar articular cartilage. We compare the sensitivity, specificity, and accuracy of conventional MR imaging, MR arthrography, and CT arthrography in detecting and staging this abnormality. Twenty-seven patients with pain in the anterior part of the knee were prospectively examined with MR imaging, including T1-weighted (650/16), proton density-weighted (2000/20), T2-weighted (2000/80), and spoiled two-dimensional gradient-recalled acquisition in the steady state (SPGR/)/35 degrees (51/10) with fat saturation pulse sequences. All were also examined with T1-weighted MR imaging after intraarticular injection of dilute gadopentetate dimeglumine and with double-contrast CT arthrography. Each imaging technique was evaluated independently by two observers, who reached a consensus interpretation. The signal characteristics of cartilage on MR images and contour abnormalities noted with all imaging techniques were evaluated and graded according to a modification of the classification of Shahriaree. Twenty-six of the 54 facets examined had chondromalacia shown by arthroscopy, which was used as the standard of reference. The sensitivity, specificity, and accuracy of each imaging technique in the diagnosis of each stage of chondromalacia patellae were determined and compared by using the McNemar two-tailed analysis. Arthroscopy showed that 28 facets were normal. Grade 1 chondromalacia patellae was diagnosed only with MR and CT arthrography in two (29%) of seven facets. Intermediate (grade 2 or 3) chondromalacia patellae was detected in two (13%) of 15 facets with T1-weighted and SPGR MR imaging, in three (20%) of 15 facets with proton density-weighted MR imaging, in seven (47%) of 15 facets with T2-weighted MR imaging, in 11 (73%) of 15 facets with CT arthrography, and in 12 (80%) of 15 facets with MR arthrography. Grade 4 was detected in three (75%) of four facets with T1-, proton

MR pyelography and conventional MR imaging in urinary tract obstruction.

PubMed

Catalano, C; Pavone, P; Laghi, A; Scipioni, A; Panebianco, V; Brillo, R; Fraioli, F; Passariello, R

1999-03-01

To evaluate the possible role of MR imaging in the assessment of patients with urinary tract obstruction by combining conventional MR imaging and MR pyelography (MRP). Forty-three patients with dilated upper urinary tract were studied with a high gradient strength 0.5 T magnet. Respiratory compensated T1-weighted, SE and T2-weighted TSE sequences were acquired in all patients. MRP images were obtained by using a respiratory compensated 3D T2-weighted TSE sequence. MRP images were reconstructed with a MIP algorithm. In all cases, urography and/or ascending pyelography were also performed. Images were independently evaluated by two radiologists. The dilated tract ureter and the level of the obstruction could be correctly demonstrated in all cases. The cause of the obstruction was correctly demonstrated by examiner 1 in 90% and by examiner 2 in 88%. The interobserver agreement was high with a kappa-value of 0.96. In cases of obstructive hydroureteronephrosis MR imaging, combining MRP and conventional sequences, can be proposed as an accurate technique in the assessment of level and cause of obstruction.

Heteronuclear Cross Polarization for Enhanced Sensitivity of in Vivo13C MR Spectroscopy on a Clinical 1.5 T MR System

NASA Astrophysics Data System (ADS)

van den Bergh, Adrianus J.; van den Boogert, Hendrikus J.; Heerschap, Arend

1998-11-01

The potential of heteronuclear {1H-13C} cross polarization was studied for optimization of the signal-to-noise ratio inin vivo13C MR spectroscopy at the clinical field strength of 1.5 T. Experiments on the human calf showed a significant chemical-shift selective signal enhancement on triglyceride signals of 3.9 by heteronuclear cross polarization, compared to a standard pulse-acquire sequence. Studies on a neonatal piglet brain showed an enhancement by cross polarization of 2.2 for the detection of13C-1-glucose. This enhancement allowed a fourfold improvement in time resolution in dynamic13C MR of13C-1-glucose inflow in piglet brain. Phantom experiments demonstrated the efficiency of this technique for interleaved detection of two spectral regions. Tests with a volume coil showed the feasibility of signal enhancement by cross polarization over a large volume of interest.

[Tolerance of magnetic resonance imaging in children and adolescents performed in a 1.5 Tesla MR scanner with an open design].

PubMed

Adamietz, B; Cavallaro, A; Radkow, T; Alibek, S; Holter, W; Bautz, W A; Staatz, G

2007-08-01

To investigate the tolerance of MR examinations in children and adolescents performed in a 1.5 Tesla MR scanner with an expanded bore diameter. 163 patients, ages 4 to 25, underwent MR examinations in a 1.5 Tesla MR scanner with an open design (MAGNETOM Espree, Siemens, Erlangen, Germany), characterized by a compact length of 125 cm and an expanded 70 cm bore diameter. MR imaging of the brain was carried out in most cases (78.5 %), followed by examinations of the spinal canal (9.8 %), the extremities (9.2 %) and the neck (2.5 %). The patients were divided into four age groups and the success rate, motion artifacts and diagnostic quality of the MR examinations were assessed using a 3-grade scale. In 119 of 163 patients (73.0 %), MR examination was possible without any motion artifacts. With respect to the different age groups, 41.7 % of the 4 - 7-year-old children, 67.6 % of the 8 - 10-year-old children, 84.1 % of the 11 - 16-year-old children and 95.8 % of the patients older than 17 showed tolerance grade I without motion artifacts and excellent diagnostic image quality. In 39 of 163 children (23.9 %), the MR images showed moderate motion artifacts but had sufficient diagnostic quality. With regard to the different age groups, 52.8 % of the 4 - 7-year-old children, 26.5 % of the 8 - 10-year-old children, 15.9 % of the 11 - 16-year-old children and none of the patients older than 17 showed tolerance grade II with moderate motion artifacts and sufficient diagnostic image quality. In only 4 of 124 children < 10 years old and 1 child > 10 years old, the MR examination was not feasible and had to be repeated under sedation. Pediatric MR imaging using a 1.5 Tesla MR scanner with an open design can be conducted in children and adolescents with excellent acceptance. The failure rate of 3.0 % of cases for pediatric MR imaging is comparable to that of a conventional low-field open MR scanner.

T1ρ-weighted Dynamic Glucose-enhanced MR Imaging in the Human Brain.

PubMed

Paech, Daniel; Schuenke, Patrick; Koehler, Christina; Windschuh, Johannes; Mundiyanapurath, Sibu; Bickelhaupt, Sebastian; Bonekamp, David; Bäumer, Philipp; Bachert, Peter; Ladd, Mark E; Bendszus, Martin; Wick, Wolfgang; Unterberg, Andreas; Schlemmer, Heinz-Peter; Zaiss, Moritz; Radbruch, Alexander

2017-12-01

Purpose To evaluate the ability to detect intracerebral regions of increased glucose concentration at T1ρ-weighted dynamic glucose-enhanced (DGE) magnetic resonance (MR) imaging at 7.0 T. Materials and Methods This prospective study was approved by the institutional review board. Nine patients with newly diagnosed glioblastoma and four healthy volunteers were included in this study from October 2015 to July 2016. Adiabatically prepared chemical exchange-sensitive spin-lock imaging was performed with a 7.0-T whole-body unit with a temporal resolution of approximately 7 seconds, yielding the time-resolved DGE contrast. T1ρ-weighted DGE MR imaging was performed with injection of 100 mL of 20% d-glucose via the cubital vein. Glucose enhancement, given by the relative signal intensity change at T1ρ-weighted MR imaging (DGEρ), was quantitatively investigated in brain gray matter versus white matter of healthy volunteers and in tumor tissue versus normal-appearing white matter of patients with glioblastoma. The median signal intensities of the assessed brain regions were compared by using the Wilcoxon rank-sum test. Results In healthy volunteers, the median signal intensity in basal ganglia gray matter (DGEρ = 4.59%) was significantly increased compared with that in white matter tissue (DGEρ = 0.65%) (P = .028). In patients, the median signal intensity in the glucose-enhanced tumor region as displayed on T1ρ-weighted DGE images (DGEρ = 2.02%) was significantly higher than that in contralateral normal-appearing white matter (DGEρ = 0.08%) (P < .0001). Conclusion T1ρ-weighted DGE MR imaging in healthy volunteers and patients with newly diagnosed, untreated glioblastoma enabled visualization of brain glucose physiology and pathophysiologically increased glucose uptake and may have the potential to provide information about glucose metabolism in tumor tissue. © RSNA, 2017 Online supplemental material is available for this article.

Cardiac Magnetic Resonance Imaging Using an Open 1.0T MR Platform: A Comparative Study with a 1.5T Tunnel System.

PubMed

Fischbach, Katharina; Kosiek, Otrud; Friebe, Björn; Wybranski, Christian; Schnackenburg, Bernhard; Schmeisser, Alexander; Smid, Jan; Ricke, Jens; Pech, Maciej

2017-01-01

Cardiac magnetic resonance imaging (cMRI) has become the non-invasive reference standard for the evaluation of cardiac function and viability. The introduction of open, high-field, 1.0T (HFO) MR scanners offers advantages for examinations of obese, claustrophobic and paediatric patients.The aim of our study was to compare standard cMRI sequences from an HFO scanner and those from a cylindrical, 1.5T MR system. Fifteen volunteers underwent cMRI both in an open HFO and in a cylindrical MR system. The protocol consisted of cine and unenhanced tissue sequences. The signal-to-noise ratio (SNR) for each sequence and blood-myocardium contrast for the cine sequences were assessed. Image quality and artefacts were rated. The location and number of non-diagnostic segments was determined. Volunteers' tolerance to examinations in both scanners was investigated. SNR was significantly lower in the HFO scanner (all p<0.001). However, the contrast of the cine sequence was significantly higher in the HFO platform compared to the 1.5T MR scanner (0.685±0.41 vs. 0.611±0.54; p<0.001). Image quality was comparable for all sequences (all p>0.05). Overall, only few non-diagnostic myocardial segments were recorded: 6/960 (0.6%) by the HFO and 17/960 (1.8%) segments by the cylindrical system. The volunteers expressed a preference for the open MR system (p<0.01). Standard cardiac MRI sequences in an HFO platform offer a high image quality that is comparable to the quality of images acquired in a cylindrical 1.5T MR scanner. An open scanner design may potentially improve tolerance of cardiac MRI and therefore allow to examine an even broader patient spectrum.

Investigating different mechanisms for biogenic selenite transformations: Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica

USGS Publications Warehouse

Pearce, C.I.; Pattrick, R.A.D.; Law, N.; Charnock, J.M.; Coker, V.S.; Fellowes, J.W.; Oremland, R.S.; Lloyd, J.R.

2009-01-01

The metal-reducing bacteria Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica, use different mechanisms to transform toxic, bioavailable sodium selenite to less toxic, non-mobile elemental selenium and then to selenide in anaerobic environments, offering the potential for in situ and ex situ bioremediation of contaminated soils, sediments, industrial effluents, and agricultural drainage waters. The products of these reductive transformations depend on both the organism involved and the reduction conditions employed, in terms of electron donor and exogenous extracellular redox mediator. The intermediary phase involves the precipitation of elemental selenium nanospheres and the potential role of proteins in the formation of these structures is discussed. The bionanomineral phases produced during these transformations, including both elemental selenium nanospheres and metal selenide nanoparticles, have catalytic, semiconducting and light-emitting properties, which may have unique applications in the realm of nanophotonics. This research offers the potential to combine remediation of contaminants with the development of environmentally friendly manufacturing pathways for novel bionanominerals. ?? 2009 Taylor & Francis.

Single-Cell Imaging and Spectroscopic Analyses of Cr(VI) Reduction on the Surface of Bacterial Cells

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

Wang, Yuanmin; Sevinc, Papatya C.; Belchik, Sara M.

2013-01-22

We investigate single-cell reduction of toxic Cr(VI) by the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), an important bioremediation process, using Raman spectroscopy and scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDX). Our experiments indicate that the toxic and highly soluble Cr(VI) can be efficiently reduced to the less toxic and non-soluble Cr2O3 nanoparticles by MR-1. Cr2O3 is observed to emerge as nanoparticles adsorbed on the cell surface and its chemical nature is identified by EDX imaging and Raman spectroscopy. Co-localization of Cr2O3 and cytochromes by EDX imaging and Raman spectroscopy suggests a terminal reductase role for MR-1more » surface-exposed cytochromes MtrC and OmcA. Our experiments revealed that the cooperation of surface proteins OmcA and MtrC makes the reduction reaction most efficient, and the sequence of the reducing reactivity of the MR-1 is: wild type > single mutant @mtrC or mutant @omcA > double mutant (@omcA-@mtrC). Moreover, our results also suggest that the direct microbial Cr(VI) reduction and Fe(II) (hematite)-mediated Cr(VI) reduction mechanisms may co-exist in the reduction processes.« less

k-t SENSE-accelerated Myocardial Perfusion MR Imaging at 3.0 Tesla - comparison with 1.5 Tesla

PubMed Central

Plein, Sven; Schwitter, Juerg; Suerder, Daniel; Greenwood, John P.; Boesiger, Peter; Kozerke, Sebastian

2008-01-01

Purpose To determine the feasibility and diagnostic accuracy of high spatial resolution myocardial perfusion MR at 3.0 Tesla using k-space and time domain undersampling with sensitivity encoding (k-t SENSE). Materials and Methods The study was reviewed and approved by the local ethic review board. k-t SENSE perfusion MR was performed at 1.5 Tesla and 3.0 Tesla (saturation recovery gradient echo pulse sequence, repetition time/echo time 3.0ms/1.0ms, flip angle 15°, 5x k-t SENSE acceleration, spatial resolution 1.3×1.3×10mm3). Fourteen volunteers were studied at rest and 37 patients during adenosine stress. In volunteers, comparison was also made with standard-resolution (2.5×2.5×10mm3) 2x SENSE perfusion MR at 3.0 Tesla. Image quality, artifact scores, signal-to-noise ratios (SNR) and contrast-enhancement ratios (CER) were derived. In patients, diagnostic accuracy of visual analysis to detect >50% diameter stenosis on quantitative coronary angiography was determined by receiver-operator-characteristics (ROC). Results In volunteers, image quality and artifact scores were similar for 3.0 Tesla and 1.5 Tesla, while SNR was higher (11.6 vs. 5.6) and CER lower (1.1 vs. 1.5, p=0.012) at 3.0 Tesla. Compared with standard-resolution perfusion MR, image quality was higher for k-t SENSE (3.6 vs. 3.1, p=0.04), endocardial dark rim artifacts were reduced (artifact thickness 1.6mm vs. 2.4mm, p<0.001) and CER similar. In patients, area under the ROC curve for detection of coronary stenosis was 0.89 and 0.80, p=0.21 for 3.0 Tesla and 1.5 Tesla, respectively. Conclusions k-t SENSE accelerated high-resolution perfusion MR at 3.0 Tesla is feasible with similar artifacts and diagnostic accuracy as at 1.5 Tesla. Compared with standard-resolution perfusion MR, image quality is improved and artifacts are reduced. PMID:18936311

Biofabrication of morphology improved cadmium sulfide nanoparticles using Shewanella oneidensis bacterial cells and ionic liquid: For toxicity against brain cancer cell lines.

PubMed

Wang, Li; Chen, Siyuan; Ding, Yiming; Zhu, Qiang; Zhang, Nijia; Yu, Shuqing

2018-01-01

The present work determines the anticancer activity of bio-mediated synthesized cadmium sulfide nanoparticles using the ionic liquid and bacterial cells (Shewanella oneidensis). Bacterial cells have been exposed to be important resources that hold huge potential as ecofriendly, cost-effective, evading toxic of dangerous chemicals and the alternative of conventional physiochemical synthesis. The Shewanella oneidensis is an important kind of metal reducing bacterium, known as its special anaerobic respiratory and sulfate reducing capacity. The crystalline nature, phase purity and surface morphology of biosynthesized cadmium sulfide nanoparticles were analyzed by Fourier transform infrared spectroscopy, X-ray diffraction, Field emission scanning electron microscopy, Energy dispersive spectroscopy and Transmission electron microscopy. The use of imidazolium based ionic liquids as soft templating agent for controlling self-assembly and crystal growth direction of metal sulfide nanoparticles has also advanced as an important method. The microscopic techniques showed that the nanoparticles are designed on the nano form and have an excellent spherical morphology, due to the self-assembled mechanism of ionic liquid assistance. The antitumor efficiency of the cadmium sulfide nanoparticles was investigated against brain cancer cell lines using rat glioma cell lines. The effectively improved nano-crystalline and morphological structure of CdS nanoparticles in the presence of IL exhibit excellent cytotoxicity and dispersion ability on the cell shape is completely spread out showing a nice toxic environment against cancer cells. The cytotoxicity effect of cadmium sulfide nanoparticles was discussed with a diagrammatic representation. Copyright © 2017. Published by Elsevier B.V.

Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

PubMed

Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

2016-07-07

A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of an automatic MR-based gold fiducial marker localisation method for MR-only prostate radiotherapy

NASA Astrophysics Data System (ADS)

Maspero, Matteo; van den Berg, Cornelis A. T.; Zijlstra, Frank; Sikkes, Gonda G.; de Boer, Hans C. J.; Meijer, Gert J.; Kerkmeijer, Linda G. W.; Viergever, Max A.; Lagendijk, Jan J. W.; Seevinck, Peter R.

2017-10-01

An MR-only radiotherapy planning (RTP) workflow would reduce the cost, radiation exposure and uncertainties introduced by CT-MRI registrations. In the case of prostate treatment, one of the remaining challenges currently holding back the implementation of an RTP workflow is the MR-based localisation of intraprostatic gold fiducial markers (FMs), which is crucial for accurate patient positioning. Currently, MR-based FM localisation is clinically performed manually. This is sub-optimal, as manual interaction increases the workload. Attempts to perform automatic FM detection often rely on being able to detect signal voids induced by the FMs in magnitude images. However, signal voids may not always be sufficiently specific, hampering accurate and robust automatic FM localisation. Here, we present an approach that aims at automatic MR-based FM localisation. This method is based on template matching using a library of simulated complex-valued templates, and exploiting the behaviour of the complex MR signal in the vicinity of the FM. Clinical evaluation was performed on seventeen prostate cancer patients undergoing external beam radiotherapy treatment. Automatic MR-based FM localisation was compared to manual MR-based and semi-automatic CT-based localisation (the current gold standard) in terms of detection rate and the spatial accuracy and precision of localisation. The proposed method correctly detected all three FMs in 15/17 patients. The spatial accuracy (mean) and precision (STD) were 0.9 mm and 0.5 mm respectively, which is below the voxel size of 1.1 × 1.1 × 1.2 mm3 and comparable to MR-based manual localisation. FM localisation failed (3/51 FMs) in the presence of bleeding or calcifications in the direct vicinity of the FM. The method was found to be spatially accurate and precise, which is essential for clinical use. To overcome any missed detection, we envision the use of the proposed method along with verification by an observer. This will result in a

The Role of Shewanella oneidensis MR-1 Outer Surface Structures in Extracellular Electron Transfer

DTIC Science & Technology

2010-01-01

Supernatants from the wells of the air-exposed VBSA that had been in operation for 220 h were harvested and planktonic cells were removed via...prepilins. In some bacteria, such as Pseudomonas aerugino- sa and Vibrio cholerae, PilD plays a dual role and processes type IVand T2SS prepilins [38 – 41... harvested from the VBSA at the times indicated by arrows in Fig. 4 (100 h data not shown). Fig. 6. Presence of riboflavin in cell-free supernatants

Characterization of the first RF coil dedicated to 1.5 T MR guided radiotherapy

NASA Astrophysics Data System (ADS)

Hoogcarspel, Stan J.; Zijlema, Stefan E.; Tijssen, Rob H. N.; Kerkmeijer, Linda G. W.; Jürgenliemk-Schulz, Ina M.; Lagendijk, Jan J. W.; Raaymakers, Bas W.

2018-01-01

The purpose of this study is to investigate the attenuation characteristics of a novel radiofrequency (RF) coil, which is the first coil that is solely dedicated to MR guided radiotherapy with a 1.5 T MR-linac. Additionally, we investigated the impact of the treatment beam on the MRI performance of this RF coil. First, the attenuation characteristics of the RF coil were characterized. Second, we investigated the impact of the treatment beam on the MRI performance of the RF coil. We additionally demonstrated the ability of the anterior coil to attenuate returning electrons and thereby reducing the dose to the skin at the distal side of the treatment beam. Intensity modulated radiation therapy simulation of a clinically viable treatment plan for spinal bone metastasis shows a decrease of the dose to the planned tumor volume of 1.8% as a result of the MR coil around the patient. Ionization chamber and film measurements show that the anterior and posterior coil attenuate the beam homogeneously by 0.4% and 2.2%, respectively. The impact of the radiation resulted in a slight drop of the time-course signal-to-noise ratio and was dependent on imaging parameters. However, we could not observe any image artifacts resulting from this irradiation in any situation. In conclusion, the investigated MR-coil can be utilized for treatments with the 1.5 T-linac system. However, there is still room for improvement when considering both the dosimetric and imaging performance of the coil.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

PubMed Central

Aigle, Axel; Bonin, Patricia; Iobbi-Nivol, Chantal; Méjean, Vincent; Michotey, Valérie

2017-01-01

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels. PMID:28317859

Chondromalacia patellae: diagnosis with MR imaging.

PubMed

McCauley, T R; Kier, R; Lynch, K J; Jokl, P

1992-01-01

Most previous studies of MR imaging for detection of chondromalacia have used T1-weighted images. We correlated findings on axial MR images of the knee with arthroscopic findings to determine MR findings of chondromalacia patellae on T2-weighted and proton density-weighted images. The study population included 52 patients who had MR examination of the knee with a 1.5-T unit and subsequent arthroscopy, which documented chondromalacia patellae in 29 patients and normal cartilage in 23. The patellar cartilage was assessed retrospectively for MR signal and contour characteristics. MR diagnosis based on the criteria of focal signal or focal contour abnormality on either the T2-weighted or proton density-weighted images yielded the highest correlation with the arthroscopic diagnosis of chondromalacia. When these criteria were used, patients with chondromalacia were detected with 86% sensitivity, 74% specificity, and 81% accuracy. MR diagnosis based on T2-weighted images alone was more sensitive and accurate than was diagnosis based on proton density-weighted images alone. In conclusion, most patients with chondromalacia patellae have focal signal or focal contour defects in the patellar cartilage on T2-weighted MR images. These findings are absent in most patients with arthroscopically normal cartilage.

MR morphology of triangular fibrocartilage complex: correlation with quantitative MR and biomechanical properties.

PubMed

Bae, Won C; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda; Chung, Christine B

2016-04-01

To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high-resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Five cadaveric wrists (22-70 years) were imaged at 3 T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques.

MR Morphology of Triangular Fibrocartilage Complex: Correlation with Quantitative MR and Biomechanical Properties

PubMed Central

Bae, Won C.; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda

2016-01-01

Objective To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Materials and Methods Five cadaveric wrists (22 to 70 yrs) were imaged at 3T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. Results On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. Conclusion These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques. PMID:26691643

The use of MR B+1 imaging for validation of FDTD electromagnetic simulations of human anatomies.

PubMed

Van den Berg, Cornelis A T; Bartels, Lambertus W; van den Bergen, Bob; Kroeze, Hugo; de Leeuw, Astrid A C; Van de Kamer, Jeroen B; Lagendijk, Jan J W

2006-10-07

In this study, MR B(+)(1) imaging is employed to experimentally verify the validity of FDTD simulations of electromagnetic field patterns in human anatomies. Measurements and FDTD simulations of the B(+)(1) field induced by a 3 T MR body coil in a human corpse were performed. It was found that MR B(+)(1) imaging is a sensitive method to measure the radiofrequency (RF) magnetic field inside a human anatomy with a precision of approximately 3.5%. A good correlation was found between the B(+)(1) measurements and FDTD simulations. The measured B(+)(1) pattern for a human pelvis consisted of a global, diagonal modulation pattern plus local B(+)(1) heterogeneties. It is believed that these local B(+)(1) field variations are the result of peaks in the induced electric currents, which could not be resolved by the FDTD simulations on a 5 mm(3) simulation grid. The findings from this study demonstrate that B(+)(1) imaging is a valuable experimental technique to gain more knowledge about the dielectric interaction of RF fields with the human anatomy.

77 FR 65545 - Mr. Jesse S. Capel and Mr. Hilton J. Cochran; EWP LLC; Notice of Transfer of Exemption

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-29

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 4815-009] Mr. Jesse S. Capel and Mr. Hilton J. Cochran; EWP LLC; Notice of Transfer of Exemption 1. By application filed on July 30, 2012 and supplemented on August 14, 2012, Mr. Jesse S. Capel and Mr. Hilton J. Cochran and EWP...

Investigating the generalisation of an atlas-based synthetic-CT algorithm to another centre and MR scanner for prostate MR-only radiotherapy

NASA Astrophysics Data System (ADS)

Wyatt, Jonathan J.; Dowling, Jason A.; Kelly, Charles G.; McKenna, Jill; Johnstone, Emily; Speight, Richard; Henry, Ann; Greer, Peter B.; McCallum, Hazel M.

2017-12-01

There is increasing interest in MR-only radiotherapy planning since it provides superb soft-tissue contrast without the registration uncertainties inherent in a CT-MR registration. However, MR images cannot readily provide the electron density information necessary for radiotherapy dose calculation. An algorithm which generates synthetic CTs for dose calculations from MR images of the prostate using an atlas of 3 T MR images has been previously reported by two of the authors. This paper aimed to evaluate this algorithm using MR data acquired at a different field strength and a different centre to the algorithm atlas. Twenty-one prostate patients received planning 1.5 T MR and CT scans with routine immobilisation devices on a flat-top couch set-up using external lasers. The MR receive coils were supported by a coil bridge. Synthetic CTs were generated from the planning MR images with (sCT1V ) and without (sCT) a one voxel body contour expansion included in the algorithm. This was to test whether this expansion was required for 1.5 T images. Both synthetic CTs were rigidly registered to the planning CT (pCT). A 6 MV volumetric modulated arc therapy plan was created on the pCT and recalculated on the sCT and sCT1V . The synthetic CTs’ dose distributions were compared to the dose distribution calculated on the pCT. The percentage dose difference at isocentre without the body contour expansion (sCT-pCT) was Δ D_sCT=(0.9 +/- 0.8) % and with (sCT1V -pCT) was Δ D_sCT1V=(-0.7 +/- 0.7) % (mean  ±  one standard deviation). The sCT1V result was within one standard deviation of zero and agreed with the result reported previously using 3 T MR data. The sCT dose difference only agreed within two standard deviations. The mean  ±  one standard deviation gamma pass rate was Γ_sCT = 96.1 +/- 2.9 % for the sCT and Γ_sCT1V = 98.8 +/- 0.5 % for the sCT1V (with 2% global dose difference and 2~mm distance to agreement gamma criteria). The one voxel body contour

Value of 3.0 T MR imaging in refractory partial epilepsy and negative 1.5 T MRI.

PubMed

Nguyen, Dang Khoa; Rochette, Emilie; Leroux, Jean-Maxime; Beaudoin, Gilles; Cossette, Patrick; Lassonde, Maryse; Guilbert, François

2010-10-01

High-field 3.0 T MR scanners provide an improved signal-to-noise ratio which can be translated in higher image resolution, possibly allowing critical detection of subtle epileptogenic lesions missed on standard-field 1.0-1.5 T MRIs. In this study, the authors explore the potential value of re-imaging at 3.0 T patients with refractory partial epilepsy and negative 1.5 T MRI. We retrospectively identified all patients with refractory partial epilepsy candidate for surgery who had undergone a 3.0 T MR study after a negative 1.5 T MR study. High-field 3.0 T MRIs were reviewed qualitatively by neuroradiologists experienced in interpreting epilepsy studies with access to clinical information. Relevance and impact on clinical management were assessed by an epileptologist. Between November 2006 and August 2009, 36 patients with refractory partial epilepsy candidate for surgery underwent 3.0 T MR study after a 1.5 T MR study failed to disclose a relevant epileptogenic lesion. A potential lesion was found only in two patients (5.6%, 95% CI: 1.5-18.1%). Both were found to have hippocampal atrophy congruent with other presurgical localization techniques which resulted in omission of an invasive EEG study and direct passage to surgery. The frequency of detection of a new lesion by re-imaging at 3.0 T patients with refractory partial epilepsy candidate for surgery was found to be low, but seems to offer the potential of a significant clinical impact for selected patients. This finding needs to be validated in a prospective controlled study. Copyright © 2010 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Microbial activity at gigapascal pressures.

PubMed

Sharma, Anurag; Scott, James H; Cody, George D; Fogel, Marilyn L; Hazen, Robert M; Hemley, Russell J; Huntress, Wesley T

2002-02-22

We observed physiological and metabolic activity of Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at pressures of 68 to 1680 megapascals (MPa) in diamond anvil cells. We measured biological formate oxidation at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system.

Investigation of multichannel phased array performance for fetal MR imaging on 1.5T clinical MR system

PubMed Central

Li, Ye; Pang, Yong; Vigneron, Daniel; Glenn, Orit; Xu, Duan; Zhang, Xiaoliang

2011-01-01

Fetal MRI on 1.5T clinical scanner has been increasingly becoming a powerful imaging tool for studying fetal brain abnormalities in vivo. Due to limited availability of dedicated fetal phased arrays, commercial torso or cardiac phased arrays are routinely used for fetal scans, which are unable to provide optimized SNR and parallel imaging performance with a small number coil elements, and insufficient coverage and filling factor. This poses a demand for the investigation and development of dedicated and efficient radiofrequency (RF) hardware to improve fetal imaging. In this work, an investigational approach to simulate the performance of multichannel flexible phased arrays is proposed to find a better solution to fetal MR imaging. A 32 channel fetal array is presented to increase coil sensitivity, coverage and parallel imaging performance. The electromagnetic field distribution of each element of the fetal array is numerically simulated by using finite-difference time-domain (FDTD) method. The array performance, including B1 coverage, parallel reconstructed images and artifact power, is then theoretically calculated and compared with the torso array. Study results show that the proposed array is capable of increasing B1 field strength as well as sensitivity homogeneity in the entire area of uterus. This would ensure high quality imaging regardless of the location of the fetus in the uterus. In addition, the paralleling imaging performance of the proposed fetal array is validated by using artifact power comparison with torso array. These results demonstrate the feasibility of the 32 channel flexible array for fetal MR imaging at 1.5T. PMID:22408747

Silicon detectors for combined MR-PET and MR-SPECT imaging

NASA Astrophysics Data System (ADS)

Studen, A.; Brzezinski, K.; Chesi, E.; Cindro, V.; Clinthorne, N. H.; Cochran, E.; Grošičar, B.; Grkovski, M.; Honscheid, K.; Kagan, H.; Lacasta, C.; Llosa, G.; Mikuž, M.; Stankova, V.; Weilhammer, P.; Žontar, D.

2013-02-01

Silicon based devices can extend PET-MR and SPECT-MR imaging to applications, where their advantages in performance outweigh benefits of high statistical counts. Silicon is in many ways an excellent detector material with numerous advantages, among others: excellent energy and spatial resolution, mature processing technology, large signal to noise ratio, relatively low price, availability, versatility and malleability. The signal in silicon is also immune to effects of magnetic field at the level normally used in MR devices. Tests in fields up to 7 T were performed in a study to determine effects of magnetic field on positron range in a silicon PET device. The curvature of positron tracks in direction perpendicular to the field's orientation shortens the distance between emission and annihilation point of the positron. The effect can be fully appreciated for a rotation of the sample for a fixed field direction, compressing range in all dimensions. A popular Ga-68 source was used showing a factor of 2 improvement in image noise compared to zero field operation. There was also a little increase in noise as the reconstructed resolution varied between 2.5 and 1.5 mm. A speculative applications can be recognized in both emission modalities, SPECT and PET. Compton camera is a subspecies of SPECT, where a silicon based scatter as a MR compatible part could inserted into the MR bore and the secondary detector could operate in less constrained environment away from the magnet. Introducing a Compton camera also relaxes requirements of the radiotracers used, extending the range of conceivable photon energies beyond 140.5 keV of the Tc-99m. In PET, one could exploit the compressed sub-millimeter range of positrons in the magnetic field. To exploit the advantage, detectors with spatial resolution commensurate to the effect must be used with silicon being an excellent candidate. Measurements performed outside of the MR achieving spatial resolution below 1 mm are reported.

Metabolically engineered glucose-utilizing Shewanella strains under anaerobic conditions.

PubMed

Choi, Donggeon; Lee, Sae Bom; Kim, Sohyun; Min, Byoungnam; Choi, In-Geol; Chang, In Seop

2014-02-01

Comparative genome analysis of Shewanella strains predicted that the strains metabolize preferably two- and three-carbon carbohydrates as carbon/electron source because many Shewanella genomes are deficient of the key enzymes in glycolysis (e.g., glucokinase). In addition, all Shewanella genomes are known to have only one set of genes associated with the phosphotransferase system required to uptake sugars. To engineer Shewanella strains that can utilize five- and six-carbon carbohydrates, we constructed glucose-utilizing Shewanella oneidensis MR-1 by introducing the glucose facilitator (glf; ZMO0366) and glucokinase (glk; ZMO0369) genes of Zymomonas mobilis. The engineered MR-1 strain was able to grow on glucose as a sole carbon/electron source under anaerobic conditions. The glucose affinity (Ks) and glucokinase activity in the engineered MR-1 strain were 299.46 mM and 0.259 ± 0.034 U/g proteins. The engineered strain was successfully applied to a microbial fuel cell system and exhibited current generation using glucose as the electron source. Copyright © 2013 Elsevier Ltd. All rights reserved.

MR Performance Comparison of a PET/MR System Before and After SiPM-Based Time-of-Flight PET Detector Insertion

NASA Astrophysics Data System (ADS)

Khalighi, Mohammad Mehdi; Delso, Gaspar; Maramraju, Sri Harsha; Deller, Timothy W.; Levin, Craig S.; Glover, Gary H.

2016-10-01

A silicon photomultiplier (SiPM)-based time-of-flight capable PET detector has been integrated with a 70 cm wide-bore 3T MR scanner for simultaneous whole-body imaging (MR750w, GE Healthcare, Waukesha, WI). After insertion of the PET detector, the final PET/MR bore is 60 cm wide (SIGNA PET/MR, GE Healthcare, Waukesha, WI). The MR performance was compared before and after the PET ring insertion. B0 homogeneity, B1+ uniformity of the body coil along with peak B1+, coherent noise, and FBIRN (Function Biomedical Informatics Research Network) tests are used to compare the MR performance. It is shown that B0 homogeneity and coherent noise have not changed according to the system specifications. Peak B1+ is increased by 33% and B1+ inhomogeneity is increased by 4% after PET ring insertion due to a smaller diameter body coil design. The FBIRN test shows similar temporal stability before and after PET ring insertion. Due to a smaller body coil on the PET/MR system, the signal fluctuation to noise ratio (SFNR) and SNR for body receive coil, are improved by 40% and 160% for Echo Planar Imaging (EPI) and spiral sequences respectively. Comparison using RF- and gradient-intensive clinical sequences shows inserting the PET detectors into the wide-bore MRI has not compromised the MR image quality according to these tests.

A synthetic microbial consortium of Shewanella and Bacillus for enhanced generation of bioelectricity.

PubMed

Liu, Ting; Yu, Yang-Yang; Chen, Tao; Chen, Wei Ning

2017-03-01

In this study, a synthetic microbial consortium containing exoelectrogen Shewanella oneidensis MR-1 and riboflavin-producing strain, Bacillus subtilis RH33, was rationally designed and successfully constructed, enabling a stable, multiple cycles of microbial fuel cells (MFCs) operation for more than 500 h. The maximum power density of MFCs with this synthetic microbial consortium was 277.4 mW/m 2 , which was 4.9 times of that with MR-1 (56.9 mW/m 2 ) and 40.2 times of RH33 (6.9 mW/m 2 ), separately. At the same time, the Coulombic efficiency of the synthetic microbial consortium (5.6%) was higher than MR-1 (4.1%) and RH33 (2.3%). Regardless the high concentration of riboflavin produced by RH33, the power density of RH33 was rather low. The low bioelectricity generation can be ascribed to the low efficiency of RH33 in utilizing riboflavin for extracellular electron transfer (EET). In the synthetic microbial consortium of MR-1 and RH33, it was found that both mediated and direct electron transfer efficiencies were enhanced. By exchanging the anolyte of MR-1 and RH33, it was confirmed that the improved MFC performance with the synthetic microbial consortium was because MR-1 could efficiently utilize the high concentration of riboflavin produced by RH33. Biotechnol. Bioeng. 2017;114: 526-532. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

T1-Weighted MR imaging of liver tumor by gadolinium-encapsulated glycol chitosan nanoparticles without non-specific toxicity in normal tissues

NASA Astrophysics Data System (ADS)

Na, Jin Hee; Lee, Sangmin; Koo, Heebeom; Han, Hyounkoo; Lee, Kyung Eun; Han, Seung Jin; Choi, Seung Hong; Kim, Hyuncheol; Lee, Seulki; Kwon, Ick Chan; Choi, Kuiwon; Kim, Kwangmeyung

2016-05-01

Herein, we have synthesized Gd(iii)-encapsulated glycol chitosan nanoparticles (Gd(iii)-CNPs) for tumor-targeted T1-weighted magnetic resonance (MR) imaging. The T1 contrast agent, Gd(iii), was successfully encapsulated into 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)-modified CNPs to form stable Gd(iii)-encapsulated CNPs (Gd(iii)-CNPs) with an average particle size of approximately 280 nm. The stable nanoparticle structure of Gd(iii)-CNPs is beneficial for liver tumor accumulation by the enhanced permeation and retention (EPR) effect. Moreover, the amine groups on the surface of Gd(iii)-CNPs could be protonated and could induce fast cellular uptake at acidic pH in tumor tissue. To assay the tumor-targeting ability of Cy5.5-labeled Gd(iii)-CNPs, near-infrared fluorescence (NIRF) imaging and MR imaging were used in a liver tumor model as well as a subcutaneous tumor model. Cy5.5-labeled Gd(iii)-CNPs generated highly intense fluorescence and T1 MR signals in tumor tissues after intravenous injection, while DOTAREM®, the commercialized control MR contrast agent, showed very low tumor-targeting efficiency on MR images. Furthermore, damaged tissues were found in the livers and kidneys of mice injected with DOTAREM®, but there were no obvious adverse effects with Gd(iii)-CNPs. Taken together, these results demonstrate the superiority of Gd(iii)-CNPs as a tumor-targeting T1 MR agent.Herein, we have synthesized Gd(iii)-encapsulated glycol chitosan nanoparticles (Gd(iii)-CNPs) for tumor-targeted T1-weighted magnetic resonance (MR) imaging. The T1 contrast agent, Gd(iii), was successfully encapsulated into 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)-modified CNPs to form stable Gd(iii)-encapsulated CNPs (Gd(iii)-CNPs) with an average particle size of approximately 280 nm. The stable nanoparticle structure of Gd(iii)-CNPs is beneficial for liver tumor accumulation by the enhanced permeation and retention (EPR) effect. Moreover, the

RGD-functionalized ultrasmall iron oxide nanoparticles for targeted T1-weighted MR imaging of gliomas

NASA Astrophysics Data System (ADS)

Luo, Yu; Yang, Jia; Yan, Yu; Li, Jingchao; Shen, Mingwu; Zhang, Guixiang; Mignani, Serge; Shi, Xiangyang

2015-08-01

We report a convenient approach to prepare ultrasmall Fe3O4 nanoparticles (NPs) functionalized with an arginylglycylaspartic acid (RGD) peptide for in vitro and in vivo magnetic resonance (MR) imaging of gliomas. In our work, stable sodium citrate-stabilized Fe3O4 NPs were prepared by a solvothermal route. Then, the carboxylated Fe3O4 NPs stabilized with sodium citrate were conjugated with polyethylene glycol (PEG)-linked RGD. The formed ultrasmall RGD-functionalized nanoprobe (Fe3O4-PEG-RGD) was fully characterized using different techniques. We show that these Fe3O4-PEG-RGD particles with a size of 2.7 nm are water-dispersible, stable, cytocompatible and hemocompatible in a given concentration range, and display targeting specificity to glioma cells overexpressing αvβ3 integrin in vitro. With the relatively high r1 relaxivity (r1 = 1.4 mM-1 s-1), the Fe3O4-PEG-RGD particles can be used as an efficient nanoprobe for targeted T1-weighted positive MR imaging of glioma cells in vitro and the xenografted tumor model in vivo via an active RGD-mediated targeting pathway. The developed RGD-functionalized Fe3O4 NPs may hold great promise to be used as a nanoprobe for targeted T1-weighted MR imaging of different αvβ3 integrin-overexpressing cancer cells or biological systems.We report a convenient approach to prepare ultrasmall Fe3O4 nanoparticles (NPs) functionalized with an arginylglycylaspartic acid (RGD) peptide for in vitro and in vivo magnetic resonance (MR) imaging of gliomas. In our work, stable sodium citrate-stabilized Fe3O4 NPs were prepared by a solvothermal route. Then, the carboxylated Fe3O4 NPs stabilized with sodium citrate were conjugated with polyethylene glycol (PEG)-linked RGD. The formed ultrasmall RGD-functionalized nanoprobe (Fe3O4-PEG-RGD) was fully characterized using different techniques. We show that these Fe3O4-PEG-RGD particles with a size of 2.7 nm are water-dispersible, stable, cytocompatible and hemocompatible in a given concentration

Geometry of magnetic rotational (MR) band-crossing phenomenon in MR bands

NASA Astrophysics Data System (ADS)

Devi, K. Rojeeta; Kumar, Suresh; Palit, R.

2018-07-01

A semiclassical (SC) approach is proposed to calculate the B( M1) transition rates in the band-crossing region of two magnetic rotational (MR) bands. In the present work, a geometry is suggested for the shear blades to govern its behaviour during the band-crossing. In the crossing region, gradual alignment of two nucleons is responsible for the crossing behaviour and it must give a quantised resultant angular momentum. As an example, it is successfully implemented for the MR bands in the mass A=110 and A=200 regions. A good agreement of the present semiclassical calculations with the experimental values is presented and furthermore, it is seen that the present proposal is also helpful to see the core contribution in the MR phenomenon.

A 1-minute full brain MR exam using a multicontrast EPI sequence.

PubMed

Skare, Stefan; Sprenger, Tim; Norbeck, Ola; Rydén, Henric; Blomberg, Lars; Avventi, Enrico; Engström, Mathias

2018-06-01

A new multicontrast echo-planar imaging (EPI)-based sequence is proposed for brain MRI, which can directly generate six MR contrasts (T 1 -FLAIR, T 2 -w, diffusion-weighted (DWI), apparent diffusion coefficient (ADC), T2*-w, T 2 -FLAIR) in 1 min with full brain coverage. This could enable clinical MR clinical screening in similar time as a conventional CT exam but with more soft-tissue information. Eleven sequence modules were created as dynamic building blocks for the sequence. Two EPI readout modules were reused throughout the sequence and were prepended by other modules to form the desired MR contrasts. Two scan protocols were optimized with scan times of 55-75 s. Motion experiments were carried out on two volunteers to investigate the robustness against head motion. Scans on patients were carried out and compared to conventional clinical images. The pulse sequence is found to be robust against motion given its single-shot nature of each contrast. For excessive out-of-plane head motion, the T 1 -FLAIR and T 2 -FLAIR contrasts suffer from incomplete inversion. Despite lower signal-to-noise ratio (SNR) and resolution, the 1-min multicontrast EPI data show promising correspondence with conventional diagnostic scans on patients. A 1 min multicontrast brain MRI scan based on EPI readouts has been presented in this feasibility study. Preliminary data show potential for clinical brain MRI use with minimal bore time for the patient. Such short examination time could be useful (e.g., for screening and acute stroke). The sequence may also help planning conventional brain MRI scans if run at the beginning of an examination. Magn Reson Med 79:3045-3054, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

MR imaging and MR cholangiopancreatography of cholangiocarcinoma developing in printing company workers.

PubMed

Koyama, Koichi; Kubo, Shoji; Ueki, Ai; Shimono, Taro; Takemura, Shigekazu; Tanaka, Shogo; Kinoshita, Masahiko; Hamano, Genya; Miki, Yukio

2017-05-01

To retrospectively investigate magnetic resonance (MR) imaging findings of occupational cholangiocarcinoma (oCC) occurring among workers in printing companies in Japan, compared to those of non-occupational cholangiocarcinoma (nCC), primary sclerosing cholangitis (PSC), and age-matched normal controls (NORs). Participants comprised 27 consecutive patients (oCC, n = 5; nCC, n = 8; PSC, n = 6; NOR, n = 8) who underwent MR imaging between May 2009 and October 2012. MR imaging was evaluated with respect to tumor characteristics, abnormal MR cholangiographic findings (PSC-like findings), bile duct stricture, and signal changes of the hepatic parenchyma. Tumors were detected in all nCCs and four oCCs. Tumors displayed a mass-forming type in all nCCs and two oCCs, and an intraductal growth type in two oCCs. Abnormal cholangiographic findings were detected in all oCCs and PSCs, but not in any nCCs or NORs. All oCCs and seven nCCs showed biliary strictures longer than 1 cm; five PSCs showed biliary strictures shorter than 1 cm. Both intra- and extrahepatic biliary strictures were detected in three PSCs and two oCCs. Peripheral hepatic hyperintensity on T2-weighted imaging was detected in two nCCs, two PSCs, and two oCCs. These results indicated that MR imaging of oCC showed findings of both PSC and nCC.

Semiautomated spleen volumetry with diffusion-weighted MR imaging.

PubMed

Lee, Jeongjin; Kim, Kyoung Won; Lee, Ho; Lee, So Jung; Choi, Sanghyun; Jeong, Woo Kyoung; Kye, Heewon; Song, Gi-Won; Hwang, Shin; Lee, Sung-Gyu

2012-07-01

In this article, we determined the relative accuracy of semiautomated spleen volumetry with diffusion-weighted (DW) MR images compared to standard manual volumetry with DW-MR or CT images. Semiautomated spleen volumetry using simple thresholding followed by 3D and 2D connected component analysis was performed with DW-MR images. Manual spleen volumetry was performed on DW-MR and CT images. In this study, 35 potential live liver donor candidates were included. Semiautomated volumetry results were highly correlated with manual volumetry results using DW-MR (r = 0.99; P < 0.0001; mean percentage absolute difference, 1.43 ± 0.94) and CT (r = 0.99; P < 0.0001; 1.76 ± 1.07). Mean total processing time for semiautomated volumetry was significantly shorter compared to that of manual volumetry with DW-MR (P < 0.0001) and CT (P < 0.0001). In conclusion, semiautomated spleen volumetry with DW-MR images can be performed rapidly and accurately when compared with standard manual volumetry. Copyright © 2011 Wiley Periodicals, Inc.

MR-1 blocks the megakaryocytic differentiation and transition of CML from chronic phase to blast crisis through MEK dephosphorylation

PubMed Central

Zhao, W; He, H; Ren, K; Li, B; Zhang, H; Lin, Y; Shao, R-g

2013-01-01

Chronic myelogenous leukemia (CML) evolves from a chronic phase characterized by the Philadelphia chromosome as the sole genetic abnormality and the accumulation of mature cells in peripheral blood into blast crisis, which is characterized by the rapid expansion of myeloid- or lymphoid-differentiation-arrested blast cells. Although ample studies have been conducted on the disease progress mechanisms, the underlying molecular mechanisms of the malignant phenotype transition are still unclear. In this study, we have shown that myofibrillogenesis regulator-1 (MR-1) was overexpressed in blast crisis patients and leukemic cells, but there was little trace expressed in healthy individuals and in most patients in CML chronic phase. MR-1 could inhibit the differentiation of myeloid cells into megakaryocytic lineages and accelerate cell proliferation. The molecular mechanism responsible for these effects was the interaction of MR-1 with MEK, which blocked the MEK/ERK signaling pathway by dephosphorylating MEK. Our results provide compelling and important evidence that MR-1 might act as a diagnostic marker and potential target of CML progression from chronic phase to blast crisis. PMID:23542180

Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.

PubMed

Elegheert, Jonathan; Brigé, Ann; Van Beeumen, Jozef; Savvides, Savvas N

2017-10-01

Shewanella oneidensis, a Gram-negative γ-proteobacterium with an extensive redox capacity, possesses four old yellow enzyme (OYE) homologs. Of these, Shewanella yellow enzyme 4 (SYE4) is implicated in resistance to oxidative stress. Here, we present a series of high-resolution crystal structures for SYE4 in the oxidized and reduced states, and in complex with phenolic ligands and the nitro-aromatic explosive picric acid. The structures unmask new features, including the identification of a binding platform for long-chain hydrophobic molecules. Furthermore, we present the first structural observation of a hydride-Meisenheimer complex of picric acid with a flavoenzyme. Overall, our study exposes the binding promiscuity of SYE4 toward a variety of electrophilic substrates and is consistent with a general detoxification function for SYE4. © 2017 Federation of European Biochemical Societies.

MR imaging of breast implants.

PubMed

Gorczyca, D P

1994-11-01

MR imaging has proved to be an excellent imaging modality in locating free silicone and evaluating an implant for rupture, with a sensitivity of approximately 94% and specificity of 97%. Silicone has a unique MR resonance frequency and long T1 and T2 relaxation times, which allows several MR sequences to provide excellent diagnostic images. The most commonly used sequences include T2-weighted, STIR, and chemical shift imaging (Figs. 3, 13, and 14). The T2-weighted and STIR sequences are often used in conjunction with chemical water suppression. The most reliable findings on MR images for detection of implant rupture include identification of the collapsed implant shell (linguine sign) and free silicone within the breast parenchyma.

Rapid Precipitation of Amorphous Silica in Experimental Systems with Nontronite (NAu-1) and Shewanella oneidensis MR-1

DTIC Science & Technology

2007-01-15

law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB...report, we focus on the rapid bio- life because much of our current understanding of early life mineralization of amorphous silica. comes from...matter. The Nanoplast-embedded sample was atomic emission spectroscopy (ICP). After pH analysis ultrathin-sectioned, and examined with JEOL3010 TEM with a

Tissue Sodium Concentration in Myocardial Infarction in Humans: A Quantitative 23Na MR Imaging Study1

PubMed Central

Ouwerkerk, Ronald; Bottomley, Paul A.; Solaiyappan, Meiyappan; Spooner, Amy E.; Tomaselli, Gordon F.; Wu, Katherine C.; Weiss, Robert G.

2008-01-01

Purpose: To prospectively determine whether the absolute tissue sodium concentration (TSC) increases in myocardial infarctions (MIs) in humans and whether TSC is related to infarct size, infarct age, ventricular dysfunction, and/or electrophysiologic inducibility of ventricular arrhythmias. Materials and Methods: Delayed contrast material–enhanced 1.5-T hydrogen 1 (1H) magnetic resonance (MR) imaging was used to measure the size and location of nonacute MIs in 20 patients (18 men, two women; mean age, 63 years ± 9 [standard deviation]; age range, 48–82 years) examined at least 90 days after MI. End-systolic and end-diastolic volumes, ejection fraction, and left ventricle (LV) mass were measured with cine MR imaging. The TSC in normal, infarcted, and adjacent myocardial tissue was measured on sodium 23 (23Na) MR images coregistered with delayed contrast-enhanced 1H MR images. Programmed electric stimulation to induce monomorphic ventricular tachycardia (MVT) was used to assess arrhythmic potential, and myocardial TSC was compared between the inducible MVT and noninducible MVT patient groups. Results: The mean TSC for MIs (59 μmol/g wet weight ± 10) was 30% higher than that for noninfarcted (remote) LV regions (45 μmol/g wet weight ± 5, P < .001) and that for healthy control subjects, and TSC did not correlate with infarct age or functional and morphologic indices. The mean TSC for tissue adjacent to the MI (50 μmol/g wet weight ± 6) was intermediate between that for the MI and that for remote regions. The elevated TSC measured in the MI at 23Na MR imaging lacked sufficient contrast and spatial resolution for routine visualization of MI. Cardiac TSC did not enable differentiation between patients in whom MVT was inducible and those in whom it was not. Conclusion: Absolute TSC is measurable with 23Na MR imaging and is significantly elevated in human MI; however, TSC increase is not related to infarct age, infarct size, or global ventricular function. In

MR-Guided Prostate Interventions

PubMed Central

Tempany, Clare; Straus, Sarah; Hata, Nobuhiko; Haker, Steven

2009-01-01

In this article the current issues of diagnosis and detection of prostate cancer are reviewed. The limitations for current techniques are highlighted and some possible solutions with MR imaging and MR-guided biopsy approaches are reviewed. There are several different biopsy approaches under investigation. These include transperineal open magnet approaches to closed-bore 1.5T transrectal biopsies. The imaging, image processing, and tracking methods are also discussed. In the arena of therapy, MR guidance has been used in conjunction with radiation methods, either brachytherapy or external delivery. The principles of the radiation treatment, the toxicities, and use of images are outlined. The future role of imaging and image-guided interventions lie with providing a noninvasive surrogate for cancer surveillance or monitoring treatment response. The shift to minimally invasive focal therapies has already begun and will be very exciting when MR-guided focused ultrasound surgery reaches its full potential. PMID:18219689

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

Sharma, Seema; Simpson, David C.; Tolic, Nikola

We investigated the combination of weak anion exchange (WAX) fractionation and on-line reversed phase liquid chromatography (RPLC) separation using a 12 T FTICR mass spectrometer for the detection of intact proteins from a Shewanella oneidensis MR-1 cell lysate. 715 intact proteins were detected and the combined results from the WAX fractions and the unfractionated cell lysate were aligned using LC-MS features to facilitate protein abundance measurements. Protein identifications and post translational modifications were assigned for ~10% of the detected proteins by comparing intact protein mass measurements to proteins identified in peptide MS/MS analysis of an aliquot of the same fraction.more » Intact proteins were also detected for S. oneidensis lysates obtained from cells grown on 13C, 15N depleted media under aerobic and sub-oxic conditions. This work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification complement. The strategy can be readily applied for measuring differential protein abundances, and provides a platform for high-throughput selection of biologically relevant targets for further characterization.« less

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

DOE PAGES

Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.; ...

2017-05-24

13C metabolic flux analysis ( 13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant ofmore » 13C MFA known as 2-Scale 13C metabolic flux analysis (2S- 13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

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

Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.

13C metabolic flux analysis ( 13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant ofmore » 13C MFA known as 2-Scale 13C metabolic flux analysis (2S- 13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

PubMed Central

Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.; Gin, Jennifer; Apel, Amanda Reider; Mukhopadhyay, Aindrila; García Martín, Héctor; Keasling, Jay D.

2017-01-01

13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of 13C MFA known as 2-Scale 13C metabolic flux analysis (2S-13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a critical

Regulation of nitrite resistance of the cytochrome cbb3 oxidase by cytochrome c ScyA in Shewanella oneidensis

PubMed Central

Yin, Jianhua; Jin, Miao; Zhang, Haiyan; Ju, Lili; Zhang, Lili; Gao, Haichun

2015-01-01

Cytochrome c proteins, as enzymes to exchange electrons with substrates or as pure electron carriers to shuttle electrons, play vital roles in bacterial respiration and photosynthesis. In Shewanella oneidensis, a research model for the respiratory diversity, at least 42 c-type cytochromes are predicted to be encoded in the genome and are regarded to be the foundation of its highly branched electron transport pathways. However, only a small number of c-type cytochromes have been extensively studied. In this study, we identify soluble cytochrome c ScyA as an important factor influencing the nitrite resistance of a strain devoid of the bd oxidase by utilizing a newly developed transposon mutagenesis vector, which enables overexpression of the gene(s) downstream of the insertion site. We show that when in overabundance ScyA facilitates growth against nitrite inhibition by enhancing nitrite resistance of the cbb3 oxidase. Based on the data presented in this study, we suggest two possible mechanisms underlying the observed effect of ScyA: (1) ScyA increases electron flow to the cbb3 oxidase; (2) ScyA promotes nitrite resistance of the cbb3 oxidase, possibly by direct interaction. PMID:25417822

Clinical Proton MR Spectroscopy in Central Nervous System Disorders

PubMed Central

Alger, Jeffry R.; Barker, Peter B.; Bartha, Robert; Bizzi, Alberto; Boesch, Chris; Bolan, Patrick J.; Brindle, Kevin M.; Cudalbu, Cristina; Dinçer, Alp; Dydak, Ulrike; Emir, Uzay E.; Frahm, Jens; González, Ramón Gilberto; Gruber, Stephan; Gruetter, Rolf; Gupta, Rakesh K.; Heerschap, Arend; Henning, Anke; Hetherington, Hoby P.; Howe, Franklyn A.; Hüppi, Petra S.; Hurd, Ralph E.; Kantarci, Kejal; Klomp, Dennis W. J.; Kreis, Roland; Kruiskamp, Marijn J.; Leach, Martin O.; Lin, Alexander P.; Luijten, Peter R.; Marjańska, Małgorzata; Maudsley, Andrew A.; Meyerhoff, Dieter J.; Mountford, Carolyn E.; Nelson, Sarah J.; Pamir, M. Necmettin; Pan, Jullie W.; Peet, Andrew C.; Poptani, Harish; Posse, Stefan; Pouwels, Petra J. W.; Ratai, Eva-Maria; Ross, Brian D.; Scheenen, Tom W. J.; Schuster, Christian; Smith, Ian C. P.; Soher, Brian J.; Tkáč, Ivan; Vigneron, Daniel B.; Kauppinen, Risto A.

2014-01-01

A large body of published work shows that proton (hydrogen 1 [1H]) magnetic resonance (MR) spectroscopy has evolved from a research tool into a clinical neuroimaging modality. Herein, the authors present a summary of brain disorders in which MR spectroscopy has an impact on patient management, together with a critical consideration of common data acquisition and processing procedures. The article documents the impact of 1H MR spectroscopy in the clinical evaluation of disorders of the central nervous system. The clinical usefulness of 1H MR spectroscopy has been established for brain neoplasms, neonatal and pediatric disorders (hypoxia-ischemia, inherited metabolic diseases, and traumatic brain injury), demyelinating disorders, and infectious brain lesions. The growing list of disorders for which 1H MR spectroscopy may contribute to patient management extends to neurodegenerative diseases, epilepsy, and stroke. To facilitate expanded clinical acceptance and standardization of MR spectroscopy methodology, guidelines are provided for data acquisition and analysis, quality assessment, and interpretation. Finally, the authors offer recommendations to expedite the use of robust MR spectroscopy methodology in the clinical setting, including incorporation of technical advances on clinical units. © RSNA, 2014 Online supplemental material is available for this article. PMID:24568703

MR-guided prostate interventions.

PubMed

Tempany, Clare; Straus, Sarah; Hata, Nobuhiko; Haker, Steven

2008-02-01

In this article the current issues of diagnosis and detection of prostate cancer are reviewed. The limitations for current techniques are highlighted and some possible solutions with MR imaging and MR-guided biopsy approaches are reviewed. There are several different biopsy approaches under investigation. These include transperineal open magnet approaches to closed-bore 1.5T transrectal biopsies. The imaging, image processing, and tracking methods are also discussed. In the arena of therapy, MR guidance has been used in conjunction with radiation methods, either brachytherapy or external delivery. The principles of the radiation treatment, the toxicities, and use of images are outlined. The future role of imaging and image-guided interventions lie with providing a noninvasive surrogate for cancer surveillance or monitoring treatment response. The shift to minimally invasive focal therapies has already begun and will be very exciting when MR-guided focused ultrasound surgery reaches its full potential. (Copyright) 2008 Wiley-Liss, Inc.

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

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

Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M.

Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved.more » Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.« less

MR Imaging of the Prostate and Adjacent Anatomic Structures before, during, and after Ejaculation: Qualitative and Quantitative Evaluation1

PubMed Central

Medved, Milica; Sammet, Steffen; Yousuf, Ambereen; Oto, Aytekin

2015-01-01

Purpose To determine the possibility of obtaining high-quality magnetic resonance (MR) images before, during, and immediately after ejaculation and detecting measurable changes in quantitative MR imaging parameters after ejaculation. Materials and Methods In this prospective, institutional review board–approved, HIPAA-compliant study, eight young healthy volunteers (median age, 22.5 years), after providing informed consent, underwent MR imaging while masturbating to the point of ejaculation. A 1.5-T MR imaging unit was used, with an eight-channel surface coil and a dynamic single-shot fast spin-echo sequence. In addition, a quantitative MR imaging protocol that allowed calculation of T1, T2, and apparent diffusion coefficient (ADC) values was applied before and after ejaculation. Volumes of the prostate and seminal vesicles (SV) were calculated by using whole-volume segmentation on T2-weighted images, both before and after ejaculation. Pre- and postejaculation changes in quantitative MR parameters and measured volumes were evaluated by using the Wilcoxon signed rank test with Bonferroni adjustment. Results There was no significant change in prostate volumes on pre- and postejaculation images, while the SV contracted by 41% on average (median, 44.5%; P = .004). No changes before and after ejaculation were observed in T1 values or in T2 and ADC values in the central gland, while T2 and ADC values were significantly reduced in the peripheral zone by 12% and 14%, respectively (median, 13% and 14.5%, respectively; P = .004). Conclusion Successful dynamic MR imaging of ejaculation events and the ability to visualize internal sphincter closure, passage of ejaculate, and significant changes in SV volumes were demonstrated. Significant changes in peripheral zone T2 and ADC values were observed. PMID:24495265

Radiofrequency Ablation, MR Thermometry, and High-Spatial-Resolution MR Parametric Imaging with a Single, Minimally Invasive Device.

PubMed

Ertürk, M Arcan; Sathyanarayana Hegde, Shashank; Bottomley, Paul A

2016-12-01

Purpose To develop and demonstrate in vitro and in vivo a single interventional magnetic resonance (MR)-active device that integrates the functions of precise identification of a tissue site with the delivery of radiofrequency (RF) energy for ablation, high-spatial-resolution thermal mapping to monitor thermal dose, and quantitative MR imaging relaxometry to document ablation-induced tissue changes for characterizing ablated tissue. Materials and Methods All animal studies were approved by the institutional animal care and use committee. A loopless MR imaging antenna composed of a tuned microcable either 0.8 or 2.2 mm in diameter with an extended central conductor was switched between a 3-T MR imaging unit and an RF power source to monitor and perform RF ablation in bovine muscle and human artery samples in vitro and in rabbits in vivo. High-spatial-resolution (250-300-μm) proton resonance frequency shift MR thermometry was interleaved with ablations. Quantitative spin-lattice (T1) and spin-spin (T2) relaxation time MR imaging mapping was performed before and after ablation. These maps were compared with findings from gross tissue examination of the region of ablated tissue after MR imaging. Results High-spatial-resolution MR imaging afforded temperature mapping in less than 8 seconds for monitoring ablation temperatures in excess of 85°C delivered by the same device. This produced irreversible thermal injury and necrosis. Quantitative MR imaging relaxation time maps demonstrated up to a twofold variation in mean regional T1 and T2 after ablation versus before ablation. Conclusion A simple, integrated, minimally invasive interventional probe that provides image-guided therapy delivery, thermal mapping of dose, and detection of ablation-associated MR imaging parametric changes was developed and demonstrated. With this single-device approach, coupling-related safety concerns associated with multiple conductor approaches were avoided. © RSNA, 2016 Online

Endogenous generation of hydrogen sulfide and its regulation in Shewanella oneidensis

PubMed Central

Wu, Genfu; Li, Ning; Mao, Yinting; Zhou, Guangqi; Gao, Haichun

2015-01-01

Hydrogen sulfide (H2S) has been recognized as a physiological mediator with a variety of functions across all domains of life. In this study, mechanisms of endogenous H2S generation in Shewanella oneidensis were investigated. As a research model with highly diverse anaerobic respiratory pathways, the microorganism is able to produce H2S by respiring on a variety of sulfur-containing compounds with SirACD and PsrABC enzymatic complexes, as well as through cysteine degradation with three enzymes, MdeA, SO_1095, and SseA. We showed that the SirACD and PsrABC complexes, which are predominantly, if not exclusively, responsible for H2S generation via respiration of sulfur species, do not interplay with each other. Strikingly, a screen for regulators controlling endogenous H2S generation by transposon mutagenesis identified global regulator Crp to be essential to all H2S-generating processes. In contrast, Fnr and Arc, two other global regulators that have a role in respiration, are dispensable in regulating H2S generation via respiration of sulfur species. Interestingly, Arc is involved in the H2S generation through cysteine degradation by repressing expression of the mdeA gene. We further showed that expression of the sirA and psrABC operons is subjected to direct regulation of Crp, but the mechanisms underlying the requirement of Crp for H2S generation through cysteine degradation remain elusive. PMID:25972854

Workflow efficiency of two 1.5 T MR scanners with and without an automated user interface for head examinations.

PubMed

Moenninghoff, Christoph; Umutlu, Lale; Kloeters, Christian; Ringelstein, Adrian; Ladd, Mark E; Sombetzki, Antje; Lauenstein, Thomas C; Forsting, Michael; Schlamann, Marc

2013-06-01

Workflow efficiency and workload of radiological technologists (RTs) were compared in head examinations performed with two 1.5 T magnetic resonance (MR) scanners equipped with or without an automated user interface called "day optimizing throughput" (Dot) workflow engine. Thirty-four patients with known intracranial pathology were examined with a 1.5 T MR scanner with Dot workflow engine (Siemens MAGNETOM Aera) and with a 1.5 T MR scanner with conventional user interface (Siemens MAGNETOM Avanto) using four standardized examination protocols. The elapsed time for all necessary work steps, which were performed by 11 RTs within the total examination time, was compared for each examination at both MR scanners. The RTs evaluated the user-friendliness of both scanners by a questionnaire. Normality of distribution was checked for all continuous variables by use of the Shapiro-Wilk test. Normally distributed variables were analyzed by Student's paired t-test, otherwise Wilcoxon signed-rank test was used to compare means. Total examination time of MR examinations performed with Dot engine was reduced from 24:53 to 20:01 minutes (P < .001) and the necessary RT intervention decreased by 61% (P < .001). The Dot engine's automated choice of MR protocols was significantly better assessed by the RTs than the conventional user interface (P = .001). According to this preliminary study, the Dot workflow engine is a time-saving user assistance software, which decreases the RTs' effort significantly and may help to automate neuroradiological examinations for a higher workflow efficiency. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS

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

Komorek, Rachel; Wei, Wenchao; Yu, Xiaofei

Bacterial biofilms are surface-associated communities that are vastly studied to understand their self-produced extracellular polymeric substances (EPS) and their roles in environmental microbiology. This study outlines a method to cultivate biofilm attachment to the System for Analysis at the Liquid Vacuum Interface (SALVI) and achieve in situ chemical mapping of a living biofilm by time-of-flight secondary ion mass spectrometry (ToF-SIMS). This is done through the culturing of bacteria both outside and within the SALVI channel with our specialized setup, as well as through optical imaging techniques to detect the biofilm presence and thickness before ToF-SIMS analysis. Our results show themore » characteristic peaks of the Shewanella biofilm in its natural hydrated state, highlighting upon its localized water cluster environment, as well as EPS fragments, which are drastically different from the same biofilm’s dehydrated state. These results demonstrate the breakthrough capability of SALVI that allows for in situ biofilm imaging with a vacuum-based chemical imaging instrument.« less

Autologous chondrocyte implantation in knee joint: MR imaging and histologic features at 1-year follow-up.

PubMed

Tins, Bernhard J; McCall, Iain W; Takahashi, Tomoki; Cassar-Pullicino, Victor; Roberts, Sally; Ashton, Brian; Richardson, James

2005-02-01

To evaluate magnetic resonance (MR) imaging features of autologous chondrocyte implantation (ACI) grafts and compare these with graft histologic features 1 year after ACI for treatment of femoral condylar defects. This study was approved by the regional ethics committee, and all patients gave informed consent. Forty-one patients (mean age, 35 years; 30 men, 11 women) underwent ACI for treatment of femoral condylar defects. One year later, knee joint MR imaging and graft biopsy were performed. Graft biopsy results were categorized into those showing hyaline, mixed fibrohyaline cartilage, fibrocartilage, and fibrous tissue. Standard T1-, T2-, T2*-, and intermediate-weighted sequences were performed, as well as three-dimensional (3D) fast low-angle shot (FLASH) and double-echo steady-state sequences for cartilage assessment. ACI grafts were assessed for signal intensity (with FLASH sequence), thickness, overgrowth, surface smoothness, integration to adjacent cartilage and underlying bone, bone marrow edema underneath graft, and contour of bone underneath graft. MR images were assessed by two observers, first independently and then in consensus. MR imaging findings were correlated with histologic findings. All 41 grafts were present at 1-year follow-up. The graft consisted of hyaline cartilage in four, mixed fibrohyaline cartilage in 10, fibrocartilage in 25, and fibrous tissue in two cases. Graft signal intensity was virtually always lower than adjacent normal cartilage signal intensity, and there was no relationship between graft signal intensity and histologic appearance (P = .34). Graft thickness (P = .83), overgrowth (P = .69), surface smoothness (P = .28), and integration with adjacent cartilage and underlying bone (P = .90); edema in bone marrow underneath graft (P = .63); and bone contour underneath graft (P = .94) at MR imaging had no correlation with graft histologic appearance. Graft overgrowth (n = 16; 39%) and edema-like signal in bone marrow underneath

Relationships between astrogliosis and 1H MR spectroscopic measures of brain choline/creatine and myo-inositol/creatine in a primate model.

PubMed

Kim, John P; Lentz, Margaret R; Westmoreland, Susan V; Greco, Jane B; Ratai, Eva M; Halpern, Elkan; Lackner, Andrew A; Masliah, Eliezer; González, R Gilberto

2005-04-01

In vivo 1H MR spectroscopy demonstrates elevated choline (Cho)/creatine (Cr) and myo-inositol (MI)/Cr in many neurologic diseases that has been ascribed to gliosis. We tested the hypotheses that in vivo Cho/Cr and/or MI/Cr levels are correlated with glial fibrillary acidic protein (GFAP) immunostains and that the changes are water-soluble metabolites. We performed postmortem 1H MR spectroscopy and GFAP immunohistochemistry in brains from seven rhesus macaques acutely infected with simian immunodeficiency virus (SIV) and in four controls and compared the findings with previous in vivo MR spectroscopic results. Changes in neuropathologic and MR spectroscopic markers after infection and relationships among plasma viral load, GFAP immunostaining results, and ex vivo and in vivo MR spectroscopic measures were statistically evaluated. On GFAP immunostaining and in vivo MR spectroscopy, GFAP, Cho/Cr and MI/Cr were highest near the time of peak plasma viral load at 11 days postinfection (dpi). Immunostains returned to baseline by 14 dpi, whereas Cho/Cr and MI/Cr had different time courses, with the former dropping below baseline and the latter remaining elevated. Viral load and immunostains were significantly correlated. No correlation was found between ex vivo Cho/Cr or MI/Cr and viral load or between metabolite ratios from in vivo and ex vivo MR spectroscopy. In acute SIV infection, plasma viral load was significantly correlated with brain GFAP immunostains and in vivo 1H MR spectroscopic Cho/Cr. In vivo changes in Cho/Cr and MI/Cr were principally due to contributions other than those of low-molecular-weight water-soluble metabolites.

Hippocampal MR volumetry

NASA Astrophysics Data System (ADS)

Haller, John W.; Botteron, K.; Brunsden, Barry S.; Sheline, Yvette I.; Walkup, Ronald K.; Black, Kevin J.; Gado, Mokhtar; Vannier, Michael W.

1994-09-01

Goal: To estimate hippocampal volumes from in vivo 3D magnetic resonance (MR) brain images and determine inter-rater and intra- rater repeatability. Objective: The precision and repeatability of hippocampal volume estimates using stereologic measurement methods is sought. Design: Five normal control and five schizophrenic subjects were MR scanned using a MPRAGE protocol. Fixed grid stereologic methods were used to estimate hippocampal volumes on a graphics workstation. The images were preprocessed using histogram analysis to standardize 3D MR image scaling from 16 to 8 bits and image volumes were interpolated to 0.5 mm3 isotropic voxels. The following variables were constant for the repeated stereologic measures: grid size, inter-slice distance (1.5 mm), voxel dimensions (0.5 mm3), number of hippocampi measured (10), total number of measurements per rater (40), and number of raters (5). Two grid sizes were tested to determine the coefficient of error associated with the number of sampled 'hits' (approximately 140 and 280) on the hippocampus. Starting slice and grid position were randomly varied to assure unbiased volume estimates. Raters were blind to subject identity, diagnosis, and side of the brain from which the image volumes were extracted and the order of subject presentation was randomized for each of the raters. Inter- and intra-rater intraclass correlation coefficients (ICC) were determined. Results: The data indicate excellent repeatability of fixed grid stereologic hippocampal volume measures when using an inter-slice distance of 1.5 mm and a 6.25 mm2 grid (inter-rater ICCs equals 0.86 - 0.97, intra- rater ICCs equals 0.85 - 0.97). One major advantage of the current study was the use of 3D MR data which significantly improved visualization of hippocampal boundaries by providing the ability to access simultaneous orthogonal views while counting stereological marks within the hippocampus. Conclusion: Stereological estimates of 3D volumes from 2D MR

Abdominopelvic 1.5-T and 3.0-T MR Imaging in Healthy Volunteers: Relationship to Formation of DNA Double-Strand Breaks.

PubMed

Suntharalingam, Saravanabavaan; Mladenov, Emil; Sarabhai, Theresia; Wetter, Axel; Kraff, Oliver; Quick, Harald H; Forsting, Michael; Iliakis, Georg; Nassenstein, Kai

2018-05-01

Purpose To investigate the relationship between abdominopelvic magnetic resonance (MR) imaging and formation of DNA double-strand breaks (DSBs) in peripheral blood lymphocytes among a cohort of healthy volunteers. Materials and Methods Blood samples were obtained from 40 healthy volunteers (23 women and 17 men; mean age, 27.2 years [range, 21-37 years]) directly before and 5 and 30 minutes after abdominopelvic MR imaging performed at 1.5 T (n = 20) or 3.0 T (n = 20). The number of DNA DSBs in isolated blood lymphocytes was quantified after indirect immunofluorescent staining of a generally accepted DSB marker, γ-H2AX, by means of high-throughput automated microscopy. As a positive control of DSB induction, blood lymphocytes from six volunteers were irradiated in vitro with x-rays at a dose of 1 Gy (70-90 keV). Statistical analysis was performed by using a Friedman test. Results No significant alteration in the frequency of DNA DSB induction was observed after MR imaging (before imaging: 0.22 foci per cell, interquartile range [IQR] = 0.54 foci per cell; 5 minutes after MR imaging: 0.08 foci per cell, IQR = 0.39 foci per cell; 30 minutes after MR imaging: 0.09 foci per cell, IQR = 0.63 foci per cell; P = .057). In vitro radiation of lymphocytes with 1 Gy led to a significant increase in DSBs (0.22 vs 3.43 foci per cell; P = .0312). The frequency of DSBs did not differ between imaging at 1.5 T and at 3.0 T (5 minutes after MR imaging: 0.23 vs 0.06 foci per cell, respectively [P = .57]; 30 minutes after MR imaging: 0.12 vs 0.08 foci per cell [P = .76]). Conclusion Abdominopelvic MR imaging performed at 1.5 T or 3.0 T does not affect the formation of DNA DSBs in peripheral blood lymphocytes. © RSNA, 2018.

Digital subtraction dark-lumen MR colonography: initial experience.

PubMed

Ajaj, Waleed; Veit, Patrick; Kuehle, Christiane; Joekel, Michaela; Lauenstein, Thomas C; Herborn, Christoph U

2005-06-01

To evaluate image subtraction for the detection of colonic pathologies in a dark-lumen MR colonography exam. A total of 20 patients (12 males; 8 females; mean 51.4 years of age) underwent MR colonography after standard cleansing and a rectal water enema on a 1.5-T whole-body MR system. After suppression of peristaltic motion, native and Gd-contrast-enhanced three-dimensional T1-w gradient echo images were acquired in the coronal plane. Two radiologists analyzed the MR data sets in consensus on two separate occasions, with and without the subtracted images for lesion detection, and assessed the value of the subtracted data set on a five-point Likert scale (1=very helpful to 5=very unhelpful). All imaging results were compared with endoscopy. Without subtracted images, MR-colonography detected a total of five polyps, two inflammatory lesions, and one carcinoma in eight patients, which were all verified by endoscopy. Using subtraction, an additional polyp was found, and readout time was significantly shorter (6:41 vs. 7:39 minutes; P<0.05). In two patients, endoscopy detected a flat adenoma and a polyp (0.4 cm) that were missed in the MR exam. Sensitivity and specificity without subtraction were 0.67/1.0, and 0.76/1.0 with the subtracted images, respectively. Subtraction was assessed as helpful in all exams (mean value 1.8+/-0.5; Likert scale). We consider subtraction of native from contrast-enhanced dark-lumen MR colonography data sets as a beneficial supplement to the exam. Copyright (c) 2005 Wiley-Liss, Inc.

Abdominal applications of 3.0-T MR imaging: comparative review versus a 1.5-T system.

PubMed

Choi, Jin-Young; Kim, Myeong-Jin; Chung, Yong Eun; Kim, Ji Youn; Jones, Alun C; de Becker, Jan; van Cauteren, Marc

2008-01-01

With the development of dedicated receiver coils and increased gradient performance, 3.0-T magnetic resonance (MR) systems are gaining wider acceptance in clinical practice. The expected twofold increase in signal-to-noise ratio (SNR) compared with that of 1.5-T MR systems may help improve spatial resolution or increase temporal resolution when used with parallel acquisition techniques. Several issues must be considered when applying 3.0-T MR in the abdomen, including the alteration of the radiofrequency field and relaxation time, increase in energy deposition and susceptibility effects, and problems associated with motion artifacts. For the evaluation of liver lesions, higher SNR and greater resolution achieved with the 3.0-T system could translate into better detection of malignant lesions on T2-weighted images obtained with adjusted imaging parameters. For the evaluation of pancreatic and biliary diseases, high-resolution T2-weighted imaging using single-shot turbo spin-echo sequences is useful; improvement in SNR was noticeable on two-dimensional MR cholangiopancreatographic images. For the preoperative imaging of rectal cancer, a single-shot sequence is useful for dramatically decreasing imaging time while maintaining image quality. Substantial modification of examination protocols, with optimized imaging parameters and sequence designs along with ongoing development of hardware, could contribute to an increased role of the 3.0-T system for abdominal MR examinations.

Dosimetric analysis of stereotactic body radiation therapy for pancreatic cancer using MR-guided Tri-60Co unit, MR-guided LINAC, and conventional LINAC-based plans.

PubMed

Ramey, Stephen James; Padgett, Kyle R; Lamichhane, Narottam; Neboori, Hanmath J; Kwon, Deukwoo; Mellon, Eric A; Brown, Karen; Duffy, Melissa; Victoria, James; Dogan, Nesrin; Portelance, Lorraine

2018-03-01

This study aims to perform a dosimetric comparison of 2 magnetic resonance (MR)-guided radiation therapy systems capable of performing online adaptive radiation therapy versus a conventional radiation therapy system for pancreas stereotactic body radiation therapy. Ten cases of patients with pancreatic adenocarcinoma previously treated in our institution were used for this analysis. MR-guided tri-cobalt 60 therapy (MR-cobalt) and MR-LINAC plans were generated and compared with conventional LINAC (volumetric modulated arc therapy) plans. The prescription dose was 40 Gy in 5 fractions covering 95% of the planning tumor volume for the 30 plans. The same organs at risk (OARs) dose constraints were used in all plans. Dose-volume-based indices were used to compare PTV coverage and OAR sparing. The conformity index of 40 Gy in 5 fractions covering 95% of the planning tumor volume demonstrated higher conformity in both LINAC-based plans compared with MR-cobalt plans. Although there was no difference in mean conformity index between LINAC and MR-LINAC plans (1.08 in both), there was a large difference between LINAC and MR-cobalt plans (1.08 vs 1.52). Overall, 79%, 72%, and 78% of critical structure dosimetric constraints were met with LINAC, MR-cobalt, and MR-LINAC plans, respectively. The MR-cobalt plans delivered more doses to all OARs compared with the LINAC plans. In contrast, the doses to the OARs of the MR-LINAC plans were similar to LINAC plans except in 2 cases: liver mean dose (MR-LINAC, 2 .8 Gy vs LINAC, 2.1 Gy) and volume of duodenum receiving at least 15 Gy (MR-LINAC, 13.2 mL vs LINAC, 15.4 mL). Both differences are likely not clinically significant. This study demonstrates that dosimetrically similar plans were achieved with conventional LINAC and MR-LINAC, whereas doses to OARs were statistically higher for MR-cobalt compared with conventional LINAC plans because of low-dose spillage. Given the improved tumor-tracking capabilities of MR-LINAC, further studies

MR Imaging-Guided Attenuation Correction of PET Data in PET/MR Imaging.

PubMed

Izquierdo-Garcia, David; Catana, Ciprian

2016-04-01

Attenuation correction (AC) is one of the most important challenges in the recently introduced combined PET/magnetic resonance (MR) scanners. PET/MR AC (MR-AC) approaches aim to develop methods that allow accurate estimation of the linear attenuation coefficients of the tissues and other components located in the PET field of view. MR-AC methods can be divided into 3 categories: segmentation, atlas, and PET based. This review provides a comprehensive list of the state-of-the-art MR-AC approaches and their pros and cons. The main sources of artifacts are presented. Finally, this review discusses the current status of MR-AC approaches for clinical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

CALiPER Report 22.1: Photoelectric Performance of LED MR16 Lamps

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

Royer, Michael P.; Poplawski, Michael E.; Brown, Charles C.

This report is a follow-up to CALiPER Application Summary Report 22, which investigated the photometric performance of LED MR16 lamps. The initial report found that many of the LED MR16 lamps did not perform as required by ENERGY STAR based on their equivalency claims, although they generally did provide substantial efficacy advantages compared to halogen MR16 lamps. All testing was completed using laboratory power supplies, with all but one product tested at 12 V AC. In contrast, this report examined the photoelectric performance of the same set of lamps, using commercially available transformers and dimmers as well as laboratory powermore » supplies providing both AC and DC power.« less

Substrates and oxygen dependent citric acid production by Yarrowia lipolytica: insights through transcriptome and fluxome analyses.

PubMed

Sabra, Wael; Bommareddy, Rajesh Reddy; Maheshwari, Garima; Papanikolaou, Seraphim; Zeng, An-Ping

2017-05-08

Unlike the well-studied backer yeast where catabolite repression represents a burden for mixed substrate fermentation, Yarrowia lipolytica, an oleaginous yeast, is recognized for its potential to produce single cell oils and citric acid from different feedstocks. These versatilities of Y. lipolytica with regards to substrate utilization make it an attractive host for biorefinery application. However, to develop a commercial process for the production of citric acid by Y. lipolytica, it is necessary to better understand the primary metabolism and its regulation, especially for growth on mixed substrate. Controlling the dissolved oxygen concentration (pO 2 ) in Y. lipolytica cultures enhanced citric acid production significantly in cultures grown on glucose in mono- or dual substrate fermentations, whereas with glycerol as mono-substrate no significant effect of pO 2 was found on citrate production. Growth on mixed substrate with glucose and glycerol revealed a relative preference of glycerol utilization by Y. lipolytica. Under optimized conditions with pO 2 control, the citric acid titer on glucose in mono- or in dual substrate cultures was 55 and 50 g/L (with productivity of 0.6 g/L*h in both cultures), respectively, compared to a maximum of 18 g/L (0.2 g/L*h) with glycerol in monosubstrate culture. Additionally, in dual substrate fermentation, glycerol limitation was found to trigger citrate consumption despite the presence of enough glucose in pO 2 -limited culture. The metabolic behavior of this yeast on different substrates was investigated at transcriptomic and 13 C-based fluxomics levels. Upregulation of most of the genes of the pentose phosphate pathway was found in cultures with highest citrate production with glucose in mono- or in dual substrate fermentation with pO 2 control. The activation of the glyoxylate cycle in the oxygen limited cultures and the imbalance caused by glycerol limitation might be the reason for the re-consumption of citrate in

Quality control for quantitative multicenter whole-body PET/MR studies: A NEMA image quality phantom study with three current PET/MR systems

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

Boellaard, Ronald, E-mail: r.boellaard@vumc.nl; European Association of Nuclear Medicine Research Ltd., Vienna 1060; European Association of Nuclear Medicine Physics Committee, Vienna 1060

2015-10-15

Purpose: Integrated positron emission tomography/magnetic resonance (PET/MR) systems derive the PET attenuation correction (AC) from dedicated MR sequences. While MR-AC performs reasonably well in clinical patient imaging, it may fail for phantom-based quality control (QC). The authors assess the applicability of different protocols for PET QC in multicenter PET/MR imaging. Methods: The National Electrical Manufacturers Association NU 2 2007 image quality phantom was imaged on three combined PET/MR systems: a Philips Ingenuity TF PET/MR, a Siemens Biograph mMR, and a GE SIGNA PET/MR (prototype) system. The phantom was filled according to the EANM FDG-PET/CT guideline 1.0 and scanned for 5more » min over 1 bed. Two MR-AC imaging protocols were tested: standard clinical procedures and a dedicated protocol for phantom tests. Depending on the system, the dedicated phantom protocol employs a two-class (water and air) segmentation of the MR data or a CT-based template. Differences in attenuation- and SUV recovery coefficients (RC) are reported. PET/CT-based simulations were performed to simulate the various artifacts seen in the AC maps (μ-map) and their impact on the accuracy of phantom-based QC. Results: Clinical MR-AC protocols caused substantial errors and artifacts in the AC maps, resulting in underestimations of the reconstructed PET activity of up to 27%, depending on the PET/MR system. Using dedicated phantom MR-AC protocols, PET bias was reduced to −8%. Mean and max SUV RC met EARL multicenter PET performance specifications for most contrast objects, but only when using the dedicated phantom protocol. Simulations confirmed the bias in experimental data to be caused by incorrect AC maps resulting from the use of clinical MR-AC protocols. Conclusions: Phantom-based quality control of PET/MR systems in a multicenter, multivendor setting may be performed with sufficient accuracy, but only when dedicated phantom acquisition and processing protocols are used for

Magnetorheological properties of sodium sulphonate capped electrolytic iron based MR fluid: a comparison with CI based MR fluid

NASA Astrophysics Data System (ADS)

Vinod, Sithara; John, Reji; Philip, John

2017-02-01

Magnetorheological fluids have numerous engineering applications due to their interesting field assisted rheological behavior. Most commonly used dispersed phase in MR fluids is carbonyl iron (CI). The relatively high cost of CI warrants the need to develop cheaper alternatives to CI, without compromising rheological properties. With the above goal in mind, we have synthesized sodium sulphonate capped electrolytic iron based MR fluid and studied their magnetorheological properties. The results are compared with that of CI based MR fluid. EI and CI particles of average particle size of ∼10 μm with fumed silica particles additives are used in the present study. The dynamic yield stress for EI and CI based MR fluid were found to vary with field strength with an exponent of roughly 1.2 and 1.24, respectively. The slightly lower static and dynamic yield stress values of EI based MR fluid is attributed to the lower magnetization and polydispersity values. The dynamic yield stress showed a decrease of 18.73% and 61.8% for field strengths of 177 mT and 531 mT, respectively as the temperature was increased from 293 to 323 K. The optorheological studies showed a peak in the loss moduli, close to the crossover point of the storage and loss moduli, due to freely moving large sized aggregates along the shear direction that are dislodged from the rheometer plates at higher strains. Our results suggests that EI based MR fluids have magnetorheological behavior comparable to that of CI based MR fluids. As EI is much cheaper than CI, our findings will have important commercial implications in producing cost effective EI based MR fluids.

Relationship Between Ktrans and K1 with Simultaneous Versus Separate MR/PET in Rabbits with VX2 Tumors.

PubMed

Lee, Kyung Hee; Kang, Seung Kwan; Goo, Jin Mo; Lee, Jae Sung; Cheon, Gi Jeong; Seo, Seongho; Hwang, Eui Jin

2017-03-01

To compare the relationship between K trans from DCE-MRI and K 1 from dynamic 13 N-NH 3 -PET, with simultaneous and separate MR/PET in the VX-2 rabbit carcinoma model. MR/PET was performed simultaneously and separately, 14 and 15 days after VX-2 tumor implantation at the paravertebral muscle. The K trans and K 1 values were estimated using an in-house software program. The relationships between K trans and K 1 were analyzed using Pearson's correlation coefficients and linear/non-linear regression function. Assuming a linear relationship, K trans and K 1 exhibited a moderate positive correlations with both simultaneous (r=0.54-0.57) and separate (r=0.53-0.69) imaging. However, while the K trans and K 1 from separate imaging were linearly correlated, those from simultaneous imaging exhibited a non-linear relationship. The amount of change in K 1 associated with a unit increase in K trans varied depending on K trans values. The relationship between K trans and K 1 may be mis-interpreted with separate MR and PET acquisition. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

A 3D MR-acquisition scheme for nonrigid bulk motion correction in simultaneous PET-MR

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

Kolbitsch, Christoph, E-mail: christoph.1.kolbitsch@kcl.ac.uk; Prieto, Claudia; Schaeffter, Tobias

Purpose: Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET-MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracermore » uptake quantification. A 3D MR-acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET-MR data. Methods: A respiratory navigated three dimensional (3D) MR-acquisition with Radial Phase Encoding (RPE) is used to obtain T1- and T2-weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters. Results: Six respiratory gated 3D data sets with T1- and T2-weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to

Whole brain myelin mapping using T1- and T2-weighted MR imaging data

PubMed Central

Ganzetti, Marco; Wenderoth, Nicole; Mantini, Dante

2014-01-01

Despite recent advancements in MR imaging, non-invasive mapping of myelin in the brain still remains an open issue. Here we attempted to provide a potential solution. Specifically, we developed a processing workflow based on T1-w and T2-w MR data to generate an optimized myelin enhanced contrast image. The workflow allows whole brain mapping using the T1-w/T2-w technique, which was originally introduced as a non-invasive method for assessing cortical myelin content. The hallmark of our approach is a retrospective calibration algorithm, applied to bias-corrected T1-w and T2-w images, that relies on image intensities outside the brain. This permits standardizing the intensity histogram of the ratio image, thereby allowing for across-subject statistical analyses. Quantitative comparisons of image histograms within and across different datasets confirmed the effectiveness of our normalization procedure. Not only did the calibrated T1-w/T2-w images exhibit a comparable intensity range, but also the shape of the intensity histograms was largely corresponding. We also assessed the reliability and specificity of the ratio image compared to other MR-based techniques, such as magnetization transfer ratio (MTR), fractional anisotropy (FA), and fluid-attenuated inversion recovery (FLAIR). With respect to these other techniques, T1-w/T2-w had consistently high values, as well as low inter-subject variability, in brain structures where myelin is most abundant. Overall, our results suggested that the T1-w/T2-w technique may be a valid tool supporting the non-invasive mapping of myelin in the brain. Therefore, it might find important applications in the study of brain development, aging and disease. PMID:25228871

Diagnostic Accuracy of Preoperative Gadoxetic Acid–enhanced 3-T MR Imaging for Malignant Liver Lesions by Using Ex Vivo MR Imaging–matched Pathologic Findings as the Reference Standard1

PubMed Central

Costa, Eduardo A. C.; Cunha, Guilherme M.; Smorodinsky, Emmanuil; Cruite, Irene; Tang, An; Marks, Robert M.; Clark, Lisa; Wolfson, Tanya; Gamst, Anthony; Sicklick, Jason K.; Hemming, Alan; Peterson, Michael R.; Middleton, Michael S.; Sirlin, Claude B.

2016-01-01

Purpose To determine per-lesion sensitivity and positive predictive value (PPV) of gadoxetic acid–enhanced 3-T magnetic resonance (MR) imaging for the diagnosis of malignant lesions by using matched (spatially correlated) hepatectomy pathologic findings as the reference standard. Materials and Methods In this prospective, institutional review board–approved, HIPAA-compliant study, 20 patients (nine men, 11 women; mean age, 59 years) with malignant liver lesions who gave written informed consent underwent preoperative gadoxetic acid–enhanced 3-T MR imaging for surgical planning. Two image sets were independently analyzed by three readers to detect liver lesions (set 1 without and set 2 with hepatobiliary phase [HBP] images). Hepatectomy specimen ex vivo MR imaging assisted in matching gadoxetic acid–enhanced 3-T MR imaging findings with pathologic findings. Interreader agreement was assessed by using the Cohen k coefficient. Per-lesion sensitivity and PPV were calculated. Results Cohen k values were 0.64–0.76 and 0.57–0.84, and overall per-lesion sensitivity was 45% (42 of 94 lesions) to 56% (53 of 94 lesions) and 58% (55 of 94 lesions) to 64% (60 of 94 lesions) for sets 1 and 2, respectively. The addition of HBP imaging did not affect interreader agreement but significantly improved overall sensitivity for one reader (P < .05) and almost for another (P = .05). Sensitivity for 0.2–0.5-cm lesions was 0% (0 of 26 lesions) to 8% (two of 26 lesions) for set 1 and 4% (one of 26 lesions) to 12% (three of 26 lesions) for set 2. Sensitivity for 0.6–1.0-cm lesions was 28% (nine of 32 lesions) to 59% (19 of 32 lesions) for set 1 and 66% (21 of 32 lesions) to 69% (22 of 32 lesions) for set 2. Sensitivity for lesions at least 1.0 cm in diameter was at least 81% (13 of 16 lesions) for set 1 and was not improved for set 2. PPV was 98% (56 of 57 lesions) to 100% (60 of 60 lesions) for all readers without differences between image sets or lesion size. Conclusion

MR imaging of intracranial hemangiopericytomas.

PubMed

Mama, N; Ben Abdallah, A; Hasni, I; Kadri, K; Arifa, N; Ladib, M; Tlili-Graiess, K

2014-12-01

To describe the MR features of primary intracranial hemangiopericytomas (HPCs) on conventional imaging, diffusion and MR spectroscopy and aim to determinate distinguishing features from meningiomas. From 2006 to 2012, seven patients with pathologically confirmed primary intracranial HPCs were included. The clinical data, conventional MR findings (n=7), DWI features (n=7) and MR spectroscopy (n=5) were retrospectively analyzed. ADC values of the HPCs (n=7) were measured on ADC map and were compared with that of contralateral normal white matter. Of the seven HPCs, four were anaplastic HPCs (WHO grade III) and three were HPCs (WHO grade II). MR pattern consisted in lobulated or irregular margin tumors in all cases with cross-leaf growth on both side of the falx in two cases. The lesions showed mainly iso signal (n=4) on T1 WI and heterogeneous high signal (n=5) on T2 WI. Heterogenity was mainly related to intra tumoral hemorrhage (n=4), and proeminent intratumoral flow voids (n=3). Marked heterogeneous enhancement (n=5) with dural tail (n=4) was noted. All tumours showed significant peritumoral edema. ADC values of the tumor tissue component range between 0.638 and 1.50×10(-3)mm/s(2) (average = 1,02). Three grade II HPCs showed higher values compared to normal parenchyma ADC (range between 0.772 and 0.930×10(-3)mm/s(2) with average of 0.830), whereas grade III HPCs showed either equal (three cases) or decreased ADC values (one case). MRS showed in all cases markedly increased Cho with lip/lac peak, decreased Cr and almost absent NAA. High mI peak with large glutamine/glutamate were noted in the three grade II HPCs. Conventional MR pattern when combined with DWI and MRS findings are highly suggestive of HPC and appear valuable data to differentiate HPCs from meningiomas. Copyright © 2014. Published by Elsevier Masson SAS.

Low-Molecular-Weight Iron Chelates May Be an Alternative to Gadolinium-based Contrast Agents for T1-weighted Contrast-enhanced MR Imaging.

PubMed

Boehm-Sturm, Philipp; Haeckel, Akvile; Hauptmann, Ralf; Mueller, Susanne; Kuhl, Christiane K; Schellenberger, Eyk A

2018-02-01

Purpose To synthesize two low-molecular-weight iron chelates and compare their T1 contrast effects with those of a commercial gadolinium-based contrast agent for their applicability in dynamic contrast material-enhanced (DCE) magnetic resonance (MR) imaging. Materials and Methods The animal experiments were approved by the local ethics committee. Two previously described iron (Fe) chelates of pentetic acid (Fe-DTPA) and of trans-cyclohexane diamine tetraacetic acid (Fe-tCDTA) were synthesized with stability constants several orders of magnitude higher than those of gadolinium-based contrast agents. The T1 contrast effects of the two chelates were compared with those of gadopentetate dimeglumine in blood serum phantoms at 1.5 T, 3 T, and 7 T. For in vivo studies, a human breast cancer cell line (MDA-231) was implanted in five mice per group. The dynamic contrast effects of the chelates were compared by performing DCE MR imaging with intravenous application of Fe-DTPA or Fe-tCDTA on day 1 and DCE MR imaging in the same tumors with gadopentetate dimeglumine on day 2. Quantitative DCE maps were generated with software and were compared by means of a one-tailed Pearson correlation test. Results Relaxivities in serum (0.94 T at room temperature) of Fe-tCDTA (r1 = 2.2 mmol -1 · sec -1 , r2 = 2.5 mmol -1 · sec -1 ) and Fe-DTPA (r1 = 0.9 mmol -1 · sec -1 , r2 = 0.9 mmol -1 · sec -1 ) were approximately twofold and fivefold lower, respectively, compared with those of gadopentetate dimeglumine (r1 = 4.1 mmol -1 · sec -1 , r2 = 4.8 mmol -1 · sec -1 ). Used at moderately higher concentrations, however, iron chelates generated similar contrast effects at T1-weighted MR imaging in vitro in serum, in vivo in blood, and for DCE MR imaging of breast cancer xenografts. The volume transfer constant values for Fe-DTPA and Fe-tCDTA in the same tumors correlated well with those observed for gadopentetate dimeglumine (Fe-tCDTA Pearson R, 0.99; P = .0003; Fe-DTPA Pearson R, 0.97; P

Design and development of MR-compatible SPECT systems for simultaneous SPECT-MR imaging of small animals

NASA Astrophysics Data System (ADS)

Tsui, Benjamin M. W.; Hugg, James W.; Xu, Jingyan; Chen, Si; Meier, Dirk; Edelstein, William; El-Sharkawy, Abdel; Wagenaar, Douglas J.; Patt, Bradley E.

2011-03-01

We describe a continuing design and development of MR-compatible SPECT systems for simultaneous SPECT-MR imaging of small animals. A first generation prototype SPECT system was designed and constructed to fit inside a MRI system with a gradient bore inner diameter of 12 cm. It consists of 3 angularly offset rings of 8 detectors (1"x1", 16x16 pixels MR-compatible solid-state CZT). A matching 24-pinhole collimator sleeve, made of a tungsten-compound, provides projections from a common FOV of ~25 mm. A birdcage RF coil for MRI data acquisition surrounds the collimator. The SPECT system was tested inside a clinical 3T MRI system. Minimal interference was observed on the simultaneously acquired SPECT and MR images. We developed a sparse-view image reconstruction method based on accurate modeling of the point response function (PRF) of each of the 24 pinholes to provide artifact-free SPECT images. The stationary SPECT system provides relatively low resolution of 3-5 mm but high geometric efficiency of 0.5- 1.2% for fast dynamic acquisition, demonstrated in a SPECT renal kinetics study using Tc-99m DTPA. Based on these results, a second generation prototype MR-compatible SPECT system with an outer diameter of 20 cm that fits inside a mid-sized preclinical MRI system is being developed. It consists of 5 rings of 19 CZT detectors. The larger ring diameter allows the use of optimized multi-pinhole collimator designs, such as high system resolution up to ~1 mm, high geometric efficiency, or lower system resolution without collimator rotation. The anticipated performance of the new system is supported by simulation data.

[Active surveillance for prostate cancer: usefulness of endorectal MR at 1.5 Tesla with pelvic phased array coil in detecting significant tumors].

PubMed

Luyckx, F; Hallouin, P; Barré, C; Aillet, G; Chauveau, P; Hétet, J-F; Bouchot, O; Rigaud, J

2011-02-01

To describe and assess MRI signs of significant tumor in a series of patients who all underwent radical prostatectomy and also fulfilled criteria to choose active surveillance according to French "SurAcaP" protocol. The clinical reports of 681 consecutive patients operated on for prostate cancer between 2002 and 2007 were reviewed retrospectively. All patients had endorectal MR (1.5 Tesla) with pelvic phased array coil. (1.5 T erMR PPA). Sixty-one patients (8.9%) fulfilled "SurAcaP" protocol criteria. Preoperative data (MR+core biopsy) were assessed by comparison to whole-mount step section pathology. 85.3% of the 61 patients entering SurAcaP protocol had significant tumor at pathology. (Non Organ Confined Disease (Non OCD)=8.2%, Gleason sum score>6=39.2%). A new exclusion criterion has been assessed: T3MRI±NPS>1 as a predictor tool of significant tumor. ("T3MRI±NPS>1"=Non OCD at MR±number of positive sextants involved in tumor at MR and/or Core Biopsy > to 1). Sensitivity, specificity, PPV, NPV of the criterion "T3MRI±NPS>1" in predicting significant tumor were, respectively: 77%, 33%, 86%, 20%. Adding this criterion to other criteria of the "SurAcaP" protocol could allow the exclusion of all Non OCD, and a decrease in Gleason sum Score>6 rates (20%). Endorectal MR at 1.5 Tesla with pelvic-phased array coil should be considered when selecting patients for active surveillance in the management of prostate cancer. A criterion based upon MR and core biopsy findings, called "T3MR±NSP>1" may represent an exclusion citeria due to its ability to predict significant tumor. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Non-contrast-enhanced MR portography and hepatic venography with time-spatial labeling inversion pulses: comparison at 1.5 Tesla and 3 Tesla

PubMed Central

Isoda, Hiroyoshi; Furuta, Akihiro; Togashi, Kaori

2015-01-01

Background A 3 Tesla (3 T) magnetic resonance (MR) scanner is a promising tool for upper abdominal MR angiography. However, there is no report focused on the image quality of non-contrast-enhanced MR portography and hepatic venography at 3 T. Purpose To compare and evaluate images of non-contrast-enhanced MR portography and hepatic venography with time-spatial labeling inversion pulses (Time-SLIP) at 1.5 Tesla (1.5 T) and 3 T. Material and Methods Twenty-five healthy volunteers were examined using respiratory-triggered three-dimensional balanced steady-state free-precession (bSSFP) with Time-SLIP. For portography, we used one tagging pulse (selective inversion recovery) and one non-selective inversion recovery pulse; for venography, two tagging pulses were used. The relative signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were quantified, and the quality of visualization was evaluated. Results The CNRs of the main portal vein, right portal vein, and left portal vein at 3 T were better than at 1.5 T. The image quality scores for the portal branches of segment 4, 5, and 8 were significantly higher at 3 T than at 1.5 T. The CNR of the right hepatic vein (RHV) at 3 T was significantly lower than at 1.5 T. The image quality scores of RHV and the middle hepatic vein were higher at 1.5 T than at 3 T. For RHV visualization, the difference was statistically significant. Conclusion Non-contrast-enhanced MR portography with Time-SLIP at 3 T significantly improved visualization of the peripheral branch in healthy volunteers compared with1.5 T. Non-contrast-enhanced MR hepatic venography at 1.5 T was better than at 3 T. PMID:26019890

Preparation and characterization of human recombinant protein 1/Clara cell M(r) 10,000 protein.

PubMed

Okutani, R; Itoh, Y; Yamada, T; Yamaguchi, T; Singh, G; Yagisawa, H; Kawai, T

1996-09-01

Protein 1, which is identical to human Clara cell M(r) 10(4) protein, is a homodimeric, low molecular mass protein (M(r) 14,000) and an effective inhibitor of phospholipase A2 activity. We have expressed this protein in E. coli and characterized its physiochemical and biological properties. Using a pET expression system, about 1.7 mg of purified recombinant protein 1 was obtained from 250 ml of E. coli culture. The amino-terminal sequence of recombinant protein 1 up to the 20th residue was identical to that of native protein 1 except for an extra methionine at the amino-terminus. On reversed-phase HPLC, recombinant protein 1 eluted at the same retention time as native protein 1. The dose-response curves of recombinant protein 1 and native protein 1 in an enzyme-linked immunosorbent assay for protein 1 were identical. Recombinant protein 1 inhibited both porcine pancreas and cobra venom phospholipase A2 activities. These results indicated that recombinant protein 1 is structurally and biologically identical to native protein 1. We found that recombinant protein 1 also inhibits phosphatidylinositol-specific phospholipase C activity.

MR Imaging in Spinocerebellar Ataxias: A Systematic Review.

PubMed

Klaes, A; Reckziegel, E; Franca, M C; Rezende, T J R; Vedolin, L M; Jardim, L B; Saute, J A

2016-08-01

Polyglutamine expansion spinocerebellar ataxias are autosomal dominant slowly progressive neurodegenerative diseases with no current treatment. MR imaging is the best-studied surrogate biomarker candidate for polyglutamine expansion spinocerebellar ataxias, though with conflicting results. We aimed to review quantitative central nervous system MR imaging technique findings in patients with polyglutamine expansion spinocerebellar ataxias and correlations with well-established clinical and molecular disease markers. We searched MEDLINE, LILACS, and Cochrane data bases of clinical trials between January 1995 and January 2016, for quantitative MR imaging volumetric approaches, MR spectroscopy, diffusion tensor imaging, or other quantitative techniques, comparing patients with polyglutamine expansion spinocerebellar ataxias (SCAs) with controls. Pertinent details for each study regarding participants, imaging methods, and results were extracted. After reviewing the 706 results, 18 studies were suitable for inclusion: 2 studies in SCA1, 1 in SCA2, 15 in SCA3, 1 in SCA7, 1 in SCA1 and SCA6 presymptomatic carriers, and none in SCA17 and dentatorubropallidoluysian atrophy. Cerebellar hemispheres and vermis, whole brain stem, midbrain, pons, medulla oblongata, cervical spine, striatum, and thalamus presented significant atrophy in SCA3. The caudate, putamen and whole brain stem presented similar sensitivity to change compared with ataxia scales after 2 years of follow-up in a single prospective study in SCA3. MR spectroscopy and DTI showed abnormalities only in cross-sectional studies in SCA3. Results from single studies in other polyglutamine expansion spinocerebellar ataxias should be replicated in different cohorts. Additional cross-sectional and prospective volumetric analysis, MR spectroscopy, and DTI studies are necessary in polyglutamine expansion spinocerebellar ataxias. The properties of preclinical disease biomarkers (presymptomatic) of MR imaging should be

Whole-body FDG PET-MR oncologic imaging: pitfalls in clinical interpretation related to inaccurate MR-based attenuation correction.

PubMed

Attenberger, Ulrike; Catana, Ciprian; Chandarana, Hersh; Catalano, Onofrio A; Friedman, Kent; Schonberg, Stefan A; Thrall, James; Salvatore, Marco; Rosen, Bruce R; Guimaraes, Alexander R

2015-08-01

Simultaneous data collection for positron emission tomography and magnetic resonance imaging (PET/MR) is now a reality. While the full benefits of concurrently acquiring PET and MR data and the potential added clinical value are still being evaluated, initial studies have identified several important potential pitfalls in the interpretation of fluorodeoxyglucose (FDG) PET/MRI in oncologic whole-body imaging, the majority of which being related to the errors in the attenuation maps created from the MR data. The purpose of this article was to present such pitfalls and artifacts using case examples, describe their etiology, and discuss strategies to overcome them. Using a case-based approach, we will illustrate artifacts related to (1) Inaccurate bone tissue segmentation; (2) Inaccurate air cavities segmentation; (3) Motion-induced misregistration; (4) RF coils in the PET field of view; (5) B0 field inhomogeneity; (6) B1 field inhomogeneity; (7) Metallic implants; (8) MR contrast agents.

Radiofrequency artefacts in echoplanar imaging induced by two 1.5 T MR scanners in close proximity.

PubMed

Li, X; Cui, J; Christopasak, S P; Kumar, A; Peng, Z-G

2014-06-01

The purpose of this study was to assess radio frequency (RF) artefacts in echoplanar imaging (EPI) induced by two 1.5 T MR scanners in close proximity and to find an effective method to correct them. Based on the intact shielding of rooms, experiments were performed by two MR scanners with similar centre frequencies. Phantom A (PA) was scanned in one scanner by EPI at different bandwidths (BWs). Simultaneously, phantom B was scanned in a fixed sequence for scanning with the other scanner. RF artefact gaps of PA, scanning time and the image signal-noise ratio (SNR) were measured and recorded. Statistical analysis was performed with the repeated-measures analysis of variance test. Based on findings obtained from PA, three healthy volunteers were studied at a conventional BW and a lower BW to observe the artefact variance. EPI RF artefacts were symmetrically situated in both sides of the image following the phase-encoding direction. The gap size of the artefact became larger and the SNR was significantly improved with a narrower BW. RF artefacts with a lower BW in volunteers presented the same characteristic as PA. For EPI RF artefacts produced by two 1.5 T MR scanners with approximately similar centre frequencies, we can reduce BWs in a suitable range to minimize the effect on MRI. MR scanners with the same field strength installed in the same vicinity might produce RF artefacts in the sequence at larger BWs. Reducing BWs properly is effective to control the position of artefacts and improve the image quality.

The mineralocorticoid receptor (MR) regulates ENaC but not NCC in mice with random MR deletion.

PubMed

Czogalla, Jan; Vohra, Twinkle; Penton, David; Kirschmann, Moritz; Craigie, Eilidh; Loffing, Johannes

2016-05-01

Aldosterone binds to the mineralocorticoid receptor (MR) and increases renal Na(+) reabsorption via up-regulation of the epithelial Na(+) channel (ENaC) and the Na(+)-K(+)-ATPase in the collecting system (CS) and possibly also via the NaCl cotransporter (NCC) in the distal convoluted tubule (DCT). However, whether aldosterone directly regulates NCC via MR or indirectly through systemic alterations remains controversial. We used mice with deletion of MR in ∼20 % of renal tubule cells (MR/X mice), in which MR-positive (MR(wt)) and -negative (MR(ko)) cells can be studied side-by-side in the same physiological context. Adult MR/X mice showed similar mRNA and protein levels of renal ion transport proteins to control mice. In MR/X mice, no differences in NCC abundance and phosphorylation was seen between MR(wt) and MR(ko) cells and dietary Na(+) restriction up-regulated NCC to similar extent in both groups of cells. In contrast, MR(ko) cells in the CS did not show any detectable alpha-ENaC abundance or apical targeting of ENaC neither on control diet nor in response to dietary Na(+) restriction. Furthermore, Na(+)-K(+)-ATPase expression was unaffected in MR(ko) cells of the DCT, while it was lost in MR(ko) cells of the CS. In conclusion, MR is crucial for ENaC and Na(+)-K(+)-ATPase regulation in the CS, but is dispensable for NCC and Na(+)-K(+)-ATPase regulation in the DCT.

Interventional MR: vascular applications.

PubMed

Smits, H F; Bos, C; van der Weide, R; Bakker, C J

1999-01-01

Three strategies for visualisation of MR-dedicated guidewires and catheters have been proposed, namely active tracking, the technique of locally induced field inhomogeneity and passive susceptibility-based tracking. In this article the pros and cons of these techniques are discussed, including the development of MR-dedicated guidewires and catheters, scan techniques, post-processing tools, and display facilities for MR tracking. Finally, some of the results obtained with MR tracking are discussed.

Enhancement of Survival and Electricity Production in an Engineered Bacterium by Light-Driven Proton Pumping▿ †

PubMed Central

Johnson, Ethan T.; Baron, Daniel B.; Naranjo, Belén; Bond, Daniel R.; Schmidt-Dannert, Claudia; Gralnick, Jeffrey A.

2010-01-01

Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments. PMID:20453141

Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping.

PubMed

Johnson, Ethan T; Baron, Daniel B; Naranjo, Belén; Bond, Daniel R; Schmidt-Dannert, Claudia; Gralnick, Jeffrey A

2010-07-01

Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

PubMed Central

Schkolnik, Gal; Schmidt, Matthias; Mazza, Marco G.; Harnisch, Falk; Musat, Niculina

2015-01-01

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats. PMID:26709923

PET/MR in oncology: an introduction with focus on MR and future perspectives for hybrid imaging

PubMed Central

Balyasnikova, Svetlana; Löfgren, Johan; de Nijs, Robin; Zamogilnaya, Yanna; Højgaard, Liselotte; Fischer, Barbara M

2012-01-01

After more than 20 years of research, a fully integrated PET/MR scanner was launched in 2010 enabling simultaneous acquisition of PET and MR imaging. Currently, no clinical indication for combined PET/MR has been established, however the expectations are high. In this paper we will discuss some of the challenges inherent in this new technology, but focus on potential applications for simultaneous PET/MR in the field of oncology. Methods and tracers for use with the PET technology will be familiar to most readers of this journal; thus this paper aims to provide a short and basic introduction to a number of different MRI techniques, such as DWI-MR (diffusion weighted imaging MR), DCE-MR (dynamic contrast enhanced MR), MRS (MR spectroscopy) and MR for attenuation correction of PET. All MR techniques presented in this paper have shown promising results in the treatment of patients with solid tumors and could be applied together with PET increasing the amount of information about the tissues of interest. The potential clinical benefit of applying PET/MR in staging, radiotherapy planning and treatment evaluation in oncology, as well as the research perspectives for the use of PET/MR in the development of new tracers and drugs will be discussed. PMID:23145362

Towards Implementing an MR-based PET Attenuation Correction Method for Neurological Studies on the MR-PET Brain Prototype

PubMed Central

Catana, Ciprian; van der Kouwe, Andre; Benner, Thomas; Michel, Christian J.; Hamm, Michael; Fenchel, Matthias; Fischl, Bruce; Rosen, Bruce; Schmand, Matthias; Sorensen, A. Gregory

2013-01-01

A number of factors have to be considered for implementing an accurate attenuation correction (AC) in a combined MR-PET scanner. In this work, some of these challenges were investigated and an AC method based entirely on the MR data obtained with a single dedicated sequence was developed and used for neurological studies performed with the MR-PET human brain scanner prototype. Methods The focus was on the bone/air segmentation problem, the bone linear attenuation coefficient selection and the RF coil positioning. The impact of these factors on the PET data quantification was studied in simulations and experimental measurements performed on the combined MR-PET scanner. A novel dual-echo ultra-short echo time (DUTE) MR sequence was proposed for head imaging. Simultaneous MR-PET data were acquired and the PET images reconstructed using the proposed MR-DUTE-based AC method were compared with the PET images reconstructed using a CT-based AC. Results Our data suggest that incorrectly accounting for the bone tissue attenuation can lead to large underestimations (>20%) of the radiotracer concentration in the cortex. Assigning a linear attenuation coefficient of 0.143 or 0.151 cm−1 to bone tissue appears to give the best trade-off between bias and variability in the resulting images. Not identifying the internal air cavities introduces large overestimations (>20%) in adjacent structures. Based on these results, the segmented CT AC method was established as the “silver standard” for the segmented MR-based AC method. Particular to an integrated MR-PET scanner, ignoring the RF coil attenuation can cause large underestimations (i.e. up to 50%) in the reconstructed images. Furthermore, the coil location in the PET field of view has to be accurately known. Good quality bone/air segmentation can be performed using the DUTE data. The PET images obtained using the MR-DUTE- and CT-based AC methods compare favorably in most of the brain structures. Conclusion An MR-DUTE-based AC

Integrin Targeted MR Imaging

PubMed Central

Tan, Mingqian; Lu, Zheng-Rong

2011-01-01

Magnetic resonance imaging (MRI) is a powerful medical diagnostic imaging modality for integrin targeted imaging, which uses the magnetic resonance of tissue water protons to display tissue anatomic structures with high spatial resolution. Contrast agents are often used in MRI to highlight specific regions of the body and make them easier to visualize. There are four main classes of MRI contrast agents based on their different contrast mechanisms, including T1, T2, chemical exchange saturation transfer (CEST) agents, and heteronuclear contrast agents. Integrins are an important family of heterodimeric transmembrane glycoproteins that function as mediators of cell-cell and cell-extracellular matrix interactions. The overexpressed integrins can be used as the molecular targets for designing suitable integrin targeted contrast agents for MR molecular imaging. Integrin targeted contrast agent includes a targeting agent specific to a target integrin, a paramagnetic agent and a linker connecting the targeting agent with the paramagnetic agent. Proper selection of targeting agents is critical for targeted MRI contrast agents to effectively bind to integrins for in vivo imaging. An ideal integrin targeted MR contrast agent should be non-toxic, provide strong contrast enhancement at the target sites and can be completely excreted from the body after MR imaging. An overview of integrin targeted MR contrast agents based on small molecular and macromolecular Gd(III) complexes, lipid nanoparticles and superparamagnetic nanoparticles is provided for MR molecular imaging. By using proper delivery systems for loading sufficient Gd(III) chelates or superparamagnetic nanoparticles, effective molecular imaging of integrins with MRI has been demonstrated in animal models. PMID:21547154

Europium-doped gadolinium sulfide nanoparticles as a dual-mode imaging agent for T1-weighted MR and photoluminescence imaging.

PubMed

Jung, Jongjin; Kim, Mi Ae; Cho, Jee-Hyun; Lee, Seung Jae; Yang, Ilseung; Cho, Janggeun; Kim, Seong Keun; Lee, Chulhyun; Park, Joung Kyu

2012-08-01

We present a facile synthesis of europium-doped gadolinium sulfide (GdS:Eu(3+)) opto-magnetic nanoparticles (NPs) via sonochemistry. Their photoluminescence and strong paramagnetic properties enable these NPs to be utilized as an in vitro cell imaging and in vivo T(1)-weighted MR imaging probe. The GdS:Eu(3+) NPs have a prominent longitudinal (r(1)) relaxivity value, which is a critical parameter for T(1)-weighted MR imaging. Here, we showed not only their strong positive contrast effect to blood vessels and organs of mice, but also blood half-life and biodistribution including clearance from organs, in order to assess the GdS:Eu(3+) NPs as a competent nanocrystal-based T(1) contrast agent. We further showed confocal images of breast cancer cells containing GdS:Eu(3+) NPs to evaluate as a photoluminescence probe. Dual-mode imaging capability obtained from the GdS:Eu(3+) NPs will allow target-oriented cellular imaging as well as the resulting disease-specific MR imaging. Copyright © 2012 Elsevier Ltd. All rights reserved.

Gadolinium-enhanced cardiac MR exams of human subjects are associated with significant increases in the DNA repair marker 53BP1, but not the damage marker γH2AX

PubMed Central

McDonald, Robert J.; Ekins, Jacob B.; Tin, Anthony S.; Costes, Sylvain; Hudson, Tamara M.; Schroeder, Dana J.; Kallmes, Kevin; Kaufmann, Scott H.; Young, Philip M.; Lu, Aiming; Kadirvel, Ramanathan; Kallmes, David F.

2018-01-01

Magnetic resonance imaging is considered low risk, yet recent studies have raised a concern of potential damage to DNA in peripheral blood leukocytes. This prospective Institutional Review Board-approved study examined potential double-strand DNA damage by analyzing changes in the DNA damage and repair markers γH2AX and 53BP1 in patients who underwent a 1.5 T gadolinium-enhanced cardiac magnetic resonance (MR) exam. Sixty patients were enrolled (median age 55 years, 39 males). Patients with history of malignancy or who were receiving chemotherapy, radiation therapy, or steroids were excluded. MR sequence data were recorded and blood samples obtained immediately before and after MR exposure. An automated immunofluorescence assay quantified γH2AX or 53BP1 foci number in isolated peripheral blood mononuclear cells. Changes in foci number were analyzed using the Wilcoxon signed-rank test. Clinical and MR procedural characteristics were compared between patients who had a >10% increase in γH2AX or 53BP1 foci numbers and patients who did not. The number of γH2AX foci did not significantly change following cardiac MR (median foci per cell pre-MR = 0.11, post-MR = 0.11, p = .90), but the number of 53BP1 foci significantly increased following MR (median foci per cell pre-MR = 0.46, post-MR = 0.54, p = .0140). Clinical and MR characteristics did not differ significantly between patients who had at least a 10% increase in foci per cell and those who did not. We conclude that MR exposure leads to a small (median 25%) increase in 53BP1 foci, however the clinical relevance of this increase is unknown and may be attributable to normal variation instead of MR exposure. PMID:29309426

Growth of Iron(III)-Reducing Bacteria on Clay Minerals as the Sole Electron Acceptor and Comparison of Growth Yields on a Variety of Oxidized Iron Forms†

PubMed Central

Kostka, Joel E.; Dalton, Dava D.; Skelton, Hayley; Dollhopf, Sherry; Stucki, Joseph W.

2002-01-01

Smectite clay minerals are abundant in soils and sediments worldwide and are typically rich in Fe. While recent investigations have shown that the structural Fe(III) bound in clay minerals is reduced by microorganisms, previous studies have not tested growth with clay minerals as the sole electron acceptor. Here we have demonstrated that a pure culture of Shewanella oneidensis strain MR-1 as well as enrichment cultures of Fe(III)-reducing bacteria from rice paddy soil and subsurface sediments are capable of conserving energy for growth with the structural Fe(III) bound in smectite clay as the sole electron acceptor. Pure cultures of S. oneidensis were used for more detailed growth rate and yield experiments on various solid- and soluble-phase electron acceptors [smectite, Fe(III) oxyhydroxide FeOOH, Fe(III) citrate, and oxygen] in the same minimal medium. Growth was assessed as direct cell counts or as an increase in cell carbon (measured as particulate organic carbon). Cell counts showed that similar growth of S. oneidensis (108 cells ml−1) occurred with smectitic Fe(III) and on other Fe forms [amorphous Fe(III) oxyhydroxide, and Fe citrate] or oxygen as the electron acceptor. In contrast, cell yields of S. oneidensis measured as the increase in cell carbon were similar on all Fe forms tested while yields on oxygen were five times higher, in agreement with thermodynamic predictions. Over a range of particle loadings (0.5 to 4 g liter−1), the increase in cell number was highly correlated to the amount of structural Fe in smectite reduced. From phylogenetic analysis of the complete 16S rRNA gene sequences, a predominance of clones retrieved from the clay mineral-reducing enrichment cultures were most closely related to the low-G+C gram-positive members of the Bacteria (Clostridium and Desulfitobacterium) and the δ-Proteobacteria (members of the Geobacteraceae). Results indicate that growth with smectitic Fe(III) is similar in magnitude to that with Fe

MR-based motion correction for PET imaging using wired active MR microcoils in simultaneous PET-MR: Phantom study

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

Huang, Chuan; Brady, Thomas J.; El Fakhri, Georges

2014-04-15

Purpose: Artifacts caused by head motion present a major challenge in brain positron emission tomography (PET) imaging. The authors investigated the feasibility of using wired active MR microcoils to track head motion and incorporate the measured rigid motion fields into iterative PET reconstruction. Methods: Several wired active MR microcoils and a dedicated MR coil-tracking sequence were developed. The microcoils were attached to the outer surface of an anthropomorphic{sup 18}F-filled Hoffman phantom to mimic a brain PET scan. Complex rotation/translation motion of the phantom was induced by a balloon, which was connected to a ventilator. PET list-mode and MR tracking datamore » were acquired simultaneously on a PET-MR scanner. The acquired dynamic PET data were reconstructed iteratively with and without motion correction. Additionally, static phantom data were acquired and used as the gold standard. Results: Motion artifacts in PET images were effectively removed by wired active MR microcoil based motion correction. Motion correction yielded an activity concentration bias ranging from −0.6% to 3.4% as compared to a bias ranging from −25.0% to 16.6% if no motion correction was applied. The contrast recovery values were improved by 37%–156% with motion correction as compared to no motion correction. The image correlation (mean ± standard deviation) between the motion corrected (uncorrected) images of 20 independent noise realizations and static reference was R{sup 2} = 0.978 ± 0.007 (0.588 ± 0.010, respectively). Conclusions: Wired active MR microcoil based motion correction significantly improves brain PET quantitative accuracy and image contrast.« less

Proton range shift analysis on brain pseudo-CT generated from T1 and T2 MR.

PubMed

Pileggi, Giampaolo; Speier, Christoph; Sharp, Gregory C; Izquierdo Garcia, David; Catana, Ciprian; Pursley, Jennifer; Amato, Francesco; Seco, Joao; Spadea, Maria Francesca

2018-05-29

In radiotherapy, MR imaging is only used because it has significantly better soft tissue contrast than CT, but it lacks electron density information needed for dose calculation. This work assesses the feasibility of using pseudo-CT (pCT) generated from T1w/T2w MR for proton treatment planning, where proton range comparisons are performed between standard CT and pCT. MR and CT data from 14 glioblastoma patients were used in this study. The pCT was generated by using conversion libraries obtained from tissue segmentation and anatomical regioning of the T1w/T2w MR. For each patient, a plan consisting of three 18 Gy beams was designed on the pCT, for a total of 42 analyzed beams. The plan was then transferred onto the CT that represented the ground truth. Range shift (RS) between pCT and CT was computed at R 80 over 10 slices. The acceptance threshold for RS was according to clinical guidelines of two institutions. A γ-index test was also performed on the total dose for each patient. Mean absolute error and bias for the pCT were 124 ± 10 and -16 ± 26 Hounsfield Units (HU), respectively. The median and interquartile range of RS was 0.5 and 1.4 mm, with highest absolute value being 4.4 mm. Of the 42 beams, 40 showed RS less than the clinical range margin. The two beams with larger RS were both in the cranio-caudal direction and had segmentation errors due to the partial volume effect, leading to misassignment of the HU. This study showed the feasibility of using T1w and T2w MRI to generate a pCT for proton therapy treatment, thus avoiding the use of a planning CT and allowing better target definition and possibilities for online adaptive therapies. Further improvements of the methodology are still required to improve the conversion from MRI intensities to HUs.

An MR-compatible neonatal incubator.

PubMed

Paley, M N J; Hart, A R; Lait, M; Griffiths, P D

2012-07-01

To develop a neonatal MR-compatible incubator for transporting babies between a neonatal intensive care unit and an MRI unit that is within the same hospital but geographically separate. The system was strapped to a standard MR-compatible patient trolley, which provides space for resuscitation outside the incubator. A constant-temperature exothermic heat pad was used to maintain temperature together with a logging fluoro-optic temperature monitor and alarm system. The system has been designed to accommodate standard knee-sized coils from the major MR manufacturers. The original incubator was constructed from carbon fibre, but this required modification to prevent radiofrequency shading artefacts due to the conducting properties of the carbon fibre. A high-tensile polyester material was used, which combined light weight with high impact strength. The system could be moved onto the patient bed with the coils and infant in place by one technologist. Studies in eight neonatal patients produced high quality 1.5 T MR images with low motion artefacts. The incubator should also be compatible with imaging in 3 T MR systems, although further work is required to establish this. Images were acquired using both rapid and high-resolution sequences, including three-dimensional volumes, proton spectra and diffusion weighting. The incubator provides a safe, quiet environment for neonates during transport and imaging, at low cost.

An MR-compatible neonatal incubator

PubMed Central

Paley, M N J; Hart, A R; Lait, M; Griffiths, P D

2012-01-01

Objectives To develop a neonatal MR-compatible incubator for transporting babies between a neonatal intensive care unit and an MRI unit that is within the same hospital but geographically separate. Methods The system was strapped to a standard MR-compatible patient trolley, which provides space for resuscitation outside the incubator. A constant-temperature exothermic heat pad was used to maintain temperature together with a logging fluoro-optic temperature monitor and alarm system. The system has been designed to accommodate standard knee-sized coils from the major MR manufacturers. The original incubator was constructed from carbon fibre, but this required modification to prevent radiofrequency shading artefacts due to the conducting properties of the carbon fibre. A high-tensile polyester material was used, which combined light weight with high impact strength. The system could be moved onto the patient bed with the coils and infant in place by one technologist. Results Studies in eight neonatal patients produced high quality 1.5 T MR images with low motion artefacts. The incubator should also be compatible with imaging in 3 T MR systems, although further work is required to establish this. Images were acquired using both rapid and high-resolution sequences, including three-dimensional volumes, proton spectra and diffusion weighting. Conclusion The incubator provides a safe, quiet environment for neonates during transport and imaging, at low cost. PMID:22167517

Coronary Artery Anomalies and Variants: Technical Feasibility of Assessment with Coronary MR Angiography at 3 T1

PubMed Central

Gharib, Ahmed M.; Ho, Vincent B.; Rosing, Douglas R.; Herzka, Daniel A.; Stuber, Matthias; Arai, Andrew E.; Pettigrew, Roderic I.

2008-01-01

The purpose of this study was to prospectively use a whole-heart three-dimensional (3D) coronary magnetic resonance (MR) angiography technique specifically adapted for use at 3 T and a parallel imaging technique (sensitivity encoding) to evaluate coronary arterial anomalies and variants (CAAV). This HIPAA-compliant study was approved by the local institutional review board, and informed consent was obtained from all participants. Twenty-two participants (11 men, 11 women; age range, 18–62 years) were included. Ten participants were healthy volunteers, whereas 12 participants were patients suspected of having CAAV. Coronary MR angiography was performed with a 3-T MR imager. A 3D free-breathing navigator-gated and vector electrocardiographically–gated segmented k-space gradient-echo sequence with adiabatic T2 preparation pulse and parallel imaging (sensitivity encoding) was used. Whole-heart acquisitions (repetition time msec/echo time msec, 4/1.35; 20° flip angle; 1 × 1 × 2-mm acquired voxel size) lasted 10–12 minutes. Mean examination time was 41 minutes ± 14 (standard deviation). Findings included aneurysms, ectasia, arteriovenous fistulas, and anomalous origins. The 3D whole-heart acquisitions developed for use with 3 T are feasible for use in the assessment of CAAV. © RSNA, 2008 PMID:18372470

Principles of PET/MR Imaging.

PubMed

Disselhorst, Jonathan A; Bezrukov, Ilja; Kolb, Armin; Parl, Christoph; Pichler, Bernd J

2014-06-01

Hybrid PET/MR systems have rapidly progressed from the prototype stage to systems that are increasingly being used in the clinics. This review provides an overview of developments in hybrid PET/MR systems and summarizes the current state of the art in PET/MR instrumentation, correction techniques, and data analysis. The strong magnetic field requires considerable changes in the manner by which PET images are acquired and has led, among others, to the development of new PET detectors, such as silicon photomultipliers. During more than a decade of active PET/MR development, several system designs have been described. The technical background of combined PET/MR systems is explained and related challenges are discussed. The necessity for PET attenuation correction required new methods based on MR data. Therefore, an overview of recent developments in this field is provided. Furthermore, MR-based motion correction techniques for PET are discussed, as integrated PET/MR systems provide a platform for measuring motion with high temporal resolution without additional instrumentation. The MR component in PET/MR systems can provide functional information about disease processes or brain function alongside anatomic images. Against this background, we point out new opportunities for data analysis in this new field of multimodal molecular imaging. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

MR-Consistent Simultaneous Reconstruction of Attenuation and Activity for Non-TOF PET/MR

NASA Astrophysics Data System (ADS)

Heußer, Thorsten; Rank, Christopher M.; Freitag, Martin T.; Dimitrakopoulou-Strauss, Antonia; Schlemmer, Heinz-Peter; Beyer, Thomas; Kachelrieß, Marc

2016-10-01

Attenuation correction (AC) is required for accurate quantification of the reconstructed activity distribution in positron emission tomography (PET). For simultaneous PET/magnetic resonance (MR), however, AC is challenging, since the MR images do not provide direct information on the attenuating properties of the underlying tissue. Standard MR-based AC does not account for the presence of bone and thus leads to an underestimation of the activity distribution. To improve quantification for non-time-of-flight PET/MR, we propose an algorithm which simultaneously reconstructs activity and attenuation distribution from the PET emission data using available MR images as anatomical prior information. The MR information is used to derive voxel-dependent expectations on the attenuation coefficients. The expectations are modeled using Gaussian-like probability functions. An iterative reconstruction scheme incorporating the prior information on the attenuation coefficients is used to update attenuation and activity distribution in an alternating manner. We tested and evaluated the proposed algorithm for simulated 3D PET data of the head and the pelvis region. Activity deviations were below 5% in soft tissue and lesions compared to the ground truth whereas standard MR-based AC resulted in activity underestimation values of up to 12%.

MO-F-CAMPUS-J-04: Tissue Segmentation-Based MR Electron Density Mapping Method for MR-Only Radiation Treatment Planning of Brain

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

Yu, H; Lee, Y; Ruschin, M

2015-06-15

Purpose: Automatically derive electron density of tissues using MR images and generate a pseudo-CT for MR-only treatment planning of brain tumours. Methods: 20 stereotactic radiosurgery (SRS) patients’ T1-weighted MR images and CT images were retrospectively acquired. First, a semi-automated tissue segmentation algorithm was developed to differentiate tissues with similar MR intensities and large differences in electron densities. The method started with approximately 12 slices of manually contoured spatial regions containing sinuses and airways, then air, bone, brain, cerebrospinal fluid (CSF) and eyes were automatically segmented using edge detection and anatomical information including location, shape, tissue uniformity and relative intensity distribution.more » Next, soft tissues - muscle and fat were segmented based on their relative intensity histogram. Finally, intensities of voxels in each segmented tissue were mapped into their electron density range to generate pseudo-CT by linearly fitting their relative intensity histograms. Co-registered CT was used as a ground truth. The bone segmentations of pseudo-CT were compared with those of co-registered CT obtained by using a 300HU threshold. The average distances between voxels on external edges of the skull of pseudo-CT and CT in three axial, coronal and sagittal slices with the largest width of skull were calculated. The mean absolute electron density (in Hounsfield unit) difference of voxels in each segmented tissues was calculated. Results: The average of distances between voxels on external skull from pseudo-CT and CT were 0.6±1.1mm (mean±1SD). The mean absolute electron density differences for bone, brain, CSF, muscle and fat are 78±114 HU, and 21±8 HU, 14±29 HU, 57±37 HU, and 31±63 HU, respectively. Conclusion: The semi-automated MR electron density mapping technique was developed using T1-weighted MR images. The generated pseudo-CT is comparable to that of CT in terms of anatomical position

Mr 40,000 and Mr 39,000 pertussis toxin substrates are increased in surgically denervated dog ventricular myocardium

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

Hershberger, R.E.; Feldman, A.M.; Anderson, F.L.

1991-04-01

To test the general hypothesis that cardiac innervation may participate in myocardial G protein regulation, we examined the effects of complete intrapericardial surgical denervation or sham operation in dogs. In particulate fractions of dog left ventricular (LV) myocardium harvested 28-33 days after denervation or sham operation, Mr 40,000 and Mr 39,000 pertussis toxin-sensitive substrates (G proteins) were increased by 31% (1.31 +/- 0.084 vs 1.00 +/- 0.058 OD, arbitrary units, p less than 0.01) and 40% (1.40 +/- 0.117 vs. 1.000 +/- 0.084 OD, arbitrary units, p less than 0.02), respectively, as compared with sham-operated controls. The Mr 40,000 pertussismore » toxin-sensitive band comigrated with a pertussis toxin-sensitive substrate in human erythrocyte membranes known to contain an alpha Gi species. In these same preparations basal, GTP and GppNHp stimulated adenylate cyclase activities were decreased in denervated heart by 20, 26, and 19%, respectively, consistent with increased activity of an inhibitory G protein. In contrast, Gs function was not altered, because cyc(-) membranes reconstituted with membrane extracts and fluoride and beta-receptor-stimulated adenylate cyclase activity were not different between groups. Furthermore, adenylate cyclase catalytic subunit function as assessed with forskolin and manganese stimulation was not different between preparations of control and denervated heart. We conclude that in preparations of surgically denervated dog myocardium Mr 40,000 and Mr 39,000 pertussis toxin-sensitive G proteins are increased by 31 and 40%, respectively, and that functional alterations in adenylate cyclase activity exist, consistent with increased inhibitory G-protein function.« less

Joint PET-MR respiratory motion models for clinical PET motion correction

NASA Astrophysics Data System (ADS)

Manber, Richard; Thielemans, Kris; Hutton, Brian F.; Wan, Simon; McClelland, Jamie; Barnes, Anna; Arridge, Simon; Ourselin, Sébastien; Atkinson, David

2016-09-01

Patient motion due to respiration can lead to artefacts and blurring in positron emission tomography (PET) images, in addition to quantification errors. The integration of PET with magnetic resonance (MR) imaging in PET-MR scanners provides complementary clinical information, and allows the use of high spatial resolution and high contrast MR images to monitor and correct motion-corrupted PET data. In this paper we build on previous work to form a methodology for respiratory motion correction of PET data, and show it can improve PET image quality whilst having minimal impact on clinical PET-MR protocols. We introduce a joint PET-MR motion model, using only 1 min per PET bed position of simultaneously acquired PET and MR data to provide a respiratory motion correspondence model that captures inter-cycle and intra-cycle breathing variations. In the model setup, 2D multi-slice MR provides the dynamic imaging component, and PET data, via low spatial resolution framing and principal component analysis, provides the model surrogate. We evaluate different motion models (1D and 2D linear, and 1D and 2D polynomial) by computing model-fit and model-prediction errors on dynamic MR images on a data set of 45 patients. Finally we apply the motion model methodology to 5 clinical PET-MR oncology patient datasets. Qualitative PET reconstruction improvements and artefact reduction are assessed with visual analysis, and quantitative improvements are calculated using standardised uptake value (SUVpeak and SUVmax) changes in avid lesions. We demonstrate the capability of a joint PET-MR motion model to predict respiratory motion by showing significantly improved image quality of PET data acquired before the motion model data. The method can be used to incorporate motion into the reconstruction of any length of PET acquisition, with only 1 min of extra scan time, and with no external hardware required.

[MR tomography of the heart].

PubMed

Hahn, D; Beer, M; Sandstede, J

2000-10-01

The introduction of magnetic resonance (MR) tomography has fundamentally changed radiological diagnosis for many diseases. Invasive digital subtraction angiography has already been widely replaced by noninvasive MR angiography for most of the vascular diseases. The rapid technical development of MR imaging in recent years has opened new functional imaging techniques. MR imaging of the heart allows simultaneous measurement of morphological and functional parameters in a single noninvasive examination without any radiation exposure. Because of the high spatial resolution and the reproducibility cine MR imaging is now the gold standard for functional analysis. With the improvement of myocardial perfusion and viability studies many diseases of the heart can be diagnosed in a single examination. MR spectroscopy is the only method which allows a view of the metabolism of the heart. New examinations for vascular imaging and flow quantification complete the goal of "one-stop-shop" imaging of the heart. MR imaging is the only diagnostic modality which allows a complete evaluation of many diseases of the heart with one technique, basic examination as well as follow-up studies. The very rapid improvement in MRI will overcome most of the limitations in the near future, especially concerning MR coronary angiography.

42 CFR 440.150 - Intermediate care facility (ICF/MR) services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false Intermediate care facility (ICF/MR) services. 440....150 Intermediate care facility (ICF/MR) services. (a) “ICF/MR services” means those items and services furnished in an intermediate care facility for the mentally retarded if the following conditions are met: (1...

Basic concepts of MR imaging, diffusion MR imaging, and diffusion tensor imaging.

PubMed

de Figueiredo, Eduardo H M S G; Borgonovi, Arthur F N G; Doring, Thomas M

2011-02-01

MR image contrast is based on intrinsic tissue properties and specific pulse sequences and parameter adjustments. A growing number of MRI imaging applications are based on diffusion properties of water. To better understand MRI diffusion-weighted imaging, a brief overview of MR physics is presented in this article followed by physics of the evolving techniques of diffusion MR imaging and diffusion tensor imaging. Copyright © 2011. Published by Elsevier Inc.

MR-assisted PET Motion Correction for eurological Studies in an Integrated MR-PET Scanner

PubMed Central

Catana, Ciprian; Benner, Thomas; van der Kouwe, Andre; Byars, Larry; Hamm, Michael; Chonde, Daniel B.; Michel, Christian J.; El Fakhri, Georges; Schmand, Matthias; Sorensen, A. Gregory

2011-01-01

Head motion is difficult to avoid in long PET studies, degrading the image quality and offsetting the benefit of using a high-resolution scanner. As a potential solution in an integrated MR-PET scanner, the simultaneously acquired MR data can be used for motion tracking. In this work, a novel data processing and rigid-body motion correction (MC) algorithm for the MR-compatible BrainPET prototype scanner is described and proof-of-principle phantom and human studies are presented. Methods To account for motion, the PET prompts and randoms coincidences as well as the sensitivity data are processed in the line or response (LOR) space according to the MR-derived motion estimates. After sinogram space rebinning, the corrected data are summed and the motion corrected PET volume is reconstructed from these sinograms and the attenuation and scatter sinograms in the reference position. The accuracy of the MC algorithm was first tested using a Hoffman phantom. Next, human volunteer studies were performed and motion estimates were obtained using two high temporal resolution MR-based motion tracking techniques. Results After accounting for the physical mismatch between the two scanners, perfectly co-registered MR and PET volumes are reproducibly obtained. The MR output gates inserted in to the PET list-mode allow the temporal correlation of the two data sets within 0.2 s. The Hoffman phantom volume reconstructed processing the PET data in the LOR space was similar to the one obtained processing the data using the standard methods and applying the MC in the image space, demonstrating the quantitative accuracy of the novel MC algorithm. In human volunteer studies, motion estimates were obtained from echo planar imaging and cloverleaf navigator sequences every 3 seconds and 20 ms, respectively. Substantially improved PET images with excellent delineation of specific brain structures were obtained after applying the MC using these MR-based estimates. Conclusion A novel MR-based MC

Advancements in MR Imaging of the Prostate: From Diagnosis to Interventions

PubMed Central

Bonekamp, David; Jacobs, Michael A.; El-Khouli, Riham; Stoianovici, Dan

2011-01-01

Prostate cancer is the most frequently diagnosed cancer in males and the second leading cause of cancer-related death in men. Assessment of prostate cancer can be divided into detection, localization, and staging; accurate assessment is a prerequisite for optimal clinical management and therapy selection. Magnetic resonance (MR) imaging has been shown to be of particular help in localization and staging of prostate cancer. Traditional prostate MR imaging has been based on morphologic imaging with standard T1-weighted and T2-weighted sequences, which has limited accuracy. Recent advances include additional functional and physiologic MR imaging techniques (diffusion-weighted imaging, MR spectroscopy, and perfusion imaging), which allow extension of the obtainable information beyond anatomic assessment. Multiparametric MR imaging provides the highest accuracy in diagnosis and staging of prostate cancer. In addition, improvements in MR imaging hardware and software (3-T vs 1.5-T imaging) continue to improve spatial and temporal resolution and the signal-to-noise ratio of MR imaging examinations. Another recent advancement in the field is MR imaging guidance for targeted prostate biopsy, which is an alternative to the current standard of transrectal ultrasonography–guided systematic biopsy. © RSNA, 2011 PMID:21571651

Interpreting findings from Mendelian randomization using the MR-Egger method.

PubMed

Burgess, Stephen; Thompson, Simon G

2017-05-01

Mendelian randomization-Egger (MR-Egger) is an analysis method for Mendelian randomization using summarized genetic data. MR-Egger consists of three parts: (1) a test for directional pleiotropy, (2) a test for a causal effect, and (3) an estimate of the causal effect. While conventional analysis methods for Mendelian randomization assume that all genetic variants satisfy the instrumental variable assumptions, the MR-Egger method is able to assess whether genetic variants have pleiotropic effects on the outcome that differ on average from zero (directional pleiotropy), as well as to provide a consistent estimate of the causal effect, under a weaker assumption-the InSIDE (INstrument Strength Independent of Direct Effect) assumption. In this paper, we provide a critical assessment of the MR-Egger method with regard to its implementation and interpretation. While the MR-Egger method is a worthwhile sensitivity analysis for detecting violations of the instrumental variable assumptions, there are several reasons why causal estimates from the MR-Egger method may be biased and have inflated Type 1 error rates in practice, including violations of the InSIDE assumption and the influence of outlying variants. The issues raised in this paper have potentially serious consequences for causal inferences from the MR-Egger approach. We give examples of scenarios in which the estimates from conventional Mendelian randomization methods and MR-Egger differ, and discuss how to interpret findings in such cases.

Phase contrast MR angiography techniques.

PubMed

Dumoulin, C L

1995-08-01

Phase contrast MR methods encode information from macroscopic motion into the phase of the MR signal. Phase contrast methods can be applied with small and large fields-of-view, can give quantitative measures of velocity, and provide excellent suppression of signals from stationary tissue. Unlike time-of-flight methods, phase contrast methods directly measure flow and thus are not hindered by the artifactual appearance of tissue having short T1. Phase contrast angiograms can be two-dimensional (thin slice or projectile), three-dimensional, and/or time resolved and have applications throughout the body.

PET/MR Imaging in Gynecologic Oncology.

PubMed

Ohliger, Michael A; Hope, Thomas A; Chapman, Jocelyn S; Chen, Lee-May; Behr, Spencer C; Poder, Liina

2017-08-01

MR imaging and PET using 2-Deoxy-2-[ 18 F]fluoroglucose (FDG) are both useful in the evaluation of gynecologic malignancies. MR imaging is superior for local staging of disease whereas fludeoxyglucose FDG PET is superior for detecting distant metastases. Integrated PET/MR imaging scanners have great promise for gynecologic malignancies by combining the advantages of each modality into a single scan. This article reviews the technology behind PET/MR imaging acquisitions and technical challenges relevant to imaging the pelvis. A dedicated PET/MR imaging protocol; the roles of PET and MR imaging in cervical, endometrial, and ovarian cancers; and future directions for PET/MR imaging are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Prognostic value of contrast-enhanced MR mammography in patients with breast cancer.

PubMed

Fischer, U; Kopka, L; Brinck, U; Korabiowska, M; Schauer, A; Grabbe, E

1997-01-01

The objective of this study was to evaluate the prognostic value of contrast-enhanced MR mammography in patients with breast cancer. A total of 190 patients with breast cancer (37 noninvasive carcinomas, 153 invasive carcinomas) underwent dynamic contrast-enhanced MR mammography preoperatively. Using 1.5-T unit, T1-weighted sequences (2D FLASH) were obtained repeatedly one time before and five times after IV administration of 0.1 mmol gadopentetate-dimeglumine per kilogram body weight. The findings on MR imaging were correlated with histopathologically defined prognostic factors (histological type, tumor size, tumor grading, metastasis in lymph nodes). In addition, immunohistochemically defined prognostic factors (c-erbB-1, c-erbB-2, p53, Ki-67) were correlated with the signal increase on MR mammogram in 40 patients. There was no significant correlation between the findings on MR mammography and the histopathological type of carcinoma, the grading, and the lymphonodular status. Noninvasive carcinomas showed a higher rate of moderate (38 %) or low (27 %) enhancement on MR imaging than invasive carcinomas (6 and 3 %). The results on MR mammography and the results of immunohistochemical stainings did not correlate significantly. Noninvasive carcinomas showed significantly lower enhancement than invasive carcinomas. However, the signal behavior of contrast-enhanced MR mammography is not related to established histopathological prognostic parameters as subtyping, grading, nodal status, and the expression of certain oncogenes/tumor suppressor genes.

Non-invasive MR-guided HIFU Therapy of TSC-Associated Renal Angiomyolipomas

DTIC Science & Technology

2012-07-01

AD_________________ Award Number: W81XWH-11-1-0299 TITLE: Non- invasive MR-guided HIFU Therapy...3. DATES COVERED 1 July 2011-30 June 2012 4. TITLE AND SUBTITLE Non- invasive MR-guided HIFU Therapy of TSC-Associated Renal Angiomyolipomas 5a... focused on technological development for thermal ablation in mice. Our goal was to establish a small-animal MR-guided HIFU experimental system that

Surveillance of Women with the BRCA1 or BRCA2 Mutation by Using Biannual Automated Breast US, MR Imaging, and Mammography.

PubMed

van Zelst, Jan C M; Mus, Roel D M; Woldringh, Gwendolyn; Rutten, Matthieu J C M; Bult, Peter; Vreemann, Suzan; de Jong, Mathijn; Karssemeijer, Nico; Hoogerbrugge, Nicoline; Mann, Ritse M

2017-11-01

Purpose To evaluate a multimodal surveillance regimen including yearly full-field digital (FFD) mammography, dynamic contrast agent-enhanced (DCE) magnetic resonance (MR) imaging, and biannual automated breast (AB) ultrasonography (US) in women with BRCA1 and BRCA2 mutations. Materials and Methods This prospective multicenter trial enrolled 296 carriers of the BRCA mutation (153 BRCA1 and 128 BRCA2 carriers, and 15 women with first-degree untested relatives) between September 2010 and November 2012, with follow-up until November 2015. Participants underwent 2 years of intensified surveillance including biannual AB US, and routine yearly DCE MR imaging and FFD mammography. The surveillance performance for each modality and possible combinations were determined. Results Breast cancer was screening-detected in 16 women (age range, 33-58 years). Three interval cancers were detected by self-examination, all in carriers of the BRCA1 mutation under age 43 years. One cancer was detected in a carrier of the BRCA1 mutation with a palpable abnormality in the contralateral breast. One incidental breast cancer was detected in a prophylactic mastectomy specimen. Respectively, sensitivity of DCE MR imaging, FFD mammography, and AB US was 68.1% (14 of 21; 95% confidence interval [CI]: 42.9%, 85.8%), 37.2% (eight of 21; 95% CI: 19.8%, 58.7%), and 32.1% (seven of 21; 95% CI: 16.1%, 53.8%); specificity was 95.0% (643 of 682; 95% CI: 92.7%, 96.5%), 98.1% (638 of 652; 95% CI: 96.7%, 98.9%), and 95.1% (1030 of 1088; 95% CI: 93.5%, 96.3%); cancer detection rate was 2.0% (14 of 702), 1.2% (eight of 671), and 1.0% (seven of 711) per 100 women-years; and positive predictive value was 25.2% (14 of 54), 33.7% (nine of 23), and 9.5% (seven of 68). DCE MR imaging and FFD mammography combined yielded the highest sensitivity of 76.3% (16 of 21; 95% CI: 53.8%, 89.9%) and specificity of 93.6% (643 of 691; 95% CI: 91.3%, 95.3%). AB US did not depict additional cancers. FFD mammography yielded no

Non-Invasive Targeted Peripheral Nerve Ablation Using 3D MR Neurography and MRI-Guided High-Intensity Focused Ultrasound (MR-HIFU): Pilot Study in a Swine Model.

PubMed

Huisman, Merel; Staruch, Robert M; Ladouceur-Wodzak, Michelle; van den Bosch, Maurice A; Burns, Dennis K; Chhabra, Avneesh; Chopra, Rajiv

2015-01-01

Ultrasound (US)-guided high intensity focused ultrasound (HIFU) has been proposed for noninvasive treatment of neuropathic pain and has been investigated in in-vivo studies. However, ultrasound has important limitations regarding treatment guidance and temperature monitoring. Magnetic resonance (MR)-imaging guidance may overcome these limitations and MR-guided HIFU (MR-HIFU) has been used successfully for other clinical indications. The primary purpose of this study was to evaluate the feasibility of utilizing 3D MR neurography to identify and guide ablation of peripheral nerves using a clinical MR-HIFU system. Volumetric MR-HIFU was used to induce lesions in the peripheral nerves of the lower limbs in three pigs. Diffusion-prep MR neurography and T1-weighted images were utilized to identify the target, plan treatment and immediate post-treatment evaluation. For each treatment, one 8 or 12 mm diameter treatment cell was used (sonication duration 20 s and 36 s, power 160-300 W). Peripheral nerves were extracted < 3 hours after treatment. Ablation dimensions were calculated from thermal maps, post-contrast MRI and macroscopy. Histological analysis included standard H&E staining, Masson's trichrome and toluidine blue staining. All targeted peripheral nerves were identifiable on MR neurography and T1-weighted images and could be accurately ablated with a single exposure of focused ultrasound, with peak temperatures of 60.3 to 85.7°C. The lesion dimensions as measured on MR neurography were similar to the lesion dimensions as measured on CE-T1, thermal dose maps, and macroscopy. Histology indicated major hyperacute peripheral nerve damage, mostly confined to the location targeted for ablation. Our preliminary results indicate that targeted peripheral nerve ablation is feasible with MR-HIFU. Diffusion-prep 3D MR neurography has potential for guiding therapy procedures where either nerve targeting or avoidance is desired, and may also have potential for post

Non-Invasive Targeted Peripheral Nerve Ablation Using 3D MR Neurography and MRI-Guided High-Intensity Focused Ultrasound (MR-HIFU): Pilot Study in a Swine Model

PubMed Central

Huisman, Merel; Staruch, Robert M.; Ladouceur-Wodzak, Michelle; van den Bosch, Maurice A.; Burns, Dennis K.; Chhabra, Avneesh; Chopra, Rajiv

2015-01-01

Purpose Ultrasound (US)-guided high intensity focused ultrasound (HIFU) has been proposed for noninvasive treatment of neuropathic pain and has been investigated in in-vivo studies. However, ultrasound has important limitations regarding treatment guidance and temperature monitoring. Magnetic resonance (MR)-imaging guidance may overcome these limitations and MR-guided HIFU (MR-HIFU) has been used successfully for other clinical indications. The primary purpose of this study was to evaluate the feasibility of utilizing 3D MR neurography to identify and guide ablation of peripheral nerves using a clinical MR-HIFU system. Methods Volumetric MR-HIFU was used to induce lesions in the peripheral nerves of the lower limbs in three pigs. Diffusion-prep MR neurography and T1-weighted images were utilized to identify the target, plan treatment and immediate post-treatment evaluation. For each treatment, one 8 or 12 mm diameter treatment cell was used (sonication duration 20 s and 36 s, power 160–300 W). Peripheral nerves were extracted < 3 hours after treatment. Ablation dimensions were calculated from thermal maps, post-contrast MRI and macroscopy. Histological analysis included standard H&E staining, Masson’s trichrome and toluidine blue staining. Results All targeted peripheral nerves were identifiable on MR neurography and T1-weighted images and could be accurately ablated with a single exposure of focused ultrasound, with peak temperatures of 60.3 to 85.7°C. The lesion dimensions as measured on MR neurography were similar to the lesion dimensions as measured on CE-T1, thermal dose maps, and macroscopy. Histology indicated major hyperacute peripheral nerve damage, mostly confined to the location targeted for ablation. Conclusion Our preliminary results indicate that targeted peripheral nerve ablation is feasible with MR-HIFU. Diffusion-prep 3D MR neurography has potential for guiding therapy procedures where either nerve targeting or avoidance is desired, and may

SU-E-T-366: Clinical Implementation of MR-Guided Vaginal Cylinder Brachytherapy

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

Owrangi, A; Jolly, S; Balter, J

2014-06-01

Purpose: To evaluate the accuracy of MR-based vaginal brachytherapy source localization using an in-house MR-visible marker versus the alignment of an applicator model to MR images. Methods: Three consecutive patients undergoing vaginal HDR brachytherapy with a plastic cylinder were scanned with both CT and MRI (including T1- and T2- weighted images). An MR-visible source localization marker, consisting of a sealed thin catheter filled with either water (for T2 contrast) or Gd-doped water (for T1 contrast), was assembled shortly before scanning. Clinically, the applicator channel was digitized on CT with an x-ray marker. To evaluate the efficacy of MR-based applicator reconstruction,more » each MR image volume was aligned locally to the CT images based on the region containing the cylinder. Applicator digitization was performed on the MR images using (1) the MR visible marker and (2) alignment of an applicator surface model from Varian's Brachytherapy Planning software to the MRI images. Resulting source positions were compared with the original CT digitization. Results: Although the source path was visualized by the MR marker, the applicator tip proved difficult to identify due to challenges in achieving a watertight seal. This resulted in observed displacements of the catheter tip, at times >1cm. Deviations between the central source positions identified via aligning the applicator surface model to MR and using the xray marker on CT ranged from 0.07 – 0.19 cm and 0.07 – 0.20 cm on T1- weighted and T2-weighted images, respectively. Conclusion: Based on the current study, aligning the applicator model to MRI provides a practical, current approach to perform MR-based brachytherapy planning. Further study is needed to produce catheters with reliably and reproducibly identifiable tips. Attempts are being made to improve catheter seals, as well as to increase the viscosity of the contrast material to decrease fluid mobility inside the catheter.« less

Prostate cancer localization with endorectal MR imaging and MR spectroscopic imaging: effect of clinical data on reader accuracy.

PubMed

Dhingsa, Rajpal; Qayyum, Aliya; Coakley, Fergus V; Lu, Ying; Jones, Kirk D; Swanson, Mark G; Carroll, Peter R; Hricak, Hedvig; Kurhanewicz, John

2004-01-01

To determine the effect of digital rectal examination findings, sextant biopsy results, and prostate-specific antigen (PSA) levels on reader accuracy in the localization of prostate cancer with endorectal magnetic resonance (MR) imaging and MR spectroscopic imaging. This was a retrospective study of 37 patients (mean age, 57 years) with biopsy-proved prostate cancer. Transverse T1-weighted, transverse high-spatial-resolution, and coronal T2-weighted MR images and MR spectroscopic images were obtained. Two independent readers, unaware of clinical data, recorded the size and location of suspicious peripheral zone tumor nodules on a standardized diagram of the prostate. Readers also recorded their degree of diagnostic confidence for each nodule on a five-point scale. Both readers repeated this interpretation with knowledge of rectal examination findings, sextant biopsy results, and PSA level. Step-section histopathologic findings were the reference standard. Logistic regression analysis with generalized estimating equations was used to correlate tumor detection with clinical data, and alternative free-response receiver operating characteristic (AFROC) curve analysis was used to examine the overall effect of clinical data on all positive results. Fifty-one peripheral zone tumor nodules were identified at histopathologic evaluation. Logistic regression analysis showed awareness of clinical data significantly improved tumor detection rate (P <.02) from 15 to 19 nodules for reader 1 and from 13 to 19 nodules for reader 2 (27%-37% overall) by using both size and location criteria. AFROC analysis showed no significant change in overall reader performance because there was an associated increase in the number of false-positive findings with awareness of clinical data, from 11 to 21 for reader 1 and from 16 to 25 for reader 2. Awareness of clinical data significantly improves reader detection of prostate cancer nodules with endorectal MR imaging and MR spectroscopic imaging

Kallman syndrome versus idiopathic hypogonadotropic hypogonadism at MR imaging

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

Vogl, T.J.; Stemmler, J.; Bergman, C.

To identify morphologic differences between Kallman syndrome (KS) and idiopathic hypogonadotropic hypogonadism (IHH) and establish a role for magnetic resonance (MR) imaging in these disorders. Twenty-eight patients were compared with 10 eugonal male volunteers. Eighteen patients had KS (hypogonadotropic hypogonadism with anosmia) and 10 had IHH. All participants underwent hormone analysis, a sniff-bottle smell test, and gadolinium-enhanced MR imaging. Changes in the hypothalamic-hypophyseal region and the rhinencephalon were evaluated. MR imaging revealed intracranial morphologic changes in all patients on plain T1-weighted sections. Seventeen patients with KS demonstrated aplasia of an olfactory bulb; one olfactory sulcus was absent in six, rudimentarymore » in four, and normal in eight. Olfactory bulbs were present in all 10 IHH patients and three showed one slightly hypoplastic bulb. Ten patients with KS and three with IHH showed an enlarged paranasal sinus system. Further MR findings were similar. MR imaging demonstrates abnormalities of the rhinencephalon present in KS patients and occasionally absent in IHH patients. 18 refs., 10 figs., 1 tab.« less

MR imaging, proton MR spectroscopy, ultrasonographic, histologic findings in patients with chronic lymphedema.

PubMed

Fumiere, E; Leduc, O; Fourcade, S; Becker, C; Garbar, C; Demeure, R; Wilputte, F; Leduc, A; Delcour, C

2007-12-01

Lymphedema is a progressive disease with multiple alterations occurring in the dermis. We undertook this study using high-frequency ultrasonography (US), magnetic resonance imaging, proton MR spectroscopy and histology to examine structural changes occurring in the subcutaneous tissue and precisely describe the nature of intralobular changes in chronic lymphedema. Four cutaneous and subcutaneous tissue biopsies from patients with chronic lymphedema during lymphonodal transplantation were studied. We performed US with a 13.5 MHz transducer, TSE T1 and TSE T2 magnetic resonance images with and without fat-suppression, MR Chemical Shift Imaging Spectroscopy and histological evaluation on these biopsies. We found that normal subcutaneous septa are seen as hyperechogenic lines in US and hyposignal lines in MRI and that hyperechogenic subcutis in US can be due to interlobular and intralobular water accumulation and/or to interlobular and intralobular fibrosis. Our study also confirms the usefulness of MR spectroscopy to assess water or fat content of soft tissue. Thus, multiple imaging modalities may be necessary to precisely delineate the nature of tissue alterations in chronic lymphedema.

Magnetic Resonance-Based Electrical Property Tomography (MR-EPT) for Prostate Cancer Grade Imaging

DTIC Science & Technology

2016-07-01

Award Number: W81XWH-13-1-0127 TITLE: Magnetic Resonance-Based Electrical Property Tomography (MR- EPT) for Prostate Cancer Grade Imaging...SUBTITLE 5a. CONTRACT NUMBER W81XWH-13-1-0127 Magnetic Resonance-Based Electrical Property Tomography (MR- EPT) for Prostate Cancer Grade Imaging...developing Magnetic Resonance – Electrical Property Tomography (MR-EPT) specifically for prostate imaging. MR-EPT is an imaging modality that may enable

Intraindividual comparison of image quality in MR urography at 1.5 and 3 tesla in an animal model.

PubMed

Regier, M; Nolte-Ernsting, C; Adam, G; Kemper, J

2008-10-01

Experimental evaluation of image quality of the upper urinary tract in MR urography (MRU) at 1.5 and 3 Tesla in a porcine model. In this study four healthy domestic pigs, weighing between 71 and 80 kg (mean 73.6 kg), were examined with a standard T1w 3D-GRE and a high-resolution (HR) T1w 3D-GRE sequence at 1.5 and 3 Tesla. Additionally, at 3 Tesla both sequences were performed with parallel imaging (SENSE factor 2). The MR urographic scans were performed after intravenous injection of gadolinium-DTPA (0.1 mmol/kg body weight (bw)) and low-dose furosemide (0.1 mg/kg bw). Image evaluation was performed by two independent radiologists blinded to sequence parameters and field strength. Image analysis included grading of image quality of the segmented collecting system based on a five-point grading scale regarding anatomical depiction and artifacts observed (1: the majority of the segment (>50%) was not depicted or was obscured by major artifacts; 5: the segment was visualized without artifacts and had sharply defined borders). Signal-to-noise (SNR) and contrast-to-noise (CNR) ratios were determined. Statistical analysis included kappa-statistics, Wilcoxon and paired student t-test. The mean scores for MR urographies at 1.5 Tesla were 2.83 for the 3D-GRE and 3.48 for the HR3D-GRE sequence. Significantly higher values were determined using the corresponding sequences at 3 Tesla, averaging 3.19 for the 3D-GRE (p = 0.047) and 3.92 for the HR3D-GRE (p = 0,023) sequence. Delineation of the pelvicaliceal system was rated significantly higher at 3 Tesla compared to 1.5 Tesla (3D-GRE: p = 0.015; HR3D-GRE: p = 0.006). At 3 Tesla the mean SNR and CNR were significantly higher (p < 0.05). A kappa of 0.67 indicated good interobserver agreement. In an experimental setup, MR urography at 3 Tesla allowed for significantly higher image quality and SNR compared to 1.5 Tesla, particularly for the visualization of the pelvicaliceal system.

Zero TE-based pseudo-CT image conversion in the head and its application in PET/MR attenuation correction and MR-guided radiation therapy planning.

PubMed

Wiesinger, Florian; Bylund, Mikael; Yang, Jaewon; Kaushik, Sandeep; Shanbhag, Dattesh; Ahn, Sangtae; Jonsson, Joakim H; Lundman, Josef A; Hope, Thomas; Nyholm, Tufve; Larson, Peder; Cozzini, Cristina

2018-02-18

To describe a method for converting Zero TE (ZTE) MR images into X-ray attenuation information in the form of pseudo-CT images and demonstrate its performance for (1) attenuation correction (AC) in PET/MR and (2) dose planning in MR-guided radiation therapy planning (RTP). Proton density-weighted ZTE images were acquired as input for MR-based pseudo-CT conversion, providing (1) efficient capture of short-lived bone signals, (2) flat soft-tissue contrast, and (3) fast and robust 3D MR imaging. After bias correction and normalization, the images were segmented into bone, soft-tissue, and air by means of thresholding and morphological refinements. Fixed Hounsfield replacement values were assigned for air (-1000 HU) and soft-tissue (+42 HU), whereas continuous linear mapping was used for bone. The obtained ZTE-derived pseudo-CT images accurately resembled the true CT images (i.e., Dice coefficient for bone overlap of 0.73 ± 0.08 and mean absolute error of 123 ± 25 HU evaluated over the whole head, including errors from residual registration mismatches in the neck and mouth regions). The linear bone mapping accounted for bone density variations. Averaged across five patients, ZTE-based AC demonstrated a PET error of -0.04 ± 1.68% relative to CT-based AC. Similarly, for RTP assessed in eight patients, the absolute dose difference over the target volume was found to be 0.23 ± 0.42%. The described method enables MR to pseudo-CT image conversion for the head in an accurate, robust, and fast manner without relying on anatomical prior knowledge. Potential applications include PET/MR-AC, and MR-guided RTP. © 2018 International Society for Magnetic Resonance in Medicine.

PET/MRI for Oncologic Brain Imaging: A Comparison of Standard MR-Based Attenuation Corrections with a Model-Based Approach for the Siemens mMR PET/MR System.

PubMed

Rausch, Ivo; Rischka, Lucas; Ladefoged, Claes N; Furtner, Julia; Fenchel, Matthias; Hahn, Andreas; Lanzenberger, Rupert; Mayerhoefer, Marius E; Traub-Weidinger, Tatjana; Beyer, Thomas

2017-09-01

The aim of this study was to compare attenuation-correction (AC) approaches for PET/MRI in clinical neurooncology. Methods: Forty-nine PET/MRI brain scans were included: brain tumor studies using 18 F-fluoro-ethyl-tyrosine ( 18 F-FET) ( n = 31) and 68 Ga-DOTANOC ( n = 7) and studies of healthy subjects using 18 F-FDG ( n = 11). For each subject, MR-based AC maps (MR-AC) were acquired using the standard DIXON- and ultrashort echo time (UTE)-based approaches. A third MR-AC was calculated using a model-based, postprocessing approach to account for bone attenuation values (BD, noncommercial prototype software by Siemens Healthcare). As a reference, AC maps were derived from patient-specific CT images (CTref). PET data were reconstructed using standard settings after AC with all 4 AC methods. We report changes in diagnosis for all brain tumor patients and the following relative differences values (RDs [%]), with regards to AC-CTref: for 18 F-FET (A)-SUVs as well as volumes of interest (VOIs) defined by a 70% threshold of all segmented lesions and lesion-to-background ratios; for 68 Ga-DOTANOC (B)-SUVs as well as VOIs defined by a 50% threshold for all lesions and the pituitary gland; and for 18 F-FDG (C)-RD of SUVs of the whole brain and 10 anatomic regions segmented on MR images. Results: For brain tumor imaging (A and B), the standard PET-based diagnosis was not affected by any of the 3 MR-AC methods. For A, the average RDs of SUV mean were -10%, -4%, and -3% and of the VOIs 1%, 2%, and 7% for DIXON, UTE, and BD, respectively. Lesion-to-background ratios for all MR-AC methods were similar to that of CTref. For B, average RDs of SUV mean were -11%, -11%, and -3% and of the VOIs 1%, -4%, and -3%, respectively. In the case of 18 F-FDG PET/MRI (C), RDs for the whole brain were -11%, -8%, and -5% for DIXON, UTE, and BD, respectively. Conclusion: The diagnostic reading of PET/MR patients with brain tumors did not change with the chosen AC method. Quantitative accuracy of

Role of MR-DWI and MR-PWI in the radiotherapy of implanted pulmonary VX-2 carcinoma in rabbits.

PubMed

Zhang, Qiang; Zhang, Mingmin; Liu, Zhaoxin; Shi, Baoqi; Qi, Fuliang; Wang, Haijiang; Lv, Yuan; Jin, Haijiao; Zhang, Weijing

2014-10-01

To detect the activity of tumor cells and tumor blood flow before and after the radiotherapy of implanted pulmonary VX-2 carcinoma in rabbit models by using magnetic resonance diffusion-weighted imaging (MR-DWI) and magnetic resonance perfusion weighted imaging (MR-PWI), and to evaluate the effectiveness and safety of the radiotherapy based on the changes in the MR-DWI and MR-PWI parameters at different treatment stages. A total of 56 rabbit models with implanted pulmonary VX-2 carcinoma were established, and then equally divided into treatment group and control group. MR-DWI and MR-PWI were separately performed using a Philips Acheiva 1.5T MRI machine (Philips, Netherland). MRI image processing was performed using special perfusion software and the WORKSPACE advanced workstation for MRI. MR-DWI was applied for the observation of tumor signals and the measurement of apparent diffusion coefficient (ADC) values; whereas MR-PWI was used for the measurement of wash in rate (WIR), wash out rate (WOR), and maximum enhancement rate (MER). The radiation treatment was performed using Siemens PRIMUS linear accelerator. In the treatment group, the radiotherapy was performed 21 days later on a once weekly dosage of 1,000 cGy to yield a total dosage of 5,000 cGy. THE ADC PARAMETERS IN THE REGION OF INTEREST ON DWI WERE AS FOLLOWS: on the treatment day for the implanted pulmonary VX-2 carcinoma, the t values at the center and the edge of the lesions were 1.352 and 1.461 in the treatment group and control group (P>0.05). During weeks 0-1 after treatment, the t values at the center and the edge of the lesions were 1.336 and 1.137 (P>0.05). During weeks 1-2, the t values were 1.731 and 1.736 (P<0.05). During weeks 2-3, the t values were 1.742 and 1.749 (P<0.05). During weeks 3-4, the t values were 2.050 and 2.127 (P<0.05). During weeks 4-5, the t values were 2.764 and 2.985 (P<0.05). The ADC values in the treatment group were significantly higher than in the control group. After

High-resolution axial MR imaging of tibial stress injuries

PubMed Central

2012-01-01

Purpose To evaluate the relative involvement of tibial stress injuries using high-resolution axial MR imaging and the correlation with MR and radiographic images. Methods A total of 33 patients with exercise-induced tibial pain were evaluated. All patients underwent radiograph and high-resolution axial MR imaging. Radiographs were taken at initial presentation and 4 weeks later. High-resolution MR axial images were obtained using a microscopy surface coil with 60 × 60 mm field of view on a 1.5T MR unit. All images were evaluated for abnormal signals of the periosteum, cortex and bone marrow. Results Nineteen patients showed no periosteal reaction at initial and follow-up radiographs. MR imaging showed abnormal signals in the periosteal tissue and partially abnormal signals in the bone marrow. In 7 patients, periosteal reaction was not seen at initial radiograph, but was detected at follow-up radiograph. MR imaging showed abnormal signals in the periosteal tissue and entire bone marrow. Abnormal signals in the cortex were found in 6 patients. The remaining 7 showed periosteal reactions at initial radiograph. MR imaging showed abnormal signals in the periosteal tissue in 6 patients. Abnormal signals were seen in the partial and entire bone marrow in 4 and 3 patients, respectively. Conclusions Bone marrow abnormalities in high-resolution axial MR imaging were related to periosteal reactions at follow-up radiograph. Bone marrow abnormalities might predict later periosteal reactions, suggesting shin splints or stress fractures. High-resolution axial MR imaging is useful in early discrimination of tibial stress injuries. PMID:22574840

Magnetically Assisted Remote-controlled Endovascular Catheter for Interventional MR Imaging: In Vitro Navigation at 1.5 T versus X-ray Fluoroscopy

PubMed Central

Losey, Aaron D.; Lillaney, Prasheel; Martin, Alastair J.; Cooke, Daniel L.; Wilson, Mark W.; Thorne, Bradford R. H.; Sincic, Ryan S.; Arenson, Ronald L.; Saeed, Maythem

2014-01-01

Purpose To compare in vitro navigation of a magnetically assisted remote-controlled (MARC) catheter under real-time magnetic resonance (MR) imaging with manual navigation under MR imaging and standard x-ray guidance in endovascular catheterization procedures in an abdominal aortic phantom. Materials and Methods The 2-mm-diameter custom clinical-grade microcatheter prototype with a solenoid coil at the distal tip was deflected with a foot pedal actuator used to deliver 300 mA of positive or negative current. Investigators navigated the catheter into branch vessels in a custom cryogel abdominal aortic phantom. This was repeated under MR imaging guidance without magnetic assistance and under conventional x-ray fluoroscopy. MR experiments were performed at 1.5 T by using a balanced steady-state free precession sequence. The mean procedure times and percentage success data were determined and analyzed with a linear mixed-effects regression analysis. Results The catheter was clearly visible under real-time MR imaging. One hundred ninety-two (80%) of 240 turns were successfully completed with magnetically assisted guidance versus 144 (60%) of 240 turns with nonassisted guidance (P < .001) and 119 (74%) of 160 turns with standard x-ray guidance (P = .028). Overall mean procedure time was shorter with magnetically assisted than with nonassisted guidance under MR imaging (37 seconds ± 6 [standard error of the mean] vs 55 seconds ± 3, P < .001), and time was comparable between magnetically assisted and standard x-ray guidance (37 seconds ± 6 vs 44 seconds ± 3, P = .045). When stratified by angle of branch vessel, magnetic assistance was faster than nonassisted MR guidance at turns of 45°, 60°, and 75°. Conclusion In this study, a MARC catheter for endovascular navigation under real-time MR imaging guidance was developed and tested. For catheterization of branch vessels arising at large angles, magnetically assisted catheterization was faster than manual catheterization

Magnetically assisted remote-controlled endovascular catheter for interventional MR imaging: in vitro navigation at 1.5 T versus X-ray fluoroscopy.

PubMed

Losey, Aaron D; Lillaney, Prasheel; Martin, Alastair J; Cooke, Daniel L; Wilson, Mark W; Thorne, Bradford R H; Sincic, Ryan S; Arenson, Ronald L; Saeed, Maythem; Hetts, Steven W

2014-06-01

To compare in vitro navigation of a magnetically assisted remote-controlled (MARC) catheter under real-time magnetic resonance (MR) imaging with manual navigation under MR imaging and standard x-ray guidance in endovascular catheterization procedures in an abdominal aortic phantom. The 2-mm-diameter custom clinical-grade microcatheter prototype with a solenoid coil at the distal tip was deflected with a foot pedal actuator used to deliver 300 mA of positive or negative current. Investigators navigated the catheter into branch vessels in a custom cryogel abdominal aortic phantom. This was repeated under MR imaging guidance without magnetic assistance and under conventional x-ray fluoroscopy. MR experiments were performed at 1.5 T by using a balanced steady-state free precession sequence. The mean procedure times and percentage success data were determined and analyzed with a linear mixed-effects regression analysis. The catheter was clearly visible under real-time MR imaging. One hundred ninety-two (80%) of 240 turns were successfully completed with magnetically assisted guidance versus 144 (60%) of 240 turns with nonassisted guidance (P < .001) and 119 (74%) of 160 turns with standard x-ray guidance (P = .028). Overall mean procedure time was shorter with magnetically assisted than with nonassisted guidance under MR imaging (37 seconds ± 6 [standard error of the mean] vs 55 seconds ± 3, P < .001), and time was comparable between magnetically assisted and standard x-ray guidance (37 seconds ± 6 vs 44 seconds ± 3, P = .045). When stratified by angle of branch vessel, magnetic assistance was faster than nonassisted MR guidance at turns of 45°, 60°, and 75°. In this study, a MARC catheter for endovascular navigation under real-time MR imaging guidance was developed and tested. For catheterization of branch vessels arising at large angles, magnetically assisted catheterization was faster than manual catheterization under MR imaging guidance and was comparable to

Quantitative MR imaging in fracture dating--Initial results.

PubMed

Baron, Katharina; Neumayer, Bernhard; Widek, Thomas; Schick, Fritz; Scheicher, Sylvia; Hassler, Eva; Scheurer, Eva

2016-04-01

For exact age determinations of bone fractures in a forensic context (e.g. in cases of child abuse) improved knowledge of the time course of the healing process and use of non-invasive modern imaging technology is of high importance. To date, fracture dating is based on radiographic methods by determining the callus status and thereby relying on an expert's experience. As a novel approach, this study aims to investigate the applicability of magnetic resonance imaging (MRI) for bone fracture dating by systematically investigating time-resolved changes in quantitative MR characteristics after a fracture event. Prior to investigating fracture healing in children, adults were examined for this study in order to test the methodology for this application. Altogether, 31 MR examinations in 17 subjects (♀: 11 ♂: 6; median age 34 ± 15 y, scanned 1-5 times over a period of up to 200 days after the fracture event) were performed on a clinical 3T MR scanner (TimTrio, Siemens AG, Germany). All subjects were treated conservatively for a fracture in either a long bone or in the collar bone. Both, qualitative and quantitative MR measurements were performed in all subjects. MR sequences for a quantitative measurement of relaxation times T1 and T2 in the fracture gap and musculature were applied. Maps of quantitative MR parameters T1, T2, and magnetisation transfer ratio (MTR) were calculated and evaluated by investigating changes over time in the fractured area by defined ROIs. Additionally, muscle areas were examined as reference regions to validate this approach. Quantitative evaluation of 23 MR data sets (12 test subjects, ♀: 7 ♂: 5) showed an initial peak in T1 values in the fractured area (T1=1895 ± 607 ms), which decreased over time to a value of 1094 ± 182 ms (200 days after the fracture event). T2 values also peaked for early-stage fractures (T2=115 ± 80 ms) and decreased to 73 ± 33 ms within 21 days after the fracture event. After that time point, no

Sampling and evaluation of specific absorption rates during patient examinations performed on 1.5-Tesla MR systems.

PubMed

Brix, G; Reinl, M; Brinker, G

2001-07-01

It was the purpose of present study, to evaluate a large number of exposure-time courses measured during patient examinations in clinical routine in relation to the current IEC standard and the draft version of the revised standard and, moreover, to investigate whether there is a correlation between the subjective heat perception of the patients during the MR examination and the intensity of RF power deposition. To this end, radiofrequency exposure to 591 patients undergoing MR examinations performed on 1.5-Tesla MR systems was monitored in five clinics and evaluated in accordance with both IEC standards. For each of the 7902 sequences applied, whole body and partial body SARs were estimated on the basis of a simple patient model. Following the examinations, 149 patients were willing to provide information in a questionnaire regarding their body weight and their subjective heat perception during the examination. Although patient masses entered into the MR system were in some cases too high, reliable masses could be estimated by the SAR monitor. In relation to our data, the revision of the IEC standard results in a tightening of the restrictions, but still more than 96% of the examinations did not exceed the SAR limits recommended for the normal operating mode. For the exposure conditions examined, no statistically significant correlation was found between the subjective heat perception of the patients and the intensity of power deposition. Taking advantage of the possibility to compute running SAR averages, MR sequences can be employed in clinical practice for which SAR levels exceed the defined IEC limits, if the acquisition time is short in relation to the averaging period and energy deposition has been low previous to the applied high-power sequence.

MR-compatible polyetheretherketone-based guide wire assisting MR-guided stenting of iliac and supraaortic arteries in swine: feasibility study.

PubMed

Kos, Sebastian; Huegli, Rolf; Hofmann, Eugen; Quick, Harald H; Kuehl, Hilmar; Aker, Stephanie; Kaiser, Gernot M; Borm, Paul J A; Jacob, Augustinus L; Bilecen, Deniz

2009-01-01

The purpose of this study was to demonstrate first magnetic resonance (MR)-guided stenting of iliac and supraaortic arteries using a polyetheretherketone-based (PEEK) MR-compatible guide wire. In vitro and animal experiments were performed in a short magnet wide-bore scanner (1.5 Tesla, Espree, Siemens Healthcare, Erlangen, Germany). For all experiments, a 0.035'' MR-compatible guide wire prototoype was used. This wire had a compound core of PEEK with reinforcing fibres, a soft and atraumatic tip and a hydrophilic coating. For its passive visualization, paramagnetic markings were attached. All experiments were performed through a vascular introducer sheath under MR-guidance. In vitro repetitive selective over the wire catheterizations of either the right carotid artery and the left subclavian artery were performed. In vivo, selective catheterization and over-the-wire stenting of the brachiocephalic trunk and the left subclavian artery were performed. The common iliac arteries were catheterized retrogradely (left) and cross-over (right). Angioplasty and stenting were performed over-the-wire. All procedures were successful. Visibility of the PEEK-based guide-wire was rated good in vitro and acceptable in vivo. Guide wire pushability and endovascular device support were good. The PEEK-based MR-compatible guide wire is well visible and usable under MR-guidance. It supports over-the-wire treatment of iliac arteries and supraaortic arteries.

Temporal Lobe Epilepsy: Quantitative MR Volumetry in Detection of Hippocampal Atrophy

PubMed Central

Farid, Nikdokht; Girard, Holly M.; Kemmotsu, Nobuko; Smith, Michael E.; Magda, Sebastian W.; Lim, Wei Y.; Lee, Roland R.

2012-01-01

Purpose: To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). Materials and Methods: This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration–cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Results: Quantitative MR imaging–derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%–89.5%) and specificity (92.2%–94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Conclusion: Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a

Focused US system for MR imaging-guided tumor ablation.

PubMed

Cline, H E; Hynynen, K; Watkins, R D; Adams, W J; Schenck, J F; Ettinger, R H; Freund, W R; Vetro, J P; Jolesz, F A

1995-03-01

To measure the performance characteristics of a focused ultrasound (US) system for magnetic resonance (MR) imaging-guided tumor ablation. The authors constructed a focused US system for MR imaging-guided tumor ablation. The location of the heated region and thermal dose were monitored with temperature-sensitive MR images obtained in phantoms and rabbit skeletal muscle after application of each sonic pulse. The region heated by the focused ultrasound beam was within 1 mm of that observed on temperature-sensitive fast gradient-echo MR images of in vivo rabbit skeletal muscle. Analysis of heat flow and the rate of coagulation necrosis provided an estimate of the size of the ablated region that was in agreement with experimental findings. MR imaging provides target definition and control for thermal therapy in regions of variable perfusion or in tissues that are not well characterized.

New advances in MR-compatible bioartificial liver

PubMed Central

Jeffries, Rex E.; Macdonald, Jeffrey M.

2015-01-01

MR-compatible bioartificial liver (BAL) studies have been performed for 30 years and are reviewed. There are two types of study: (i) metabolism and drug studies using multinuclear MRS; primarily short-term (< 8 h) studies; (ii) the use of multinuclear MRS and MRI to noninvasively define the features and functions of BAL systems for long-term liver tissue engineering. In the latter, these systems often undergo not only modification of the perfusion system, but also the construction of MR radiofrequency probes around the bioreactor. We present novel MR-compatible BALs and the use of multinuclear MRS (13C, 19F, 31P) for the noninvasive monitoring of their growth, metabolism and viability, as well as 1H MRI methods for the determination of flow profiles, diffusion, cell distribution, quality assurance and bioreactor integrity. Finally, a simple flexible coil design and circuit, and life support system, are described that can make almost any BAL MR-compatible. PMID:22351642

Effect of Exercise on the Creatine Resonances in 1H MR Spectra of Human Skeletal Muscle

NASA Astrophysics Data System (ADS)

Kreis, R.; Jung, B.; Slotboom, J.; Felblinger, J.; Boesch, C.

1999-04-01

1H MR spectra of human muscles were recorded before, during, and after fatiguing exercise. In contrast to expectations, it was found that the spectral contributions of creatine/phosphocreatine (Cr/PCr) were subject to change as a function of exercise. In particular, the dipolar-coupled methylene protons of Cr/PCr were found to be reduced in intensity in proportion to the co-registered PCr levels. Recovery after exercise and behavior under ischemic conditions provide further evidence to suggest that the contributions of the CH2protons of Cr/PCr to1H MR spectra of human musclein vivoreflect PCr rather than Cr levels. Variation of experimental parameters showed that this effect is not due to a trivial change in relaxation times. At present it can only be speculated about why the Cr resonances have reduced NMR visibility. If temporary binding to macromolecules should be involved, the free Cr concentration-important for equilibrium calculations of the creatine kinase reaction-might be different from what was previously assumed.

Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures.

PubMed

Zhang, Yingdan; Ng, Chun Kiat; Cohen, Yehuda; Cao, Bin

2014-05-01

The performance of biofilm-based bioprocesses is difficult to predict and control because of the intrinsic heterogeneous and dynamic properties of microbial biofilms. Biofilm mimics, such as microbial cells entrapped in polymeric scaffolds that are permeable for nutrients, have been proposed to replace real biofilms to achieve long-term robust performance in engineering applications. However, the physiological differences between cells that are physically entrapped in a synthetic polymeric matrix and biofilm cells that are encased in a self-produced polymeric matrix remain unknown. In this study, using Shewanella oneidensis as a model organism and alginate hydrogel as a model synthetic matrix, we compared the cell growth and protein expression in entrapped cultures and biofilms. The hydrogel-entrapped cultures were found to exhibit a growth rate comparable with biofilms. There was no substantial difference in cell viability, surface charge, as well as hydrophobicity between the cells grown in alginate hydrogel and those grown in biofilms. However, the gel-entrapped cultures were found to be physiologically different from biofilms. The gel-entrapped cultures had a higher demand for metabolic energy. The siderophore-mediated iron uptake was repressed in the gel-entrapped cells. The presence of the hydrogel matrix decreased the expression of proteins involved in biofilm formation, while inducing the production of extracellular DNA (eDNA) in the gel-entrapped cultures. These results advance the fundamental understanding of the physiology of hydrogel-entrapped cells, which can lead to more efficient biofilm mimic-based applications.

Proton MR spectroscopy in predicting the increase of perfusion MR imaging for WHO grade II gliomas.

PubMed

Guillevin, Remy; Menuel, Carole; Abud, Lucas; Costalat, Robert; Capelle, Laurent; Hoang-Xuan, Khê; Habas, Christophe; Chiras, Jacques; Vallée, Jean-Noel

2012-03-01

To investigate the correlation between the metabolite ratios obtained from proton magnetic resonance (MR) spectroscopy and those obtained from MR perfusion parameters (relative cerebral blood volume [rCBV]) in a cohort of low-grade glioma (LGG). Patients underwent prospectively conventional MR, proton magnetic resonance spectroscopy ((1) HMRS), and perfusion-weighted images (PWI). Statistical analyses were performed to determine the correlative and independent predictive factors of rCBVmax and the metabolite ratio thresholds with optimum sensitivity and specificity. Thirty-one patients were included in this study. Linear correlations were observed between the metabolic ratios (lactate [Lac]/creatine [Cr], choline [Cho]/N-acetyl-aspartate [NAA], free-lipids/Cr) and rCBVmax (P < 0.05). These metabolic ratios were determined to be independent predictive factors of rCBVmax (P = 0.027, 0.011 and 0.032, respectively). According to the receiver operating characteristic curves, the cutoff values of the metabolic ratios to discriminate between the two populations of rCBVmax (<1.7 versus = 1.7) were 1.72, 1.54, and 1.40, respectively, with a sensitivity = 75% and a specificity >95% for Lac/Cr. This study demonstrated consistent correlations between the data from (1) HMRS and PWI. The Lac/Cr ratio predicts regional hemodynamic changes, which are themselves a useful biomarker of clinical prognosis in patients with LGG. As such, this ratio may provide a new parameter for making improved clinical decisions. Copyright © 2011 Wiley-Liss, Inc.

A miniature microbial fuel cell with conducting nanofibers-based 3D porous biofilm

NASA Astrophysics Data System (ADS)

Jiang, Huawei; Halverson, Larry J.; Dong, Liang

2015-12-01

Miniature microbial fuel cell (MFC) technology has received growing interest due to its potential applications in high-throughput screening of bacteria and mutants to elucidate mechanisms of electricity generation. This paper reports a novel miniature MFC with an improved output power density and short startup time, utilizing electrospun conducting poly(3,4-ethylenedioxythiophene) (PEDOT) nanofibers as a 3D porous anode within a 12 μl anolyte chamber. This device results in 423 μW cm-3 power density based on the volume of the anolyte chamber, using Shewanella oneidensis MR-1 as a model biocatalyst without any optimization of bacterial culture. The device also excels in a startup time of only 1hr. The high conductivity of the electrospun nanofibers makes them suitable for efficient electron transfer. The mean pore size of the conducting nanofibers is several micrometers, which is favorable for bacterial penetration and colonization of surfaces of the nanofibers. We demonstrate that S. oneidensis can fully colonize the interior region of this nanofibers-based porous anode. This work represents a new attempt to explore the use of electrospun PEDOT nanofibers as a 3D anode material for MFCs. The presented miniature MFC potentially will provide a high-sensitivity, high-throughput tool to screen suitable bacterial species and mutant strains for use in large-size MFCs.

Biliary epithelium and liver B cells exposed to bacteria activate intrahepatic MAIT cells through MR1

PubMed Central

Jeffery, Hannah C.; van Wilgenburg, Bonnie; Kurioka, Ayako; Parekh, Krishan; Stirling, Kathryn; Roberts, Sheree; Dutton, Emma E.; Hunter, Stuart; Geh, Daniel; Braitch, Manjit K.; Rajanayagam, Jeremy; Iqbal, Tariq; Pinkney, Thomas; Brown, Rachel; Withers, David R.; Adams, David H.; Klenerman, Paul; Oo, Ye H.

2016-01-01

Background & Aims Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells characterised by the invariant TCR-chain, Vα7.2-Jα33, and are restricted by MR1, which presents bacterial vitamin B metabolites. They are important for antibacterial immunity at mucosal sites; however, detailed characteristics of liver-infiltrating MAIT (LI-MAIT) and their role in biliary immune surveillance remain unexplored. Methods The phenotype and intrahepatic localisation of human LI-MAIT cells was examined in diseased and normal livers. MAIT cell activation in response to E. coli-exposed macrophages, biliary epithelial cells (BEC) and liver B cells was assessed with/without anti-MR1. Results Intrahepatic MAIT cells predominantly localised to bile ducts in the portal tracts. Consistent with this distribution, they expressed biliary tropic chemokine receptors CCR6, CXCR6, and integrin αEβ7. LI-MAIT cells were also present in the hepatic sinusoids and possessed tissue-homing chemokine receptor CXCR3 and integrins LFA-1 and VLA-4, suggesting their recruitment via hepatic sinusoids. LI-MAIT cells were enriched in the parenchyma of acute liver failure livers compared to chronic diseased livers. LI-MAIT cells had an activated, effector memory phenotype, expressed α4β7 and receptors for IL-12, IL-18, and IL-23. Importantly, in response to E. coli-exposed macrophages, liver B cells and BEC, MAIT cells upregulated IFN-γ and CD40 Ligand and degranulated in an MR1-dependent, cytokine-independent manner. In addition, diseased liver MAIT cells expressed T-bet and RORγt and the cytokines IFN-γ, TNF-α, and IL-17. Conclusions Our findings provide the first evidence of an immune surveillance effector response for MAIT cells towards BEC in human liver; thus they could be manipulated for treatment of biliary disease in the future. PMID:26743076

Quantitative myocardial blood flow imaging with integrated time-of-flight PET-MR.

PubMed

Kero, Tanja; Nordström, Jonny; Harms, Hendrik J; Sörensen, Jens; Ahlström, Håkan; Lubberink, Mark

2017-12-01

The use of integrated PET-MR offers new opportunities for comprehensive assessment of cardiac morphology and function. However, little is known on the quantitative accuracy of cardiac PET imaging with integrated time-of-flight PET-MR. The aim of the present work was to validate the GE Signa PET-MR scanner for quantitative cardiac PET perfusion imaging. Eleven patients (nine male; mean age 59 years; range 46-74 years) with known or suspected coronary artery disease underwent 15 O-water PET scans at rest and during adenosine-induced hyperaemia on a GE Discovery ST PET-CT and a GE Signa PET-MR scanner. PET-MR images were reconstructed using settings recommended by the manufacturer, including time-of-flight (TOF). Data were analysed semi-automatically using Cardiac VUer software, resulting in both parametric myocardial blood flow (MBF) images and segment-based MBF values. Correlation and agreement between PET-CT-based and PET-MR-based MBF values for all three coronary artery territories were assessed using regression analysis and intra-class correlation coefficients (ICC). In addition to the cardiac PET-MR reconstruction protocol as recommended by the manufacturer, comparisons were made using a PET-CT resolution-matched reconstruction protocol both without and with TOF to assess the effect of time-of-flight and reconstruction parameters on quantitative MBF values. Stress MBF data from one patient was excluded due to movement during the PET-CT scanning. Mean MBF values at rest and stress were (0.92 ± 0.12) and (2.74 ± 1.37) mL/g/min for PET-CT and (0.90 ± 0.23) and (2.65 ± 1.15) mL/g/min for PET-MR (p = 0.33 and p = 0.74). ICC between PET-CT-based and PET-MR-based regional MBF was 0.98. Image quality was improved with PET-MR as compared to PET-CT. ICC between PET-MR-based regional MBF with and without TOF and using different filter and reconstruction settings was 1.00. PET-MR-based MBF values correlated well with PET-CT-based MBF values and

Marrow Adipose Tissue Quantification of the Lumbar Spine by Using Dual-Energy CT and Single-Voxel 1H MR Spectroscopy: A Feasibility Study

PubMed Central

Daley, Scott M.; Kalra, Mannudeep K.; Brown, J. Keenan; Miller, Karen K.; Torriani, Martin

2015-01-01

Purpose To test the performance of dual-energy computed tomography (CT) in the assessment of marrow adipose tissue (MAT) content of the lumbar spine by using proton (hydrogen 1 [1H]) magnetic resonance (MR) spectroscopy as a reference standard and to determine the influence of MAT on the assessment of bone mineral density (BMD). Materials and Methods This study was institutional review board approved and complied with HIPAA guidelines. Written informed consent was obtained. Twelve obese osteopenic but otherwise healthy subjects (mean age ± standard deviation, 43 years ± 13) underwent 3-T 1H MR spectroscopy of the L2 vertebra by using a point-resolved spatially localized spectroscopy sequence without water suppression. The L2 vertebra was scanned with dual-energy CT (80 and 140 kV) by using a dual-source multi–detector row CT scanner with a calibration phantom. Mean basis material composition relative to the phantom was estimated in the L2 vertebra. Volumetric BMD was measured with and without correction for MAT. Bland-Altman 95% limits of agreement and Pearson correlation coefficients were calculated. Results There was excellent agreement between 1H MR spectroscopy and dual-energy CT, with a mean difference in fat fraction of −0.02 between the techniques, with a 95% confidence interval of −0.24, 0.20. There was a strong correlation between marrow fat fraction obtained with 1H MR spectroscopy and that obtained with dual-energy CT (r = 0.91, P < .001). The presence of MAT led to underestimation of BMD, and this bias increased with increasing MAT content (P < .001). Conclusion Dual-energy CT can be used to assess MAT content and BMD of the lumbar spine in a single examination and provides data that closely agree and correlate with 1H MR spectroscopy data. © RSNA, 2015 PMID:25988401

Volume comparison of radiofrequency ablation at 3- and 5-cm target volumes for four different radiofrequency generators: MR volumetry in an open 1-T MRI system versus macroscopic measurement.

PubMed

Rathke, Hendrik; Hamm, Bernd; Guettler, Felix; Lohneis, Philipp; Stroux, Andrea; Suttmeyer, Britta; Jonczyk, Martin; Teichgräber, Ulf; de Bucourt, Maximilian

2015-12-01

In a patient, it is usually not macroscopically possible to estimate the non-viable volume induced by radiofrequency ablation (RFA) after the procedure. The purpose of this study was to use an ex vivo bovine liver model to perform magnetic resonance (MR) volumetry of the visible tissue signal change induced by RFA and to correlate the MR measurement with the actual macroscopic volume measured in the dissected specimens. Sixty-four liver specimens cut from 16 bovine livers were ablated under constant simulated, close physiological conditions with target volumes set to 14.14 ml (3-cm lesion) and 65.45 ml (5-cm lesion). Four commercially available radiofrequency (RF) systems were tested (n=16 for each system; n=8 for 3 cm and n=8 for 5 cm). A T1-weighted turbo spin echo (TSE) sequence with inversion recovery and a proton-density (PD)-weighted TSE sequence were acquired in a 1.0-T open magnetic resonance imaging (MRI) system. After manual dissection, actual macroscopic ablation diameters were measured and volumes calculated. MR volumetry was performed using a semiautomatic software tool. To validate the correctness and feasibility of the volume formula in macroscopic measurements, MR multiplanar reformation diameter measurements with subsequent volume calculation and semiautomatic MR volumes were correlated. Semiautomatic MR volumetry yielded smaller volumes than manual measurement after dissection, irrespective of RF system used, target lesion size, and MR sequence. For the 3-cm lesion, only 43.3% (T1) and 41.5% (PD) of the entire necrosis are detectable. For the 5-cm lesion, only 40.8% (T1) and 37.2% (PD) are visualized in MRI directly after intervention. The correlation between semiautomatic MR volumes and calculated MR volumes was 0.888 for the T1-weighted sequence and 0.875 for the PD sequence. After correlation of semiautomatic MR volumes and calculated MR volumes, it seems reasonable to use the respective volume formula for macroscopic volume calculation

MR Fingerprinting of Adult Brain Tumors: Initial Experience.

PubMed

Badve, C; Yu, A; Dastmalchian, S; Rogers, M; Ma, D; Jiang, Y; Margevicius, S; Pahwa, S; Lu, Z; Schluchter, M; Sunshine, J; Griswold, M; Sloan, A; Gulani, V

2017-03-01

MR fingerprinting allows rapid simultaneous quantification of T1 and T2 relaxation times. This study assessed the utility of MR fingerprinting in differentiating common types of adult intra-axial brain tumors. MR fingerprinting acquisition was performed in 31 patients with untreated intra-axial brain tumors: 17 glioblastomas, 6 World Health Organization grade II lower grade gliomas, and 8 metastases. T1, T2 of the solid tumor, immediate peritumoral white matter, and contralateral white matter were summarized within each ROI. Statistical comparisons on mean, SD, skewness, and kurtosis were performed by using the univariate Wilcoxon rank sum test across various tumor types. Bonferroni correction was used to correct for multiple-comparison testing. Multivariable logistic regression analysis was performed for discrimination between glioblastomas and metastases, and area under the receiver operator curve was calculated. Mean T2 values could differentiate solid tumor regions of lower grade gliomas from metastases (mean, 172 ± 53 ms, and 105 ± 27 ms, respectively; P = .004, significant after Bonferroni correction). The mean T1 of peritumoral white matter surrounding lower grade gliomas differed from peritumoral white matter around glioblastomas (mean, 1066 ± 218 ms, and 1578 ± 331 ms, respectively; P = .004, significant after Bonferroni correction). Logistic regression analysis revealed that the mean T2 of solid tumor offered the best separation between glioblastomas and metastases with an area under the curve of 0.86 (95% CI, 0.69-1.00; P < .0001). MR fingerprinting allows rapid simultaneous T1 and T2 measurement in brain tumors and surrounding tissues. MR fingerprinting-based relaxometry can identify quantitative differences between solid tumor regions of lower grade gliomas and metastases and between peritumoral regions of glioblastomas and lower grade gliomas. © 2017 by American Journal of Neuroradiology.

Bimodal MR-PET agent for quantitative pH imaging

PubMed Central

Frullano, Luca; Catana, Ciprian; Benner, Thomas; Sherry, A. Dean; Caravan, Peter

2010-01-01

Activatable or “smart” magnetic resonance contrast agents have relaxivities that depend on environmental factors such as pH or enzymatic activity, but the MR signal depends on relaxivity and agent concentration – two unknowns. A bimodal approach, incorporating a positron emitter, solves this problem. Simultaneous positron emission tomography (PET) and MR imaging with the biomodal, pH-responsive MR-PET agent GdDOTA-4AMP-F allows direct determination of both concentration (PET) and T1 (MRI), and hence pH. PMID:20191650

MR safety and compatibility of a noninvasively expandable total-joint endoprosthesis.

PubMed

Ogg, Robert J; McDaniel, C Brian; Wallace, Donald; Pitot, Pierre; Neel, Michael D; Kaste, Sue C

2005-09-01

A noninvasively expandable total-joint endoprosthesis is now available for pediatric patients; the prosthesis can be lengthened by external application of a magnetic field. We investigated the risks of unintentional heating or lengthening of the prosthesis during MR imaging and evaluated the effect of the device on the diagnostic efficacy of MR imaging of surrounding tissues. We performed MR imaging at 1.5 T by using standard pulse sequences and pulse sequences with high-gradient and high-radiofrequency duty cycle. MR imaging caused no measurable change in prosthesis length, and the temperature of the prosthesis increased by less than 1 degrees C during repeated 14-min exposures. Despite significant signal loss and image distortion around the prosthetic joint, clinically useful images were obtained as close as 12 cm from the ends of the prosthetic stems, measured toward the body of the device. Thus, the prosthesis can be safely exposed to MR imaging pulse sequences at 1.5 T, and the visualization of some tissue surrounding the device is clinically useful.

An MR-compatible stereoscopic in-room 3D display for MR-guided interventions.

PubMed

Brunner, Alexander; Groebner, Jens; Umathum, Reiner; Maier, Florian; Semmler, Wolfhard; Bock, Michael

2014-08-01

A commercial three-dimensional (3D) monitor was modified for use inside the scanner room to provide stereoscopic real-time visualization during magnetic resonance (MR)-guided interventions, and tested in a catheter-tracking phantom experiment at 1.5 T. Brightness, uniformity, radio frequency (RF) emissions and MR image interferences were measured. Due to modifications, the center luminance of the 3D monitor was reduced by 14%, and the addition of a Faraday shield further reduced the remaining luminance by 31%. RF emissions could be effectively shielded; only a minor signal-to-noise ratio (SNR) decrease of 4.6% was observed during imaging. During the tracking experiment, the 3D orientation of the catheter and vessel structures in the phantom could be visualized stereoscopically.

Detection and differentiation of early acute and following age stages of myocardial infarction with quantitative post-mortem cardiac 1.5T MR.

PubMed

Schwendener, Nicole; Jackowski, Christian; Persson, Anders; Warntjes, Marcel J; Schuster, Frederick; Riva, Fabiano; Zech, Wolf-Dieter

2017-01-01

Recently, quantitative MR sequences have started being used in post-mortem imaging. The goal of the present study was to evaluate if early acute and following age stages of myocardial infarction can be detected and discerned by quantitative 1.5T post-mortem cardiac magnetic resonance (PMCMR) based on quantitative T1, T2 and PD values. In 80 deceased individuals (25 female, 55 male), a cardiac MR quantification sequence was performed prior to cardiac dissection at autopsy in a prospective study. Focal myocardial signal alterations detected in synthetically generated MR images were MR quantified for their T1, T2 and PD values. The locations of signal alteration measurements in PMCMR were targeted at autopsy heart dissection and cardiac tissue specimens were taken for histologic examinations. Quantified signal alterations in PMCMR were correlated to their according histologic age stage of myocardial infarction. In PMCMR seventy-three focal myocardial signal alterations were detected in 49 of 80 investigated hearts. These signal alterations were diagnosed histologically as early acute (n=39), acute (n=14), subacute (n=10) and chronic (n=10) age stages of myocardial infarction. Statistical analysis revealed that based on their quantitative T1, T2 and PD values, a significant difference between all defined age groups of myocardial infarction can be determined. It can be concluded that quantitative 1.5T PMCMR quantification based on quantitative T1, T2 and PD values is feasible for characterization and differentiation of early acute and following age stages of myocardial infarction. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Spiral MR fingerprinting at 7T with simultaneous B1 estimation.

PubMed

Buonincontri, Guido; Schulte, Rolf F; Cosottini, Mirco; Tosetti, Michela

2017-09-01

Magnetic resonance fingerprinting is an efficient, new approach for quantitative imaging with MR. We aimed to extend this technique to cases with B1+ inhomogeneities within the imaging volume. Previous approaches have used abrupt changes in flip angles to estimate the B1+ field simultaneously with T1 and T2, using a Cartesian approach in a small-animal scanner at 4.7T. Here, we evaluated whether a similar approach would be suitable for imaging human brains using spiral readouts with a 7T scanner. We found that our modified scheme could significantly reduce the adverse effects of B1+ inhomogeneities even in extreme cases, reducing both the bias and the variance in T2 estimations by an order of magnitude when compared to literature methods. Acquisitions used less than 1.5W/kg SAR and could be performed in 12s per slice. In conclusion, our approach can be used to perform quantitative imaging of the brain at 7T in a short time, simultaneously estimating the B1+ profile. Copyright © 2017 Elsevier Inc. All rights reserved.

Deep embedding convolutional neural network for synthesizing CT image from T1-Weighted MR image.

PubMed

Xiang, Lei; Wang, Qian; Nie, Dong; Zhang, Lichi; Jin, Xiyao; Qiao, Yu; Shen, Dinggang

2018-07-01

Recently, more and more attention is drawn to the field of medical image synthesis across modalities. Among them, the synthesis of computed tomography (CT) image from T1-weighted magnetic resonance (MR) image is of great importance, although the mapping between them is highly complex due to large gaps of appearances of the two modalities. In this work, we aim to tackle this MR-to-CT synthesis task by a novel deep embedding convolutional neural network (DECNN). Specifically, we generate the feature maps from MR images, and then transform these feature maps forward through convolutional layers in the network. We can further compute a tentative CT synthesis from the midway of the flow of feature maps, and then embed this tentative CT synthesis result back to the feature maps. This embedding operation results in better feature maps, which are further transformed forward in DECNN. After repeating this embedding procedure for several times in the network, we can eventually synthesize a final CT image in the end of the DECNN. We have validated our proposed method on both brain and prostate imaging datasets, by also comparing with the state-of-the-art methods. Experimental results suggest that our DECNN (with repeated embedding operations) demonstrates its superior performances, in terms of both the perceptive quality of the synthesized CT image and the run-time cost for synthesizing a CT image. Copyright © 2018. Published by Elsevier B.V.

Acute interstitial edematous pancreatitis: Findings on non-enhanced MR imaging

PubMed Central

Zhang, Xiao-Ming; Feng, Zhi-Song; Zhao, Qiong-Hui; Xiao, Chun-Ming; Mitchell, Donald G; Shu, Jian; Zeng, Nan-Lin; Xu, Xiao-Xue; Lei, Jun-Yang; Tian, Xiao-Bing

2006-01-01

AIM: To study the appearances of acute interstitial edematous pancreatitis (IEP) on non-enhanced MR imaging. METHODS: A total of 53 patients with IEP diagnosed by clinical features and laboratory findings were underwent MR imaging. MR imaging sequences included fast spoiled gradient echo (FSPGR) fat saturation axial T1-weighted imaging, gradient echo T1-weighted (in phase), single shot fast spin echo (SSFSE) T2-weighted, respiratory triggered (R-T) T2-weighted with fat saturation, and MR cholangiopancreatography. Using the MR severity score index, pancreatitis was graded as mild (0-2 points), moderate (3-6 points) and severe (7-10 points). RESULTS: Among the 53 patients, IEP was graded as mild in 37 patients and as moderate in 16 patients. Forty-seven of 53 (89%) patients had at least one abnormality on MR images. Pancreas was hypointense relative to liver on FSPGR T1-weighted images in 18.9% of patients, and hyperintense in 25% and 30% on SSFSE T2-weighted and R-T T2-weighted images, respectively. The prevalences of the findings of IEP on R-T T2-weighted images were, respectively, 85% for pancreatic fascial plane, 77% for left renal fascial plane, 55% for peripancreatic fat stranding, 42% for right renal fascial plane, 45% for perivascular fluid, 40% for thickened pancreatic lobular septum and 25% for peripancreatic fluid, which were markedly higher than those on in-phase or SSFSE T2-weighted images (P < 0.001). CONCLUSION: IEP primarily manifests on non-enhanced MR images as thickened pancreatic fascial plane, left renal fascial plane, peripancreatic fat stranding, and peripancreatic fluid. R-T T2-weighted imaging is more sensitive than in-phase and SSFSE T2-weighted imaging for depicting IEP. PMID:17007053

Acute interstitial edematous pancreatitis: Findings on non-enhanced MR imaging.

PubMed

Zhang, Xiao-Ming; Feng, Zhi-Song; Zhao, Qiong-Hui; Xiao, Chun-Ming; Mitchell, Donald-G; Shu, Jian; Zeng, Nan-Lin; Xu, Xiao-Xue; Lei, Jun-Yang; Tian, Xiao-Bing

2006-09-28

To study the appearances of acute interstitial edematous pancreatitis (IEP) on non-enhanced MR imaging. A total of 53 patients with IEP diagnosed by clinical features and laboratory findings were underwent MR imaging. MR imaging sequences included fast spoiled gradient echo (FSPGR) fat saturation axial T1-weighted imaging, gradient echo T1-weighted (in phase), single shot fast spin echo (SSFSE) T2-weighted, respiratory triggered (R-T) T2-weighted with fat saturation, and MR cholangiopancreatography. Using the MR severity score index, pancreatitis was graded as mild (0-2 points), moderate (3-6 points) and severe (7-10 points). Among the 53 patients, IEP was graded as mild in 37 patients and as moderate in 16 patients. Forty-seven of 53 (89%) patients had at least one abnormality on MR images. Pancreas was hypointense relative to liver on FSPGR T1-weighted images in 18.9% of patients, and hyperintense in 25% and 30% on SSFSE T2-weighted and R-T T2-weighted images, respectively. The prevalences of the findings of IEP on R-T T2-weighted images were, respectively, 85% for pancreatic fascial plane, 77% for left renal fascial plane, 55% for peripancreatic fat stranding, 42% for right renal fascial plane, 45% for perivascular fluid, 40% for thickened pancreatic lobular septum and 25% for peripancreatic fluid, which were markedly higher than those on in-phase or SSFSE T2-weighted images (P<0.001). IEP primarily manifests on non-enhanced MR images as thickened pancreatic fascial plane, left renal fascial plane, peripancreatic fat stranding, and peripancreatic fluid. R-T T2-weighted imaging is more sensitive than in-phase and SSFSE T2-weighted imaging for depicting IEP.

Temporal lobe epilepsy: quantitative MR volumetry in detection of hippocampal atrophy.

PubMed

Farid, Nikdokht; Girard, Holly M; Kemmotsu, Nobuko; Smith, Michael E; Magda, Sebastian W; Lim, Wei Y; Lee, Roland R; McDonald, Carrie R

2012-08-01

To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration-cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Quantitative MR imaging-derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%-89.5%) and specificity (92.2%-94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a useful and viable means for translating volumetric analysis into

MR images from fewer data

NASA Astrophysics Data System (ADS)

Vafadar, Bahareh; Bones, Philip J.

2012-10-01

There is a strong motivation to reduce the amount of acquired data necessary to reconstruct clinically useful MR images, since less data means faster acquisition sequences, less time for the patient to remain motionless in the scanner and better time resolution for observing temporal changes within the body. We recently introduced an improvement in image quality for reconstructing parallel MR images by incorporating a data ordering step with compressed sensing (CS) in an algorithm named `PECS'. That method requires a prior estimate of the image to be available. We are extending the algorithm to explore ways of utilizing the data ordering step without requiring a prior estimate. The method presented here first reconstructs an initial image x1 by compressed sensing (with scarcity enhanced by SVD), then derives a data ordering from x1, R'1 , which ranks the voxels of x1 according to their value. A second reconstruction is then performed which incorporates minimization of the first norm of the estimate after ordering by R'1 , resulting in a new reconstruction x2. Preliminary results are encouraging.

Direct Evaluation of MR-Derived Attenuation Correction Maps for PET/MR of the Mouse Myocardium

NASA Astrophysics Data System (ADS)

Evans, Eleanor; Buonincontri, Guido; Hawkes, Rob C.; Ansorge, Richard E.; Carpenter, T. Adrian; Sawiak, Stephen J.

2016-02-01

Attenuation correction (AC) must be applied to provide accurate measurements of PET tracer activity concentrations. Due to the limited space available in PET/MR scanners, MR-derived AC (MRAC) is used as a substitute for transmission source scanning. In preclinical PET/MR, there has been limited exploration of MRAC, as the magnitude of AC in murine imaging is much smaller than that required in clinical scans. We investigated if a simple 2 class (air and tissue) segmentation-based MRAC approach could provide adequate AC for mouse PET imaging. To construct the default MRAC μ maps, MR images were thresholded and segmented using ASIPRO software (Siemens Molecular Imaging), which defined the mouse body region as tissue with a uniform linear attenuation coefficient ( μ) of 0.095 cm - 1, and the background and lungs as air, with a μ value of 0 cm - 1. To correct for the misassignment of the lungs as air, two further MRAC μ maps were tested: 1) MRAC (tissue) approach, which changed the lung region designation from air to tissue ( μ = 0.095 cm - 1) and 2) MRAC (lung) approach, which treated the lungs as an additional tissue class, with a μ value of 0.032 cm - 1. All μ maps were then forward projected to create attenuation sinograms for image reconstruction. Standard uptake value (SUV) maps of the myocardium were derived for 10 mice with and without AC applied using gold standard transmission scans (TXAC), the 3 MRAC methods and PET emission scans (EmAC). All AC methods produced significantly different myocardial SUVs to those produced without AC when compared across the mouse group ( ). Similar ( ) SUV were derived with all AC methods, with the best agreement to TXAC achieved using the MRAC (tissue) method, giving a mean difference of 0.9±2.4% in myocardial SUV when compared across all mice. SUV differences of up to 40%, however, were seen in areas adjacent to the RF coil in images produced using all AC methods, except for TXAC. A 2 class MRAC approach can therefore

Peripheral Vasculature: High-Temporal- and High-Spatial-Resolution Three-dimensional Contrast-enhanced MR Angiography1

PubMed Central

Haider, Clifton R.; Glockner, James F.; Stanson, Anthony W.; Riederer, Stephen J.

2009-01-01

Purpose: To prospectively evaluate the feasibility of performing high-spatial-resolution (1-mm isotropic) time-resolved three-dimensional (3D) contrast material–enhanced magnetic resonance (MR) angiography of the peripheral vasculature with Cartesian acquisition with projection-reconstruction–like sampling (CAPR) and eightfold accelerated two-dimensional (2D) sensitivity encoding (SENSE). Materials and Methods: All studies were approved by the institutional review board and were HIPAA compliant; written informed consent was obtained from all participants. There were 13 volunteers (mean age, 41.9; range, 27–53 years). The CAPR sequence was adapted to provide 1-mm isotropic spatial resolution and a 5-second frame time. Use of different receiver coil element sizes for those placed on the anterior-to-posterior versus left-to-right sides of the field of view reduced signal-to-noise ratio loss due to acceleration. Results from eight volunteers were rated independently by two radiologists according to prominence of artifact, arterial to venous separation, vessel sharpness, continuity of arterial signal intensity in major arteries (anterior and posterior tibial, peroneal), demarcation of origin of major arteries, and overall diagnostic image quality. MR angiographic results in two patients with peripheral vascular disease were compared with their results at computed tomographic angiography. Results: The sequence exhibited no image artifact adversely affecting diagnostic image quality. Temporal resolution was evaluated to be sufficient in all cases, even with known rapid arterial to venous transit. The vessels were graded to have excellent sharpness, continuity, and demarcation of the origins of the major arteries. Distal muscular branches and the communicating and perforating arteries were routinely seen. Excellent diagnostic quality rating was given for 15 (94%) of 16 evaluations. Conclusion: The feasibility of performing high-diagnostic-quality time-resolved 3D

Fat suppression at three-dimensional T1-weighted MR imaging of the hands: Dixon method versus CHESS technique.

PubMed

Kirchgesner, T; Perlepe, V; Michoux, N; Larbi, A; Vande Berg, B

2018-01-01

To compare the effectiveness of fat suppression and the image quality of the Dixon method with those of the chemical shift-selective (CHESS) technique in hands of normal subjects at non-enhanced three-dimensional (3D) T1-weighted MR imaging. Both hands of 14 healthy volunteers were imaged with 3D fast spoiled gradient echo (FSPGR) T1-weighted Dixon, 3D FSPGR T1-weighted CHESS and 3D T1-weighted fast spin echo (FSE) CHESS sequences in a 1.5T MR scanner. Three radiologists scored the effectiveness of fat suppression in bone marrow (EFS BM ) and soft tissues (EFS ST ) in 20 joints per subject. One radiologist measured the signal-to-noise ratio (SNR) in 10 bones per subject. Statistical analysis used two-way ANOVA with random effects (P<0.0083), paired t-test (P<0.05) and observed agreement to assess differences in effectiveness of fat suppression, differences in SNR and interobserver agreement. EFS BM was statistically significantly higher for the 3D FSPGR T1-weighted Dixon than for the 3D FSPGR T1-weighted CHESS sequence and the 3D FSE T1-weighted CHESS sequence (P<0.0001). EFS ST was statistically significantly higher for the 3D FSPGR T1-weighted Dixon than for the 3D FSPGR T1-weighted CHESS sequence (P<0.0011) and for the 3D FSE T1-weighted CHESS sequence in the axial plane (P=0.0028). Mean SNR was statistically significantly higher for 3D FSPGR T1-weighted Dixon sequence than for 3D FSPGR T1-weighted CHESS and 3D FSE T1-weighted CHESS sequences (P<0.0001). The Dixon method yields more effective fat suppression and higher SNR than the CHESS technique at 3D T1-weighted MR imaging of the hands. Copyright © 2017 Éditions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Assessing the potential of spectral induced polarization to detect in situ changes in iron reduction

NASA Astrophysics Data System (ADS)

Rosier, C. L.; Price, A.; Sharma, S.; Atekwana, E. A.

2016-12-01

The near surface geophysical technique Spectral Induced Polarization (SIP), provides promise as an effective method measuring in situ biofilm formation/development. Yet, potential mechanisms responsible for observed shifts in SIP response due to biofilm are not clearly understood. In order to address possible mechanisms we assessed the influence of Shewanella oneidensis (MR1) cell density (colony forming units; CFU), biofilm production (Bradford assay) and iron reduction metabolism (colorimetric assay) on SIP response. Laboratory measurements were collected over three months on columns packed with either iron-coated or iron-free sands and amended with artificial ground water and acetate in order to stimulate biofilm production and microbial iron reduction. Additionally, scanning electron microscopy (SEM) was used to confirm the presence of S. oneidensis cells and biofilm. Our results suggest that during early/initial stage (<30 days) of the iron-coated column incubations, both phase and imaginary conductivity response increased 4-fold as concentrations of reduced iron increased from 0-50 mM. In the later stages (>75 days) of column incubation, SIP measurements revealed that phase and imaginary conductivity responses decreased as the concentration of reduced iron decreased below 2.0 mM. In contrast, we observed only a moderate increase in phase and imaginary conductivity ( 30%) within iron-free columns as a result of increases in S. oneidensis cells (CFU 1.5 x 1011) and biofilm production (7.0 mg ml-1). SEM analysis confirmed the presence of biofilm and cells within both iron-coated and iron-free columns. We hypothesize that the production of microbial metabolic byproducts is a potential mechanism explaining large phase shits observed in previous studies ( 50 mrads) rather than the conductivity of cells or biofilm. Our findings provide support for the following: i) ratio of cells to biofilm production only moderately influences both phase and imaginary conductivity

Joint estimation of activity and attenuation for PET using pragmatic MR-based prior: application to clinical TOF PET/MR whole-body data for FDG and non-FDG tracers

NASA Astrophysics Data System (ADS)

Ahn, Sangtae; Cheng, Lishui; Shanbhag, Dattesh D.; Qian, Hua; Kaushik, Sandeep S.; Jansen, Floris P.; Wiesinger, Florian

2018-02-01

Accurate and robust attenuation correction remains challenging in hybrid PET/MR particularly for torsos because it is difficult to segment bones, lungs and internal air in MR images. Additionally, MR suffers from susceptibility artifacts when a metallic implant is present. Recently, joint estimation (JE) of activity and attenuation based on PET data, also known as maximum likelihood reconstruction of activity and attenuation, has gained considerable interest because of (1) its promise to address the challenges in MR-based attenuation correction (MRAC), and (2) recent advances in time-of-flight (TOF) technology, which is known to be the key to the success of JE. In this paper, we implement a JE algorithm using an MR-based prior and evaluate the algorithm using whole-body PET/MR patient data, for both FDG and non-FDG tracers, acquired from GE SIGNA PET/MR scanners with TOF capability. The weight of the MR-based prior is spatially modulated, based on MR signal strength, to control the balance between MRAC and JE. Large prior weights are used in strong MR signal regions such as soft tissue and fat (i.e. MR tissue classification with a high degree of certainty) and small weights are used in low MR signal regions (i.e. MR tissue classification with a low degree of certainty). The MR-based prior is pragmatic in the sense that it is convex and does not require training or population statistics while exploiting synergies between MRAC and JE. We demonstrate the JE algorithm has the potential to improve the robustness and accuracy of MRAC by recovering the attenuation of metallic implants, internal air and some bones and by better delineating lung boundaries, not only for FDG but also for more specific non-FDG tracers such as 68Ga-DOTATOC and 18F-Fluoride.

Principles of Quantitative MR Imaging with Illustrated Review of Applicable Modular Pulse Diagrams.

PubMed

Mills, Andrew F; Sakai, Osamu; Anderson, Stephan W; Jara, Hernan

2017-01-01

Continued improvements in diagnostic accuracy using magnetic resonance (MR) imaging will require development of methods for tissue analysis that complement traditional qualitative MR imaging studies. Quantitative MR imaging is based on measurement and interpretation of tissue-specific parameters independent of experimental design, compared with qualitative MR imaging, which relies on interpretation of tissue contrast that results from experimental pulse sequence parameters. Quantitative MR imaging represents a natural next step in the evolution of MR imaging practice, since quantitative MR imaging data can be acquired using currently available qualitative imaging pulse sequences without modifications to imaging equipment. The article presents a review of the basic physical concepts used in MR imaging and how quantitative MR imaging is distinct from qualitative MR imaging. Subsequently, the article reviews the hierarchical organization of major applicable pulse sequences used in this article, with the sequences organized into conventional, hybrid, and multispectral sequences capable of calculating the main tissue parameters of T1, T2, and proton density. While this new concept offers the potential for improved diagnostic accuracy and workflow, awareness of this extension to qualitative imaging is generally low. This article reviews the basic physical concepts in MR imaging, describes commonly measured tissue parameters in quantitative MR imaging, and presents the major available pulse sequences used for quantitative MR imaging, with a focus on the hierarchical organization of these sequences. © RSNA, 2017.

New-Generation Laser-lithographed Dual-Axis Magnetically Assisted Remote-controlled Endovascular Catheter for Interventional MR Imaging: In Vitro Multiplanar Navigation at 1.5 T and 3 T versus X-ray Fluoroscopy.

PubMed

Moftakhar, Parham; Lillaney, Prasheel; Losey, Aaron D; Cooke, Daniel L; Martin, Alastair J; Thorne, Bradford R H; Arenson, Ronald L; Saeed, Maythem; Wilson, Mark W; Hetts, Steven W

2015-12-01

To assess the feasibility of multiplanar vascular navigation with a new magnetically assisted remote-controlled (MARC) catheter with real-time magnetic resonance (MR) imaging at 1.5 T and 3 T and to compare it with standard x-ray guidance in simulated endovascular catheterization procedures. A 1.6-mm-diameter custom clinical-grade microcatheter prototype with lithographed double-saddle coils at the distal tip was deflected with real-time MR imaging. Two inexperienced operators and two experienced operators catheterized anteroposterior (celiac, superior mesenteric, and inferior mesenteric arteries) and mediolateral (renal arteries) branch vessels in a cryogel abdominal aortic phantom. This was repeated with conventional x-ray fluoroscopy by using clinical catheters and guidewires. Mean procedure times and percentage success data were analyzed with linear mixed-effects regression. The MARC catheter tip was visible at 1.5 T and 3 T. Among inexperienced operators, MARC MR imaging guidance was not statistically different from x-ray guidance at 1.5 T (67% successful vessel selection turns with MR imaging vs 76% with x-ray guidance, P = .157) and at 3 T (75% successful turns with MR imaging vs 76% with x-ray guidance, P = .869). Experienced operators were more successful in catheterizing vessels with x-ray guidance (98% success within 60 seconds) than with 1.5-T (65%, P < .001) or 3-T (75%) MR imaging. Among inexperienced operators, mean procedure time was nearly equivalent by using MR imaging (31 seconds) and x-ray guidance (34 seconds, P = .436). Among experienced operators, catheterization was faster with x-ray guidance (20 seconds) compared with 1.5-T MR imaging (42 seconds, P < .001), but MARC guidance improved at 3 T (31 seconds). MARC MR imaging guidance at 3 T was not significantly different from x-ray guidance for the celiac (P = .755), superior mesenteric (P = .358), and inferior mesenteric (P = .065) arteries. Multiplanar navigation with a new MARC catheter

New-Generation Laser-lithographed Dual-Axis Magnetically Assisted Remote-controlled Endovascular Catheter for Interventional MR Imaging: In Vitro Multiplanar Navigation at 1.5 T and 3 T versus X-ray Fluoroscopy

PubMed Central

Moftakhar, Parham; Lillaney, Prasheel; Losey, Aaron D.; Cooke, Daniel L.; Martin, Alastair J.; Thorne, Bradford R. H.; Arenson, Ronald L.; Saeed, Maythem; Wilson, Mark W.

2015-01-01

Purpose To assess the feasibility of multiplanar vascular navigation with a new magnetically assisted remote-controlled (MARC) catheter with real-time magnetic resonance (MR) imaging at 1.5 T and 3 T and to compare it with standard x-ray guidance in simulated endovascular catheterization procedures. Materials and Methods A 1.6-mm–diameter custom clinical-grade microcatheter prototype with lithographed double-saddle coils at the distal tip was deflected with real-time MR imaging. Two inexperienced operators and two experienced operators catheterized anteroposterior (celiac, superior mesenteric, and inferior mesenteric arteries) and mediolateral (renal arteries) branch vessels in a cryogel abdominal aortic phantom. This was repeated with conventional x-ray fluoroscopy by using clinical catheters and guidewires. Mean procedure times and percentage success data were analyzed with linear mixed-effects regression. Results The MARC catheter tip was visible at 1.5 T and 3 T. Among inexperienced operators, MARC MR imaging guidance was not statistically different from x-ray guidance at 1.5 T (67% successful vessel selection turns with MR imaging vs 76% with x-ray guidance, P = .157) and at 3 T (75% successful turns with MR imaging vs 76% with x-ray guidance, P = .869). Experienced operators were more successful in catheterizing vessels with x-ray guidance (98% success within 60 seconds) than with 1.5-T (65%, P < .001) or 3-T (75%) MR imaging. Among inexperienced operators, mean procedure time was nearly equivalent by using MR imaging (31 seconds) and x-ray guidance (34 seconds, P = .436). Among experienced operators, catheterization was faster with x-ray guidance (20 seconds) compared with 1.5-T MR imaging (42 seconds, P < .001), but MARC guidance improved at 3 T (31 seconds). MARC MR imaging guidance at 3 T was not significantly different from x-ray guidance for the celiac (P = .755), superior mesenteric (P = .358), and inferior mesenteric (P = .065) arteries. Conclusion

Breast imaging with ultrasound tomography: update on a comparative study with MR

NASA Astrophysics Data System (ADS)

Ranger, Bryan; Littrup, Peter; Duric, Neb; Li, Cuiping; Schmidt, Steven; Rama, Olsi; Bey-Knight, Lisa

2011-03-01

The objective of this study is to present imaging parameters and display thresholds of an ultrasound tomography (UST) prototype in order to demonstrate analogous visualization of overall breast anatomy and lesions relative to magnetic resonance (MR). Thirty-six women were imaged with MR and our UST prototype. The UST scan generated sound speed, attenuation, and reflection images and were subjected to variable thresholds then fused together into a single UST image. Qualitative and quantitative comparisons of MR and UST images were utilized to identify anatomical similarities and mass characteristics. Overall, UST demonstrated the ability to visualize and characterize breast tissues in a manner comparable to MR without the use of IV contrast. For optimal visualization, fused images utilized thresholds of 1.46+/-0.1 km/s for sound speed to represent architectural features of the breast including parenchyma. An arithmetic combination of images using the logical .AND. and .OR. operators, along with thresholds of 1.52+/-0.03 km/s for sound speed and 0.16+/-0.04 dB/cm for attenuation, allowed for mass detection and characterization similar to MR.

High resolution MR microscopy

NASA Astrophysics Data System (ADS)

Ciobanu, Luisa

Magnetic resonance imaging (MRI) microscopy [1] has the potential to bring the full capabilities of NMR to arbitrarily specified localized positions within small samples. The most interesting target of study is the living biological cell, with typical dimensions ˜100 mum, but with substructures that are much smaller, such as the cell nucleus (typically ˜10 mu m) and mitochondria (1--10 mum). One anticipates that the development of MR microscopy with resolution at the level of these substructures or better and with a wide, three dimensional field-of-view could open a new avenue of investigation into the biology of the living cell. Although the first MR image of a single biological cell was reported in 1987 [2], the cell imaged had quite large (˜1 mm diameter) spatial dimensions and the resolution obtained (on the order of 10 mu m) was not adequate for meaningful imaging of more typically sized cells. The quest for higher resolution has continued. In 1989 Zhou et al. [3] obtained fully three dimensional images with spatial resolution of (6.37 mum)3, or 260 femtoliters. While better "in-plane" resolutions (i.e., the resolution in 2 of the 3 spatial dimensions) have since been obtained, [4, 5] this volume resolution was not exceeded until quite recently by Lee et al., [6] who report 2D images having volume resolution of 75 mum 3 and in-plane resolution of 1 mum. In parallel with these advances in raw resolution several investigators [7, 8, 9] have focused on localized spectroscopy and/or chemical shift imaging. The key obstacles to overcome in MR microscopy are (1) the loss of signal to noise that occurs when observing small volumes and (2) molecular diffusion during the measurement or encoding. To date the problem of sensitivity has typically been addressed by employing small micro-coil receivers. [10] The problem of molecular diffusion can only be defeated with strong magnetic field gradients that can encode spatial information quickly. We report MR microscopy

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy†

PubMed Central

Gunsolus, Ian L.; Hu, Dehong; Mihai, Cosmin; Lohse, Samuel E.; Lee, Chang-soo; Torelli, Marco D.; Hamers, Robert J.; Murhpy, Catherine J.; Orr, Galya

2015-01-01

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate eficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localization patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells. PMID:24816810

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy

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

Gunsolus, Ian L.; Hu, Dehong; Mihai, Cosmin

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate efficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localizationmore » patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells.« less

The Molecular Density of States in Bacterial Nanowires

PubMed Central

El-Naggar, Mohamed Y.; Gorby, Yuri A.; Xia, Wei; Nealson, Kenneth H.

2008-01-01

The recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. We here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells and bioremediation of heavy metals and radionuclides. The Shewanella nanowires display a surprising nonlinear electrical transport behavior, where the voltage dependence of the conductance reveals peaks indicating discrete energy levels with higher electronic density of states. Our results indicate that the molecular constituents along the Shewanella nanowires possess an intricate electronic structure that plays a role in mediating transport. PMID:18441026

MR-based field-of-view extension in MR/PET: B0 homogenization using gradient enhancement (HUGE).

PubMed

Blumhagen, Jan O; Ladebeck, Ralf; Fenchel, Matthias; Scheffler, Klaus

2013-10-01

In whole-body MR/PET, the human attenuation correction can be based on the MR data. However, an MR-based field-of-view (FoV) is limited due to physical restrictions such as B0 inhomogeneities and gradient nonlinearities. Therefore, for large patients, the MR image and the attenuation map might be truncated and the attenuation correction might be biased. The aim of this work is to explore extending the MR FoV through B0 homogenization using gradient enhancement in which an optimal readout gradient field is determined to locally compensate B0 inhomogeneities and gradient nonlinearities. A spin-echo-based sequence was developed that computes an optimal gradient for certain regions of interest, for example, the patient's arms. A significant distortion reduction was achieved outside the normal MR-based FoV. This FoV extension was achieved without any hardware modifications. In-plane distortions in a transaxially extended FoV of up to 600 mm were analyzed in phantom studies. In vivo measurements of the patient's arms lying outside the normal specified FoV were compared with and without the use of B0 homogenization using gradient enhancement. In summary, we designed a sequence that provides data for reducing the image distortions due to B0 inhomogeneities and gradient nonlinearities and used the data to extend the MR FoV. Copyright © 2011 Wiley Periodicals, Inc.

Biliary epithelium and liver B cells exposed to bacteria activate intrahepatic MAIT cells through MR1.

PubMed

Jeffery, Hannah C; van Wilgenburg, Bonnie; Kurioka, Ayako; Parekh, Krishan; Stirling, Kathryn; Roberts, Sheree; Dutton, Emma E; Hunter, Stuart; Geh, Daniel; Braitch, Manjit K; Rajanayagam, Jeremy; Iqbal, Tariq; Pinkney, Thomas; Brown, Rachel; Withers, David R; Adams, David H; Klenerman, Paul; Oo, Ye H

2016-05-01

Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells characterised by the invariant TCR-chain, Vα7.2-Jα33, and are restricted by MR1, which presents bacterial vitamin B metabolites. They are important for antibacterial immunity at mucosal sites; however, detailed characteristics of liver-infiltrating MAIT (LI-MAIT) and their role in biliary immune surveillance remain unexplored. The phenotype and intrahepatic localisation of human LI-MAIT cells was examined in diseased and normal livers. MAIT cell activation in response to E. coli-exposed macrophages, biliary epithelial cells (BEC) and liver B cells was assessed with/without anti-MR1. Intrahepatic MAIT cells predominantly localised to bile ducts in the portal tracts. Consistent with this distribution, they expressed biliary tropic chemokine receptors CCR6, CXCR6, and integrin αEβ7. LI-MAIT cells were also present in the hepatic sinusoids and possessed tissue-homing chemokine receptor CXCR3 and integrins LFA-1 and VLA-4, suggesting their recruitment via hepatic sinusoids. LI-MAIT cells were enriched in the parenchyma of acute liver failure livers compared to chronic diseased livers. LI-MAIT cells had an activated, effector memory phenotype, expressed α4β7 and receptors for IL-12, IL-18, and IL-23. Importantly, in response to E. coli-exposed macrophages, liver B cells and BEC, MAIT cells upregulated IFN-γ and CD40 Ligand and degranulated in an MR1-dependent, cytokine-independent manner. In addition, diseased liver MAIT cells expressed T-bet and RORγt and the cytokines IFN-γ, TNF-α, and IL-17. Our findings provide the first evidence of an immune surveillance effector response for MAIT cells towards BEC in human liver; thus they could be manipulated for treatment of biliary disease in the future. Copyright © 2016 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Dose Optimization in TOF-PET/MR Compared to TOF-PET/CT

PubMed Central

Queiroz, Marcelo A.; Delso, Gaspar; Wollenweber, Scott; Deller, Timothy; Zeimpekis, Konstantinos; Huellner, Martin; de Galiza Barbosa, Felipe; von Schulthess, Gustav; Veit-Haibach, Patrick

2015-01-01

Purpose To evaluate the possible activity reduction in FDG-imaging in a Time-of-Flight (TOF) PET/MR, based on cross-evaluation of patient-based NECR (noise equivalent count rate) measurements in PET/CT, cross referencing with phantom-based NECR curves as well as initial evaluation of TOF-PET/MR with reduced activity. Materials and Methods A total of 75 consecutive patients were evaluated in this study. PET/CT imaging was performed on a PET/CT (time-of-flight (TOF) Discovery D 690 PET/CT). Initial PET/MR imaging was performed on a newly available simultaneous TOF-PET/MR (Signa PET/MR). An optimal NECR for diagnostic purposes was defined in clinical patients (NECRP) in PET/CT. Subsequent optimal activity concentration at the acquisition time ([A]0) and target NECR (NECRT) were obtained. These data were used to predict the theoretical FDG activity requirement of the new TOF-PET/MR system. Twenty-five initial patients were acquired with (retrospectively reconstructed) different imaging times equivalent for different activities on the simultaneous PET/MR for the evaluation of clinically realistic FDG-activities. Results The obtained values for NECRP, [A]0 and NECRT were 114.6 (± 14.2) kcps (Kilocounts per second), 4.0 (± 0.7) kBq/mL and 45 kcps, respectively. Evaluating the NECRT together with the phantom curve of the TOF-PET/MR device, the theoretical optimal activity concentration was found to be approximately 1.3 kBq/mL, which represents 35% of the activity concentration required by the TOF-PET/CT. Initial evaluation on patients in the simultaneous TOF-PET/MR shows clinically realistic activities of 1.8 kBq/mL, which represent 44% of the required activity. Conclusion The new TOF-PET/MR device requires significantly less activity to generate PET-images with good-to-excellent image quality, due to improvements in detector geometry and detector technologies. The theoretically achievable dose reduction accounts for up to 65% but cannot be fully translated into clinical

Simultaneous radiofrequency (RF) heating and magnetic resonance (MR) thermal mapping using an intravascular MR imaging/RF heating system.

PubMed

Qiu, Bensheng; El-Sharkawy, Abdel-Monem; Paliwal, Vaishali; Karmarkar, Parag; Gao, Fabao; Atalar, Ergin; Yang, Xiaoming

2005-07-01

Previous studies have confirmed the possibility of using an intravascular MR imaging guidewire (MRIG) as a heating source to enhance vascular gene transfection/expression. This motivated us to develop a new intravascular system that can perform MR imaging, radiofrequncy (RF) heating, and MR temperature monitoring simultaneously in an MR scanner. To validate this concept, a series of mathematical simulations of RF power loss along a 0.032-inch MRIG and RF energy spatial distribution were performed to determine the optimum RF heating frequency. Then, an RF generator/amplifier and a filter box were built. The possibility for simultaneous RF heating and MR thermal mapping of the system was confirmed in vitro using a phantom, and the obtained thermal mapping profile was compared with the simulated RF power distribution. Subsequently, the feasibility of simultaneous RF heating and temperature monitoring was successfully validated in vivo in the aorta of living rabbits. This MR imaging/RF heating system offers a potential tool for intravascular MR-mediated, RF-enhanced vascular gene therapy.

Evaluation and automatic correction of metal-implant-induced artifacts in MR-based attenuation correction in whole-body PET/MR imaging

NASA Astrophysics Data System (ADS)

Schramm, G.; Maus, J.; Hofheinz, F.; Petr, J.; Lougovski, A.; Beuthien-Baumann, B.; Platzek, I.; van den Hoff, J.

2014-06-01

The aim of this paper is to describe a new automatic method for compensation of metal-implant-induced segmentation errors in MR-based attenuation maps (MRMaps) and to evaluate the quantitative influence of those artifacts on the reconstructed PET activity concentration. The developed method uses a PET-based delineation of the patient contour to compensate metal-implant-caused signal voids in the MR scan that is segmented for PET attenuation correction. PET emission data of 13 patients with metal implants examined in a Philips Ingenuity PET/MR were reconstructed with the vendor-provided method for attenuation correction (MRMaporig, PETorig) and additionally with a method for attenuation correction (MRMapcor, PETcor) developed by our group. MRMaps produced by both methods were visually inspected for segmentation errors. The segmentation errors in MRMaporig were classified into four classes (L1 and L2 artifacts inside the lung and B1 and B2 artifacts inside the remaining body depending on the assigned attenuation coefficients). The average relative SUV differences (\\varepsilon _{rel}^{av}) between PETorig and PETcor of all regions showing wrong attenuation coefficients in MRMaporig were calculated. Additionally, relative SUVmean differences (ɛrel) of tracer accumulations in hot focal structures inside or in the vicinity of these regions were evaluated. MRMaporig showed erroneous attenuation coefficients inside the regions affected by metal artifacts and inside the patients' lung in all 13 cases. In MRMapcor, all regions with metal artifacts, except for the sternum, were filled with the soft-tissue attenuation coefficient and the lung was correctly segmented in all patients. MRMapcor only showed small residual segmentation errors in eight patients. \\varepsilon _{rel}^{av} (mean ± standard deviation) were: ( - 56 ± 3)% for B1, ( - 43 ± 4)% for B2, (21 ± 18)% for L1, (120 ± 47)% for L2 regions. ɛrel (mean ± standard deviation) of hot focal structures were

Automatic detection of pelvic lymph nodes using multiple MR sequences

NASA Astrophysics Data System (ADS)

Yan, Michelle; Lu, Yue; Lu, Renzhi; Requardt, Martin; Moeller, Thomas; Takahashi, Satoru; Barentsz, Jelle

2007-03-01

A system for automatic detection of pelvic lymph nodes is developed by incorporating complementary information extracted from multiple MR sequences. A single MR sequence lacks sufficient diagnostic information for lymph node localization and staging. Correct diagnosis often requires input from multiple complementary sequences which makes manual detection of lymph nodes very labor intensive. Small lymph nodes are often missed even by highly-trained radiologists. The proposed system is aimed at assisting radiologists in finding lymph nodes faster and more accurately. To the best of our knowledge, this is the first such system reported in the literature. A 3-dimensional (3D) MR angiography (MRA) image is employed for extracting blood vessels that serve as a guide in searching for pelvic lymph nodes. Segmentation, shape and location analysis of potential lymph nodes are then performed using a high resolution 3D T1-weighted VIBE (T1-vibe) MR sequence acquired by Siemens 3T scanner. An optional contrast-agent enhanced MR image, such as post ferumoxtran-10 T2*-weighted MEDIC sequence, can also be incorporated to further improve detection accuracy of malignant nodes. The system outputs a list of potential lymph node locations that are overlaid onto the corresponding MR sequences and presents them to users with associated confidence levels as well as their sizes and lengths in each axis. Preliminary studies demonstrates the feasibility of automatic lymph node detection and scenarios in which this system may be used to assist radiologists in diagnosis and reporting.

Effect of carbonyl iron particles composition on the physical characteristics of MR grease

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

Mohamad, Norzilawati, E-mail: mnorzilawati@gmail.com; Mazlan, Saiful Amri, E-mail: amri.kl@utm.my; Ubaidillah, E-mail: ubaidillah@uns.ac.id

2016-03-29

Magnetorheological (MR) grease is an extension of the study of magnetorheological materials. The MR grease can help to reduce the particles sedimentation problem occurred in the MR fluids. Within this study, an effort has been taken to investigate the effect of different weight compositions of carbonyl iron particles on the physical and chemical characteristics of the MR grease under off-state condition (no magnetic field). The MR grease is prepared by mixing carbonyl iron particles having a size range of 1 to 10 µm with commercial NPC Highrex HD-3 grease. Characterizations of MR grease are investigated using Vibrating Sample Magnetometer (VSM), Environmentalmore » Scanning Electron Microscopy (ESEM), Differential Scanning Calorimeter (DSC) and rheometer. The dependency of carbonyl iron particles weight towards the magnetic properties of MR grease and other characterizations are investigated.« less

PET Imaging Stability Measurements During Simultaneous Pulsing of Aggressive MR Sequences on the SIGNA PET/MR System.

PubMed

Deller, Timothy W; Khalighi, Mohammad Mehdi; Jansen, Floris P; Glover, Gary H

2018-01-01

The recent introduction of simultaneous whole-body PET/MR scanners has enabled new research taking advantage of the complementary information obtainable with PET and MRI. One such application is kinetic modeling, which requires high levels of PET quantitative stability. To accomplish the required PET stability levels, the PET subsystem must be sufficiently isolated from the effects of MR activity. Performance measurements have previously been published, demonstrating sufficient PET stability in the presence of MR pulsing for typical clinical use; however, PET stability during radiofrequency (RF)-intensive and gradient-intensive sequences has not previously been evaluated for a clinical whole-body scanner. In this work, PET stability of the GE SIGNA PET/MR was examined during simultaneous scanning of aggressive MR pulse sequences. Methods: PET performance tests were acquired with MR idle and during simultaneous MR pulsing. Recent system improvements mitigating RF interference and gain variation were used. A fast recovery fast spin echo MR sequence was selected for high RF power, and an echo planar imaging sequence was selected for its high heat-inducing gradients. Measurements were performed to determine PET stability under varying MR conditions using the following metrics: sensitivity, scatter fraction, contrast recovery, uniformity, count rate performance, and image quantitation. A final PET quantitative stability assessment for simultaneous PET scanning during functional MRI studies was performed with a spiral in-and-out gradient echo sequence. Results: Quantitation stability of a 68 Ge flood phantom was demonstrated within 0.34%. Normalized sensitivity was stable during simultaneous scanning within 0.3%. Scatter fraction measured with a 68 Ge line source in the scatter phantom was stable within the range of 40.4%-40.6%. Contrast recovery and uniformity were comparable for PET images acquired simultaneously with multiple MR conditions. Peak noise equivalent count

SU-E-J-214: MR Protocol Development to Visualize Sirius MRI Markers in Prostate Brachytherapy Patients for MR-Based Post-Implant Dosimetry

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

Lim, T; Wang, J; Frank, S

Purpose: The current CT-based post-implant dosimetry allows precise seed localization but limited anatomical delineation. Switching to MR-based post-implant dosimetry is confounded by imprecise seed localization. One approach is to place positive-contrast markers (Sirius) adjacent to the negative-contrast seeds. This patient study aims to assess the utility of a 3D fast spoiled gradient-recalled echo (FSPGR) sequence to visualize Sirius markers for post-implant dosimetry. Methods: MRI images were acquired in prostate implant patients (n=10) on Day 0 (day-of-implant) and Day 30. The post-implant MR protocol consisted of 3D T2-weighted fast-spin-echo (FSE), T2-weighted 2D-FSE (axial) and T1-weighted 2D-FSE (axial/sagittal/coronal). We incorporated a 3D-FSPGRmore » sequence into the post-implant MR protocol to visualize the Sirius markers. Patients were scanned with different number-of-excitations (6, 8, 10), field-of-view (10cm, 14cm, 18cm), slice thickness (1mm, 0.8mm), flip angle (14 degrees, 20 degrees), bandwidth (122.070 Hz/pixel, 325.508 Hz/pixel, 390.625 Hz/pixel), phase encoding steps (160, 192, 224, 256), frequency-encoding direction (right/left, anterior/posterior), echo-time type (minimum-full, out-of-phase), field strength (1.5T, 3T), contrast (with, without), scanner vendor (Siemens, GE), coil (endorectal-coil only, endorectal-and-torso-coil, torsocoil only), endorectal-coil filling (30cc, 50cc) and endorectal-coil filling type (air, perfluorocarbon [PFC]). For post-implant dosimetric evaluation with greater anatomical detail, 3D-FSE images were fused with 3D-FSPGR images. For comparison with CT-based post-implant dosimetry, CT images were fused with 3D-FSPGR images. Results: The 3D-FSPGR sequence facilitated visualization of markers in patients. Marker visualization helped distinguish signal voids as seeds versus needle tracks for more definitive MR-based post-implant dosimetry. On the CT-MR fused images, the distance between the seed on CT to MR

MR signal intensity: staying on the bright side in MR image interpretation

PubMed Central

Bloem, Johan L; Reijnierse, Monique; Huizinga, Tom W J

2018-01-01

In 2003, the Nobel Prize for Medicine was awarded for contribution to the invention of MRI, reflecting the incredible value of MRI for medicine. Since 2003, enormous technical advancements have been made in acquiring MR images. However, MRI has a complicated, accident-prone dark side; images are not calibrated and respective images are dependent on all kinds of subjective choices in the settings of the machine, acquisition technique parameters, reconstruction techniques, data transmission, filtering and postprocessing techniques. The bright side is that understanding MR techniques increases opportunities to unravel characteristics of tissue. In this viewpoint, we summarise the different subjective choices that can be made to generate MR images and stress the importance of communication between radiologists and rheumatologists to correctly interpret images.

MR findings in athletes with pubalgia.

PubMed

Albers, S L; Spritzer, C E; Garrett, W E; Meyers, W C

2001-05-01

To describe the MR findings in athletes with pubalgia. Pelvic MR images of 32 athletes (30 men, 2 women) with pubalgia were studied. T1-weighted and T2-weighted (SE and FSE) and STIR images in the axial and coronal planes were obtained on a 1.5-T system. Images were reviewed for general pelvic pathology. Special attention was given to the pubic symphysis, groin and pelvic musculature, and to the abdominal wall musculature. Thirty surgically confirmed cases comprise the study group. Abnormalities in the following were found: pubic symphysis (21/30), abdominal wall (27/30), groin musculature, including rectus abdominis (21/30), pectineus (6/30), and adductor muscle group (18/30). Pubalgia is a complex process which is frequently multifactorial. The MRI findings can alter the surgical approach.

Pediatric Sarcomas Are Targetable by MR-Guided High Intensity Focused Ultrasound (MR-HIFU): Anatomical Distribution and Radiological Characteristics.

PubMed

Shim, Jenny; Staruch, Robert M; Koral, Korgun; Xie, Xian-Jin; Chopra, Rajiv; Laetsch, Theodore W

2016-10-01

Despite intensive therapy, children with metastatic and recurrent sarcoma or neuroblastoma have a poor prognosis. Magnetic resonance guided high intensity focused ultrasound (MR-HIFU) is a noninvasive technique allowing the delivery of targeted ultrasound energy under MR imaging guidance. MR-HIFU may be used to ablate tumors without ionizing radiation or target chemotherapy using hyperthermia. Here, we evaluated the anatomic locations of tumors to assess the technical feasibility of MR-HIFU therapy for children with solid tumors. Patients with sarcoma or neuroblastoma with available cross-sectional imaging were studied. Tumors were classified based on the location and surrounding structures within the ultrasound beam path as (i) not targetable, (ii) completely or partially targetable with the currently available MR-HIFU system, and (iii) potentially targetable if a respiratory motion compensation technique was used. Of the 121 patients with sarcoma and 61 patients with neuroblastoma, 64% and 25% of primary tumors were targetable at diagnosis, respectively. Less than 20% of metastases at diagnosis or relapse were targetable for both sarcoma and neuroblastoma. Most targetable lesions were located in extremities or in the pelvis. Respiratory motion compensation may increase the percentage of targetable tumors by 4% for sarcomas and 10% for neuroblastoma. Many pediatric sarcomas are localized at diagnosis and are targetable by current MR-HIFU technology. Some children with neuroblastoma have bony tumors targetable by MR-HIFU at relapse, but few newly diagnosed children with neuroblastoma have tumors amenable to MR-HIFU therapy. Clinical trials of MR-HIFU should focus on patients with anatomically targetable tumors. © 2016 Wiley Periodicals, Inc.

Real-time active MR-tracking of metallic stylets in MR-guided radiation therapy

PubMed Central

Wang, Wei; Dumoulin, Charles L.; Viswanathan, Akila N.; Tse, Zion T. H.; Mehrtash, Alireza; Loew, Wolfgang; Norton, Isaiah; Tokuda, Junichi; Seethamraju, Ravi T.; Kapur, Tina; Damato, Antonio L.; Cormack, Robert A.; Schmidt, Ehud J.

2014-01-01

Purpose To develop an active MR-tracking system to guide placement of metallic devices for radiation therapy. Methods An actively tracked metallic stylet for brachytherapy was constructed by adding printed-circuit micro-coils to a commercial stylet. The coil design was optimized by electromagnetic simulation, and has a radio-frequency lobe pattern extending ~5 mm beyond the strong B0 inhomogeneity region near the metal surface. An MR-tracking sequence with phase-field dithering was used to overcome residual effects of B0 and B1 inhomogeneities caused by the metal, as well as from inductive coupling to surrounding metallic stylets. The tracking system was integrated with a graphical workstation for real-time visualization. 3T MRI catheter-insertion procedures were tested in phantoms and ex-vivo animal tissue, and then performed in three patients during interstitial brachytherapy. Results The tracking system provided high-resolution (0.6 × 0.6 × 0.6 mm3) and rapid (16 to 40 frames per second, with three to one phase-field dithering directions) catheter localization in phantoms, animals, and three gynecologic cancer patients. Conclusion This is the first demonstration of active tracking of the shaft of metallic stylet in MR-guided brachytherapy. It holds the promise of assisting physicians to achieve better targeting and improving outcomes in interstitial brachytherapy. PMID:24903165

Spin-echo Echo-planar Imaging MR Elastography versus Gradient-echo MR Elastography for Assessment of Liver Stiffness in Children and Young Adults Suspected of Having Liver Disease.

PubMed

Serai, Suraj D; Dillman, Jonathan R; Trout, Andrew T

2017-03-01

Purpose To compare two-dimensional (2D) gradient-recalled echo (GRE) and 2D spin-echo (SE) echo-planar imaging (EPI) magnetic resonance (MR) elastography for measurement of hepatic stiffness in pediatric and young adult patients suspected of having liver disease. Materials and Methods In this institutional review board-approved, HIPAA-compliant study, 58 patients underwent both 2D GRE and 2D SE-EPI MR elastography at 1.5 T during separate breath holds. Liver stiffness (mean of means; in kilopascals) was measured by five blinded reviewers. Pooled mean liver stiffness and region-of-interest (ROI) size were compared by using paired t tests. Intraclass correlation coefficients (ICCs) were used to assess agreement between techniques. Respiratory motion artifacts were compared across sequences by using the Fisher exact test. Results Mean patient age was 14.7 years ± 5.2 (standard deviation; age range, 0.7-20.5 years), and 55.2% (32 of 58) of patients were male. Mean liver stiffness was 2.92 kPa ± 1.29 measured at GRE MR elastography and 2.76 kPa ± 1.39 at SE-EPI MR elastography (n = 290; P = .15). Mean ROI sizes were 8495 mm 2 ± 4482 for 2D GRE MR elastography and 15 176 mm 2 ± 7609 for 2D SE-EPI MR elastography (n = 290; P < .001). Agreement was excellent for measured stiffness between five reviewers for both 2D GRE (ICC, 0.97; 95% confidence interval: 0.95, 0.98) and 2D SE-EPI (ICC, 0.98; 95% confidence interval: 0.96, 0.99). Mean ICC (n = 5) for agreement between 2D GRE and 2D SE-EPI MR elastography was 0.93 (range, 0.91-0.95). Moderate or severe breathing artifacts were observed on 27.5% (16 of 58) of 2D GRE images versus 0% 2D SE-EPI images (P < .001). Conclusion There is excellent agreement on measured hepatic stiffness between 2D GRE and 2D SE-EPI MR elastography across multiple reviewers. SE-EPI MR elastography allowed for stiffness measurement across larger areas of the liver and can be performed in a single breath hold. © RSNA, 2016.

Evaluation of thermometric monitoring for intradiscal laser ablation in an open 1.0 T MR scanner.

PubMed

Wonneberger, Uta; Schnackenburg, Bernhard; Wlodarczyk, Waldemar; Rump, Jens; Walter, Thula; Streitparth, Florian; Teichgräber, Ulf Karl Mart

2010-01-01

The purpose of this study was to evaluate different methods of magnetic resonance thermometry (MRTh) for the monitoring of intradiscal laser ablation therapy in an open 1.0 Tesla magnetic resonance (MR) scanner. MRTh methods based on the two endogenous MR temperature indicators of spin-lattice relaxation time T1 and water proton resonance frequency (PRF) shift were optimised and compared in vitro. For the latter, we measured the effective spin-spin relaxation times T2* in intervertebral discs of volunteers. Then we compared four gradient echo-based imaging techniques to monitor laser ablations in human disc specimens. Criteria of assessment were outline of anatomic detail, immunity against needle artefacts, signal-to-noise ratio (SNR) and accuracy of the calculated temperature. T2* decreased in an inverse and almost linear manner with the patients' age (r = 0.9) from 70 to 30 ms (mean of 49 ms). The optimum image quality (anatomic details, needle artefacts, SNR) and temperature accuracy (+/-1.09 degrees C for T1-based and +/-1.11 degrees C for PRF-based MRTh) was achieved with a non-spoiled gradient-echo sequence with an echo time of TE = 10 ms. Combination of anatomic and thermometric non-invasive monitoring of laser ablations in the lumbar spine is feasible. The temperature accuracy of the investigated T1- and PRF-based MRTh methods in vitro is high enough and promises to be reliable in vivo as well.

Athletic pubalgia and the "sports hernia": MR imaging findings.

PubMed

Zoga, Adam C; Kavanagh, Eoin C; Omar, Imran M; Morrison, William B; Koulouris, George; Lopez, Hector; Chaabra, Avneesh; Domesek, John; Meyers, William C

2008-06-01

To retrospectively determine the sensitivity and specificity of magnetic resonance (MR) imaging findings in patients with clinical athletic pubalgia, with either surgical or physical examination findings as the reference standard. Institutional review board approval was granted for this HIPAA-compliant study, and informed consent was waived. MR imaging studies in 141 patients (134 male patients, seven female patients; mean age, 30.1 years; range, 17-71 years) who had been referred to a subspecialist because of groin pain were reviewed for findings including hernia, pubic bone marrow edema, secondary cleft sign, and rectus abdominis and adductor tendon injury. MR imaging findings were compared with surgical findings for 102 patients, physical examination findings for all 141 patients, and MR imaging findings in an asymptomatic control group of 25 men (mean age, 29.8 years; range, 18-39 years). Sensitivity and specificity of MR imaging for rectus abdominis and adductor tendon injury were determined by using a chi(2) analysis, and significance of the findings was analyzed with an unpaired Student t test. Disease patterns seen at MR imaging were compared with those reported in the surgical and sports medicine literature. One hundred thirty-eight (98%) of 141 patients had findings at MR imaging that could cause groin pain. Compared with surgery, MR imaging had a sensitivity and specificity, respectively, of 68% and 100% for rectus abdominis tendon injury and 86% and 89% for adductor tendon injury. Injury in each of these structures was significantly more common in the patient group than in the control group (P < .001). Only two patients had hernias at surgery. At MR imaging, injury or disease could be fit into distinct groups, including osteitis pubis, adductor compartment injury, rectus abdominis tendon injury, and injury or disease remote from the pubic symphysis. Patients with injury involving the rectus abdominis insertion were most likely to go on to surgical

Interventional-Cardiovascular MR: Role of the Interventional MR Technologist

PubMed Central

Mazal, Jonathan R; Rogers, Toby; Schenke, William H; Faranesh, Anthony Z; Hansen, Michael; O’Brien, Kendall; Ratnayaka, Kanishka; Lederman, Robert J

2016-01-01

Background Interventional-cardiovascular magnetic resonance (iCMR) is a promising clinical tool for adults and children who need a comprehensive hemodynamic catheterization of the heart. Magnetic resonance (MR) imaging-guided cardiac catheterization offers radiation-free examination with increased soft tissue contrast and unconstrained imaging planes for catheter guidance. The interventional MR technologist plays an important role in the care of patients undergoing such procedures. It is therefore helpful for technologists to under-stand the unique iCMR preprocedural preparation, procedural and imaging workflows, and management of emergencies. The authors report their team’s experience from the National Institutes of Health Clinical Center and a collaborating pediatric site. PMID:26721838

TH-AB-BRA-04: Dosimetric Evaluation of MR-Guided HDR Brachytherapy Planning for Cervical Cancer

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

Kamio, Y; Barkati, M; Beliveau-Nadeau, D

2016-06-15

Purpose: To perform a retrospective study on 16 patients that had both CT and T2-weighted MR scans done at first fraction using the Utrecht CT/MR applicator (Elekta Brachytherapy) in order to evaluate uncertainties associated with an MR-only planning workflow. Methods: MR-workflow uncertainties were classified in three categories: reconstruction, registration and contouring. A systematic comparison of the CT and MR contouring, manual reconstruction and optimization process was performed to evaluate the impact of these uncertainties on the recommended GEC ESTRO DVH parameters: D90% and V100% for HR-CTV as well as D2cc for bladder, rectum, sigmoid colon and small bowel. This comparisonmore » was done using the following four steps: 1. Catheter reconstruction done on MR images with original CT-plan contours and dwell times. 2. OAR contours adjusted on MR images with original CT-plan reconstruction and dwell times. 3. Both reconstruction and contours done on MR images with original CT-plan dwell times. 4. Entire MR-based workflow optimized dwell times reimported to the original CT-plan. Results: The MR-based reconstruction process showed average D2cc deviations of 4.5 ± 3.0%, 1.5 ± 2.0%, 2.5 ± 2.0% and 2.0 ± 1.0% for the bladder, rectum, sigmoid colon and small bowels respectively with a maximum of 10%, 6%, 6% and 4%. The HR-CTV’s D90% and V100% average deviations was found to be 4.0 ± 3.0%, and 2.0 ± 2.0% respectively with a maximum of 10% and 6%. Adjusting contours on MR-images was found to have a similar impact. Finally, the optimized MR-based workflow dwell times were found to still give acceptable plans when re-imported to the original CT-plan which validated the entire workflow. Conclusion: This work illustrates a systematic validation method for centers wanting to move towards an MR-only workflow. This work will be expanded to model based reconstruction, PD-weighted images and other types of applicators.« less

Effect of electrode sub-micron surface feature size on current generation of Shewanella oneidensis in microbial fuel cells

NASA Astrophysics Data System (ADS)

Ye, Zhou; Ellis, Michael W.; Nain, Amrinder S.; Behkam, Bahareh

2017-04-01

Microbial fuel cells (MFCs) are envisioned to serve as compact and sustainable sources of energy; however, low current and power density have hindered their widespread use. Introduction of 3D micro/nanostructures on the MFC anode is known to improve its performance by increasing the surface area available for bacteria attachment; however, the role of the feature size remains poorly understood. To delineate the role of feature size from the ensuing surface area increase, nanostructures with feature heights of 115 nm and 300 nm, both at a height to width aspect ratio of 0.3, are fabricated in a grid pattern on glassy carbon electrodes (GCEs). Areal current densities and bacteria attachment densities of the patterned and unpatterned GCEs are compared using Shewanella oneidensis Δbfe in a three-electrode bioreactor. The 115 nm features elicit a remarkable 40% increase in current density and a 78% increase in bacterial attachment density, whereas the GCE with 300 nm pattern does not exhibit significant change in current density or bacterial attachment density. The current density dependency on feature size is maintained over the entire 160 h experiment. Thus, optimally sized surface features have a substantial effect on current production that is independent of their effect on surface area.

Craniofacial duplication (diprosopus): CT, MR imaging, and MR angiography findings case report.

PubMed

Hähnel, Stefan; Schramm, Peter; Hassfeld, Stefan; Steiner, Hans H; Seitz, Angelika

2003-01-01

Diprosopus is one of the rarest malformations in humans. In addition to the facial structures, the cerebral frontal lobes were duplicated in this case. Three pairs of anterior cerebral arteries were detected, and the rostral parts of the superior sagittal sinus were duplicated. Computed tomography, magnetic resonance (MR) imaging, and MR angiography allowed study of the degree of duplicative changes in diprosopus, especially for planning cosmetic correction. Copyright RSNA, 2002

Endovascular Catheter for Magnetic Navigation under MR Imaging Guidance: Evaluation of Safety in Vivo at 1.5T

PubMed Central

Hetts, S.W.; Saeed, M.; Martin, A.J.; Evans, L.; Bernhardt, A.F.; Malba, V.; Settecase, F.; Do, L.; Yee, E.J.; Losey, A.; Sincic, R.; Roy, S.; Arenson, R.L.; Wilson, M.W.

2013-01-01

BACKGROUND AND PURPOSE: Endovascular navigation under MR imaging guidance can be facilitated by a catheter with steerable microcoils on the tip. Not only do microcoils create visible artifacts allowing catheter tracking, but also they create a small magnetic moment permitting remote-controlled catheter tip deflection. A side product of catheter tip electrical currents, however, is the heat that might damage blood vessels. We sought to determine the upper boundary of electrical currents safely usable at 1.5T in a coil-tipped microcatheter system. MATERIALS AND METHODS: Alumina tubes with solenoid copper coils were attached to neurovascular microcatheters with heat shrink-wrap. Catheters were tested in carotid arteries of 8 pigs. The catheters were advanced under x-ray fluoroscopy and MR imaging. Currents from 0 mA to 700 mA were applied to test heating and potential vascular damage. Postmortem histologic analysis was the primary endpoint. RESULTS: Several heat-mitigation strategies demonstrated negligible vascular damage compared with control arteries. Coil currents ≤300 mA resulted in no damage (0/58 samples) compared with 9 (25%) of 36 samples for > 300-mA activations (P = .0001). Tip coil activation ≤1 minute and a proximal carotid guide catheter saline drip > 2 mL/minute also had a nonsignificantly lower likelihood of vascular damage. For catheter tip coil activations ≤300 mA for ≤1 minute in normal carotid flow, 0 of 43 samples had tissue damage. CONCLUSIONS: Activations of copper coils at the tip of microcatheters at low currents in 1.5T MR scanners can be achieved without significant damage to blood vessel walls in a controlled experimental setting. Further optimization of catheter design and procedure protocols is necessary for safe remote control magnetic catheter guidance. PMID:23846795

Dynamic susceptibility contrast-enhanced perfusion MR imaging at 1.5 T predicts final infarct size in a rat stroke model.

PubMed

Chen, Feng; Suzuki, Yasuhiro; Nagai, Nobuo; Peeters, Ronald; Marchal, Guy; Ni, Yicheng

2005-01-30

The purpose of the present animal experiment was to determine whether source images from dynamic susceptibility contrast-enhanced perfusion weighted imaging (DSC-PWI) at a 1.5T MR scanner, performed early after photochemically induced thrombosis (PIT) of cerebral middle artery (MCA), is feasible to predict final cerebral infarct size in a rat stroke model. Fifteen rats were subjected to PIT of proximal MCA. T2 weighted imaging (T2WI), diffusion-weighted imaging (DWI), and contrast-enhanced PWI were obtained at 1 h and 24 h after MCA occlusion. The relative lesion size (RLS) was defined as lesion volume/brain volume x 100% and measured for MR images, and compared with the final RLS on the gold standard triphenyl tetrazolium chloride (TTC) staining at 24 h. One hour after MCA occlusion, the RLS with DSC-PWI was 24.9 +/- 6.3%, which was significantly larger than 17.6 +/- 4.8% with DWI (P < 0.01). At 24 h, the final RLS on TTC was 24.3 +/- 4.8%, which was comparable to 25.1 +/- 3.5%, 24.6 +/- 3.6% and 27.9 +/- 6.8% with T2WI, DWI and DSC-PWI respectively (P > 0.05). The fact that at 1 h after MCA occlusion only the displayed perfusion deficit was similar to the final infarct size on TTC (P > 0.05) suggests that early source images from DSC-PWI at 1.5T MR scanner is feasible to noninvasively predict the final infarct size in rat models of stroke.

Muscle MR Imaging in Tubular Aggregate Myopathy

PubMed Central

Beltrame, Valeria; Ortolan, Paolo; Coran, Alessandro; Zanato, Riccardo; Gazzola, Matteo; Frigo, Annachiara; Bello, Luca; Pegoraro, Elena; Stramare, Roberto

2014-01-01

Purpose To evaluate with Magnetic Resonance (MR) the degree of fatty replacement and edematous involvement in skeletal muscles in patients with Tubular Aggregate Myopathy (TAM). To asses the inter-observer agreement in evaluating muscle involvement and the symmetry index of fatty replacement. Materials and Methods 13 patients were evaluated by MR to ascertain the degree of fatty replacement (T1W sequences) according to Mercuri's scale, and edema score (STIR sequences) according to extent and site. Results Fatty replacement mainly affects the posterior superficial compartment of the leg; the anterior compartment is generally spared. Edema was generally poor and almost only in the superficial compartment of the leg. The inter-observer agreement is very good with a Krippendorff's coefficient >0.9. Data show a total symmetry in the muscular replacement (McNemar-Bowker test with p = 1). Conclusions MR reveals characteristic muscular involvement, and is a reproducible technique for evaluation of TAM. There may also be a characteristic involvement of the long and short heads of the biceps femoris. It is useful for aimed biopsies, diagnostic hypotheses and evaluation of disease progression. PMID:24722334

Practical Considerations for Clinical PET/MR Imaging.

PubMed

Galgano, Samuel; Viets, Zachary; Fowler, Kathryn; Gore, Lael; Thomas, John V; McNamara, Michelle; McConathy, Jonathan

2018-01-01

Clinical PET/MR imaging is currently performed at a number of centers around the world as part of routine standard of care. This article focuses on issues and considerations for a clinical PET/MR imaging program, focusing on routine standard-of-care studies. Although local factors influence how clinical PET/MR imaging is implemented, the approaches and considerations described here intend to apply to most clinical programs. PET/MR imaging provides many more options than PET/computed tomography with diagnostic advantages for certain clinical applications but with added complexity. A recurring theme is matching the PET/MR imaging protocol to the clinical application to balance diagnostic accuracy with efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Practical Considerations for Clinical PET/MR Imaging.

PubMed

Galgano, Samuel; Viets, Zachary; Fowler, Kathryn; Gore, Lael; Thomas, John V; McNamara, Michelle; McConathy, Jonathan

2017-05-01

Clinical PET/MR imaging is currently performed at a number of centers around the world as part of routine standard of care. This article focuses on issues and considerations for a clinical PET/MR imaging program, focusing on routine standard-of-care studies. Although local factors influence how clinical PET/MR imaging is implemented, the approaches and considerations described here intend to apply to most clinical programs. PET/MR imaging provides many more options than PET/computed tomography with diagnostic advantages for certain clinical applications but with added complexity. A recurring theme is matching the PET/MR imaging protocol to the clinical application to balance diagnostic accuracy with efficiency. Copyright © 2016 Elsevier Inc. All rights reserved.

Fibrolipomatous hamartoma: pathognomonic on MR imaging.

PubMed

Marom, E M; Helms, C A

1999-05-01

To assess the MR imaging characteristics, presenting symptoms, age and nerve distribution of fibrolipomatous hamartoma. A computer search was performed of the term fibrolipomatous hamartoma through the musculoskeletal section MR imaging results at our institution from June 7, 1996 to January 21, 1998 followed by a search of the terms lipomatous hamartoma, median nerve, surrounding fat, increased fatty signal, coaxial, and neuroma. MR images and medical files were retrospectively reviewed by two experienced musculoskeletal radiologists for imaging characteristics, nerve and age distribution as well as for history of trauma. In addition three consultation cases from outside institutions were added for determination of image characteristics. Ten fibrolipomatous hamartomas were identified: eight in the median nerve, one in the ulnar nerve and one in the sciatic nerve. Mean age was 32.3 years (range 4-75 years, SD 21 years). Imaging characteristics were serpiginous low-intensity structures representing thickened nerve fascicles, surrounded by evenly distributed fat, high signal intensity on T1-weighted sequences and low signal intensity on T2-weighted sequences. The amount of fat varied; however, distribution in eight cases (80%) was predominantly between nerve fibers rather than surrounding them peripherally. All had a coaxial-cable-like appearance on axial planes and a spaghetti-like appearance on coronal planes that was not seen in any other type of median nerve abnormality imaged during the study period. The MR imaging characteristics of fibrolipomatous hamartoma are pathognomonic, obviating the need for biopsy for diagnosis.

Investigation of MR scanning, image registration, and image processing techniques to visualize cortical veins for neurosurgery

NASA Astrophysics Data System (ADS)

Noordmans, Herke J.; Rutten, G. J. M.; Willems, Peter W. A.; Hoogduin, J.; Viergever, Max A.

2001-01-01

The visualization of brain vessels on the cortex helps the neurosurgeon in two ways: To avoid blood vessels when specifying the trepanation entry, and to overcome errors in the surgical navigation system due to brain shift. We compared 3D T1 MR, 3D T1 MR with gadolinium contrast, MR venography and MR phase contrast angiography as scanning techniques, mutual information as registration technique, and thresholding and multi-vessel enhancement as image processing techniques. We evaluated the volume rendered results based on their quality and correspondence with photos took during surgery. It appears that with 3D T1 MR scans, gadolinium is required to show cortical veins. The visibility of small cortical veins is strongly enhanced by subtracting a 3D T1 MR baseline scan, which should be registered to the scan with gadolinium contrast, even when the scans are made during the same session. Multi-vessel enhancement helps to clarify the view on small vessels by reducing the noise level, but strikingly does not reveal more. MR venography does show intracerebral veins with high detail, but is, as is, unsuited to show cortical veins due to the low contrast with CSF. MR phase contrast angiography can perform equally well as the subtraction technique, but its quality seems to show more inter-patient variability.

Rosen's (M,R) system in process algebra.

PubMed

Gatherer, Derek; Galpin, Vashti

2013-11-17

Robert Rosen's Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has been claimed to be non-reducible to its components and algorithmically non-computable, in the sense of not being evaluable as a function by a Turing machine. If (M,R)-like structures are present in real biological networks, this suggests that many biological networks will be non-computable, with implications for those branches of systems biology that rely on in silico modelling for predictive purposes. We instantiate (M,R) using the process algebra Bio-PEPA, and discuss the extent to which our model represents a true realization of (M,R). We observe that under some starting conditions and parameter values, stable states can be achieved. Although formal demonstration of algorithmic computability remains elusive for (M,R), we discuss the extent to which our Bio-PEPA representation of (M,R) allows us to sidestep Rosen's fundamental objections to computational systems biology. We argue that the behaviour of (M,R) in Bio-PEPA shows life-like properties.

Endovascular MR-guided Renal Embolization by Using a Magnetically Assisted Remote-controlled Catheter System

PubMed Central

Lillaney, Prasheel V.; Yang, Jeffrey K.; Losey, Aaron D.; Martin, Alastair J.; Cooke, Daniel L.; Thorne, Bradford R. H.; Barry, David C.; Chu, Andrew; Stillson, Carol; Do, Loi; Arenson, Ronald L.; Saeed, Maythem; Wilson, Mark W.

2016-01-01

Purpose To assess the feasibility of a magnetically assisted remote-controlled (MARC) catheter system under magnetic resonance (MR) imaging guidance for performing a simple endovascular procedure (ie, renal artery embolization) in vivo and to compare with x-ray guidance to determine the value of MR imaging guidance and the specific areas where the MARC system can be improved. Materials and Methods In concordance with the Institutional Animal Care and Use Committee protocol, in vivo renal artery navigation and embolization were tested in three farm pigs (mean weight 43 kg ± 2 [standard deviation]) under real-time MR imaging at 1.5 T. The MARC catheter device was constructed by using an intramural copper-braided catheter connected to a laser-lithographed saddle coil at the distal tip. Interventionalists controlled an in-room cart that delivered electrical current to deflect the catheter in the MR imager. Contralateral kidneys were similarly embolized under x-ray guidance by using standard clinical catheters and guidewires. Changes in renal artery flow and perfusion were measured before and after embolization by using velocity-encoded and perfusion MR imaging. Catheter navigation times, renal parenchymal perfusion, and renal artery flow rates were measured for MR-guided and x-ray–guided embolization procedures and are presented as means ± standard deviation in this pilot study. Results Embolization was successful in all six kidneys under both x-ray and MR imaging guidance. Mean catheterization time with MR guidance was 93 seconds ± 56, compared with 60 seconds ± 22 for x-ray guidance. Mean changes in perfusion rates were 4.9 au/sec ± 0.8 versus 4.6 au/sec ± 0.6, and mean changes in renal flow rate were 2.1 mL/min/g ± 0.2 versus 1.9 mL/min/g ± 0.2 with MR imaging and x-ray guidance, respectively. Conclusion The MARC catheter system is feasible for renal artery catheterization and embolization under real-time MR imaging in vivo, and quantitative physiologic

Endovascular MR-guided Renal Embolization by Using a Magnetically Assisted Remote-controlled Catheter System.

PubMed

Lillaney, Prasheel V; Yang, Jeffrey K; Losey, Aaron D; Martin, Alastair J; Cooke, Daniel L; Thorne, Bradford R H; Barry, David C; Chu, Andrew; Stillson, Carol; Do, Loi; Arenson, Ronald L; Saeed, Maythem; Wilson, Mark W; Hetts, Steven W

2016-10-01

Purpose To assess the feasibility of a magnetically assisted remote-controlled (MARC) catheter system under magnetic resonance (MR) imaging guidance for performing a simple endovascular procedure (ie, renal artery embolization) in vivo and to compare with x-ray guidance to determine the value of MR imaging guidance and the specific areas where the MARC system can be improved. Materials and Methods In concordance with the Institutional Animal Care and Use Committee protocol, in vivo renal artery navigation and embolization were tested in three farm pigs (mean weight 43 kg ± 2 [standard deviation]) under real-time MR imaging at 1.5 T. The MARC catheter device was constructed by using an intramural copper-braided catheter connected to a laser-lithographed saddle coil at the distal tip. Interventionalists controlled an in-room cart that delivered electrical current to deflect the catheter in the MR imager. Contralateral kidneys were similarly embolized under x-ray guidance by using standard clinical catheters and guidewires. Changes in renal artery flow and perfusion were measured before and after embolization by using velocity-encoded and perfusion MR imaging. Catheter navigation times, renal parenchymal perfusion, and renal artery flow rates were measured for MR-guided and x-ray-guided embolization procedures and are presented as means ± standard deviation in this pilot study. Results Embolization was successful in all six kidneys under both x-ray and MR imaging guidance. Mean catheterization time with MR guidance was 93 seconds ± 56, compared with 60 seconds ± 22 for x-ray guidance. Mean changes in perfusion rates were 4.9 au/sec ± 0.8 versus 4.6 au/sec ± 0.6, and mean changes in renal flow rate were 2.1 mL/min/g ± 0.2 versus 1.9 mL/min/g ± 0.2 with MR imaging and x-ray guidance, respectively. Conclusion The MARC catheter system is feasible for renal artery catheterization and embolization under real-time MR imaging in vivo, and quantitative physiologic

Abbreviated Combined MR Protocol: A New Faster Strategy for Characterizing Breast Lesions.

PubMed

Moschetta, Marco; Telegrafo, Michele; Rella, Leonarda; Stabile Ianora, Amato Antonio; Angelelli, Giuseppe

2016-06-01

The use of an abbreviated magnetic resonance (MR) protocol has been recently proposed for cancer screening. The aim of our study is to evaluate the diagnostic accuracy of an abbreviated MR protocol combining short TI inversion recovery (STIR), turbo-spin-echo (TSE)-T2 sequences, a pre-contrast T1, and a single intermediate (3 minutes after contrast injection) post-contrast T1 sequence for characterizing breast lesions. A total of 470 patients underwent breast MR examination for screening, problem solving, or preoperative staging. Two experienced radiologists evaluated both standard and abbreviated protocols in consensus. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy for both protocols were calculated (with the histological findings and 6-month ultrasound follow-up as the reference standard) and compared with the McNemar test. The post-processing and interpretation times for the MR images were compared with the paired t test. In 177 of 470 (38%) patients, the MR sequences detected 185 breast lesions. Standard and abbreviated protocols obtained sensitivity, specificity, diagnostic accuracy, PPV, and NPV values respectively of 92%, 92%, 92%, 68%, and 98% and of 89%, 91%, 91%, 64%, and 98% with no statistically significant difference (P < .0001). The mean post-processing and interpretation time were, respectively, 7 ± 1 minutes and 6 ± 3.2 minutes for the standard protocol and 1 ± 1.2 minutes and 2 ± 1.2 minutes for the abbreviated protocol, with a statistically significant difference (P < .01). An abbreviated combined MR protocol represents a time-saving tool for radiologists and patients with the same diagnostic potential as the standard protocol in patients undergoing breast MRI for screening, problem solving, or preoperative staging. Copyright © 2016 Elsevier Inc. All rights reserved.

MR spectroscopy and MR perfusion character of cerebral sparganosis: a case report.

PubMed

Chiu, C-H; Chiou, T-L; Hsu, Y-H; Yen, P-S

2010-02-01

The authors report the case of a 46-year-old woman with cerebral sparganosis resulting from infection with a larva of Spirometra. Computed tomography and magnetic resonance imaging revealed a mass lesion with prominent perifocal oedema in the left parietal lobe. Advanced imaging pulse sequences, including MR spectroscopy and MR perfusion, were performed. During surgery for the removal of a granuloma, the parasite was discovered and excised. Following treatment, the patient's neurological deficits markedly improved.

MR images of mouse brain using clinical 3T MR scanner and 4CH-Mouse coil

NASA Astrophysics Data System (ADS)

Lim, Soo Mee; Park, Eun Mi; Lyoo, In Kyoon; Lee, Junghyun; Han, Bo Mi; Lee, Jeong Kyong; Lee, Su Bin

2015-07-01

Objectives: Although small-bore high-field magnets are useful for research in small rodent models,this technology, however, has not been easily accessible to most researchers. This current study, thus,tried to evaluate the usability of 4CH-Mouse coil (Philips Healthcare, Best, the Netherlands) forpreclinical investigations in clinical 3T MR scan environment. We evaluated the effects of ischemicpreconditioning (IP) in the mouse stroke model with clinical 3T MR scanner and 4CH-Mouse coil. Materials and Methods: Experiments were performed on male C57BL/6 mice that either received the IP or sham operation (control). Three different MR sequences including diffusion weighted images (DWI), T2-weighted images (T2WI), and fluid attenuated inversion recovery (FLAIR) were performed on the mouse brains following 24, 72 hours of middle cerebral artery occlusion (MCAO) and analyzed for infarct lesions. Results: The images showed that the IP-treated mouse brains had significantly smaller infarct volumes compared to the control group. Of the MR sequences employed, the T2WI showed the highest level of correlations with postmortem infarct volume measurements. Conclusions: The clinical 3T MR scanner turned out to have a solid potential as a practical tool for imaging small animal brains. MR sequences including DWI, T2WI, FLAIR were obtained with acceptable resolution and in a reasonable time constraint in evaluating a mouse stroke model brain.

Brain MR imaging at ultra-low radiofrequency power.

PubMed

Sarkar, Subhendra N; Alsop, David C; Madhuranthakam, Ananth J; Busse, Reed F; Robson, Philip M; Rofsky, Neil M; Hackney, David B

2011-05-01

To explore the lower limits for radiofrequency (RF) power-induced specific absorption rate (SAR) achievable at 1.5 T for brain magnetic resonance (MR) imaging without loss of tissue signal or contrast present in high-SAR clinical imaging in order to create a potentially viable MR method at ultra-low RF power to image tissues containing implanted devices. An institutional review board-approved HIPAA-compliant prospective MR study design was used, with written informed consent from all subjects prior to MR sessions. Seven healthy subjects were imaged prospectively at 1.5 T with ultra-low-SAR optimized three-dimensional (3D) fast spin-echo (FSE) and fluid-attenuated inversion-recovery (FLAIR) T2-weighted sequences and an ultra-low-SAR 3D spoiled gradient-recalled acquisition in the steady state T1-weighted sequence. Corresponding high-SAR two-dimensional (2D) clinical sequences were also performed. In addition to qualitative comparisons, absolute signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) for multicoil, parallel imaging acquisitions were generated by using a Monte Carlo method for quantitative comparison between ultra-low-SAR and high-SAR results. There were minor to moderate differences in the absolute tissue SNR and CNR values and in qualitative appearance of brain images obtained by using ultra-low-SAR and high-SAR techniques. High-SAR 2D T2-weighted imaging produced slightly higher SNR, while ultra-low-SAR 3D technique not only produced higher SNR for T1-weighted and FLAIR images but also higher CNRs for all three sequences for most of the brain tissues. The 3D techniques adopted here led to a decrease in the absorbed RF power by two orders of magnitude at 1.5 T, and still the image quality was preserved within clinically acceptable imaging times. RSNA, 2011

Imaging Human Brain Perfusion with Inhaled Hyperpolarized 129Xe MR Imaging.

PubMed

Rao, Madhwesha R; Stewart, Neil J; Griffiths, Paul D; Norquay, Graham; Wild, Jim M

2018-02-01

Purpose To evaluate the feasibility of directly imaging perfusion of human brain tissue by using magnetic resonance (MR) imaging with inhaled hyperpolarized xenon 129 ( 129 Xe). Materials and Methods In vivo imaging with 129 Xe was performed in three healthy participants. The combination of a high-yield spin-exchange optical pumping 129 Xe polarizer, custom-built radiofrequency coils, and an optimized gradient-echo MR imaging protocol was used to achieve signal sensitivity sufficient to directly image hyperpolarized 129 Xe dissolved in the human brain. Conventional T1-weighted proton (hydrogen 1 [ 1 H]) images and perfusion images by using arterial spin labeling were obtained for comparison. Results Images of 129 Xe uptake were obtained with a signal-to-noise ratio of 31 ± 9 and demonstrated structural similarities to the gray matter distribution on conventional T1-weighted 1 H images and to perfusion images from arterial spin labeling. Conclusion Hyperpolarized 129 Xe MR imaging is an injection-free means of imaging the perfusion of cerebral tissue. The proposed method images the uptake of inhaled xenon gas to the extravascular brain tissue compartment across the intact blood-brain barrier. This level of sensitivity is not readily available with contemporary MR imaging methods. © RSNA, 2017.

Low-cost high-resolution fast spin-echo MR of acoustic schwannoma: an alternative to enhanced conventional spin-echo MR?

PubMed

Allen, R W; Harnsberger, H R; Shelton, C; King, B; Bell, D A; Miller, R; Parkin, J L; Apfelbaum, R I; Parker, D

1996-08-01

To determine whether unenhanced high-resolution T2-weighted fast spin-echo MR imaging provides an acceptable and less expensive alternative to contrast-enhanced conventional T1-weighted spin-echo MR techniques in the diagnosis of acoustic schwannoma. We reviewed in a blinded fashion the records of 25 patients with pathologically documented acoustic schwannoma and of 25 control subjects, all of whom had undergone both enhanced conventional spin-echo MR imaging and unenhanced fast spin-echo MR imaging of the cerebellopontine angle/internal auditory canal region. The patients were imaged with the use of a quadrature head receiver coil for the conventional spin-echo sequences and dual 3-inch phased-array receiver coils for the fast spin-echo sequences. The size of the acoustic schwannomas ranged from 2 to 40 mm in maximum dimension. The mean maximum diameter was 12 mm, and 12 neoplasms were less than 10 mm in diameter. Acoustic schwannoma was correctly diagnosed on 98% of the fast spin-echo images and on 100% of the enhanced conventional spin-echo images. Statistical analysis of the data using the kappa coefficient demonstrated agreement beyond chance between these two imaging techniques for the diagnosis of acoustic schwannoma. There is no statistically significant difference in the sensitivity and specificity of unenhanced high-resolution fast spin-echo imaging and enhance T1-weighted conventional spin-echo imaging in the detection of acoustic schwannoma. We believe that the unenhanced high-resolution fast spin-echo technique provides a cost-effective method for the diagnosis of acoustic schwannoma.

Quantitative analysis of cardiovascular MR images.

PubMed

van der Geest, R J; de Roos, A; van der Wall, E E; Reiber, J H

1997-06-01

The diagnosis of cardiovascular disease requires the precise assessment of both morphology and function. Nearly all aspects of cardiovascular function and flow can be quantified nowadays with fast magnetic resonance (MR) imaging techniques. Conventional and breath-hold cine MR imaging allow the precise and highly reproducible assessment of global and regional left ventricular function. During the same examination, velocity encoded cine (VEC) MR imaging provides measurements of blood flow in the heart and great vessels. Quantitative image analysis often still relies on manual tracing of contours in the images. Reliable automated or semi-automated image analysis software would be very helpful to overcome the limitations associated with the manual and tedious processing of the images. Recent progress in MR imaging of the coronary arteries and myocardial perfusion imaging with contrast media, along with the further development of faster imaging sequences, suggest that MR imaging could evolve into a single technique ('one stop shop') for the evaluation of many aspects of heart disease. As a result, it is very likely that the need for automated image segmentation and analysis software algorithms will further increase. In this paper the developments directed towards the automated image analysis and semi-automated contour detection for cardiovascular MR imaging are presented.

Towards integration of PET/MR hybrid imaging into radiation therapy treatment planning

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

Paulus, Daniel H., E-mail: daniel.paulus@imp.uni-erlangen.de; Thorwath, Daniela; Schmidt, Holger

2014-07-15

Purpose: Multimodality imaging has become an important adjunct of state-of-the-art radiation therapy (RT) treatment planning. Recently, simultaneous PET/MR hybrid imaging has become clinically available and may also contribute to target volume delineation and biological individualization in RT planning. For integration of PET/MR hybrid imaging into RT treatment planning, compatible dedicated RT devices are required for accurate patient positioning. In this study, prototype RT positioning devices intended for PET/MR hybrid imaging are introduced and tested toward PET/MR compatibility and image quality. Methods: A prototype flat RT table overlay and two radiofrequency (RF) coil holders that each fix one flexible body matrixmore » RF coil for RT head/neck imaging have been evaluated within this study. MR image quality with the RT head setup was compared to the actual PET/MR setup with a dedicated head RF coil. PET photon attenuation and CT-based attenuation correction (AC) of the hardware components has been quantitatively evaluated by phantom scans. Clinical application of the new RT setup in PET/MR imaging was evaluated in anin vivo study. Results: The RT table overlay and RF coil holders are fully PET/MR compatible. MR phantom and volunteer imaging with the RT head setup revealed high image quality, comparable to images acquired with the dedicated PET/MR head RF coil, albeit with 25% reduced SNR. Repositioning accuracy of the RF coil holders was below 1 mm. PET photon attenuation of the RT table overlay was calculated to be 3.8% and 13.8% for the RF coil holders. With CT-based AC of the devices, the underestimation error was reduced to 0.6% and 0.8%, respectively. Comparable results were found within the patient study. Conclusions: The newly designed RT devices for hybrid PET/MR imaging are PET and MR compatible. The mechanically rigid design and the reproducible positioning allow for straightforward CT-based AC. The systematic evaluation within this study

Inter‐station intensity standardization for whole‐body MR data

PubMed Central

Staring, Marius; Reijnierse, Monique; Lelieveldt, Boudewijn P. F.; van der Geest, Rob J.

2016-01-01

Purpose To develop and validate a method for performing inter‐station intensity standardization in multispectral whole‐body MR data. Methods Different approaches for mapping the intensity of each acquired image stack into the reference intensity space were developed and validated. The registration strategies included: “direct” registration to the reference station (Strategy 1), “progressive” registration to the neighboring stations without (Strategy 2), and with (Strategy 3) using information from the overlap regions of the neighboring stations. For Strategy 3, two regularized modifications were proposed and validated. All methods were tested on two multispectral whole‐body MR data sets: a multiple myeloma patients data set (48 subjects) and a whole‐body MR angiography data set (33 subjects). Results For both data sets, all strategies showed significant improvement of intensity homogeneity with respect to vast majority of the validation measures (P < 0.005). Strategy 1 exhibited the best performance, closely followed by Strategy 2. Strategy 3 and its modifications were performing worse, in majority of the cases significantly (P < 0.05). Conclusions We propose several strategies for performing inter‐station intensity standardization in multispectral whole‐body MR data. All the strategies were successfully applied to two types of whole‐body MR data, and the “direct” registration strategy was concluded to perform the best. Magn Reson Med 77:422–433, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine PMID:26834001

[Current practice in MR imaging of the liver].

PubMed

Kanematsu, M; Kondo, H; Matsuo, M; Hoshi, H

2001-12-01

MR imaging, which is able to evaluate T1- and T2-relaxation time, fat, hemorrhage, metal deposition, blood flow, perfusion, diffusion, and so on, has offered more information for the diagnosis of diffuse and focal hepatic diseases than CT. The spoiled-GRE sequence with high contrast resolution and ease of the aimed contrast capture derived from the k-space property, with the use of a phased-array multicoil, have remarkably increased the value of gadolinium-enhanced dynamic MR diagnosis of the liver. In recent years, the clinical use of ferumoxide has begun, and issues concerning the superiority or inferiority and combination of contrast media are being debated. This paper describes the value, role, and clinical practice of unenhanced, gadolinium-enhanced, and ferumoxide-enhanced MR imaging of the liver based on knowledge obtained in our institution, with some reference to the literature.

Morbidity of direct MR arthrography.

PubMed

Giaconi, Joseph C; Link, Thomas M; Vail, Thomas P; Fisher, Zachary; Hong, Richard; Singh, Ravi; Steinbach, Lynne S

2011-04-01

The purpose of this study was to determine the incidence and severity of arthrographic pain after intraarticular injection of a gadolinium mixture diluted in normal saline for direct MR arthrography. From March 2009 until January 2010, 155 consecutive patients underwent direct MR arthrography; 20 patients were lost to follow-up. Patients were contacted by telephone between 3 and 7 days after joint injection. Using an 11-point numeric pain rating scale, patients were asked to report if they had experienced joint pain that was different or more intense than their preinjection baseline, the severity of pain, the duration of pain, time to onset of pain, and eventual resolution of pain. The incidence of postarthrographic pain was 66% (89/135), with an average intensity of pain of 4.8 ± 2.4 (range, 1-10). Postarthrographic pain lasted an average of 44.4 ± 30.5 hours (range, 6-168 hours). The time to onset of pain after joint injection was on average 16.6 ± 13.1 hours (range, 4-72 hours). There was no significant difference regarding the severity or incidence of postarthrographic pain between groups on the basis of patient age (p = 0.20 and 0.26), patient sex (p = 0.20 and 0.86), contrast mixture contents (p = 0.83 and 0.49), or joint injected (p = 0.51 and 0.47). No patients experienced any other serious side effects. Sixty-six percent of patients who undergo direct MR arthrography will experience a fairly severe delayed onset of pain that completely resolves over the course of several days.

Feasibility and safety of adenosine cardiovascular magnetic resonance in patients with MR conditional pacemaker systems at 1.5 Tesla.

PubMed

Klein-Wiele, Oliver; Garmer, Marietta; Urbien, Rhyan; Busch, Martin; Kara, Kaffer; Mateiescu, Serban; Grönemeyer, Dietrich; Schulte-Hermes, Michael; Garbrecht, Marc; Hailer, Birgit

2015-12-22

Cardiovascular Magnetic Resonance (CMR) with adenosine stress is a valuable diagnostic tool in coronary artery disease (CAD). However, despite the development of MR conditional pacemakers CMR is not yet established in clinical routine for pacemaker patients with known or suspected CAD. A possible reason is that adenosine stress perfusion for ischemia detection in CMR has not been studied in patients with cardiac conduction disease requiring pacemaker therapy. Other than under resting conditions it is unclear whether MR safe pacing modes (paused pacing or asynchronous mode) can be applied safely because the effect of adenosine on heart rate is not precisely known in this entity of patients. We investigate for the first time feasibility and safety of adenosine stress CMR in pacemaker patients in clinical routine and evaluate a pacing protocol that considers heart rate changes under adenosine. We retrospectively analyzed CMR scans of 24 consecutive patients with MR conditional pacemakers (mean age 72.1 ± 11.0 years) who underwent CMR in clinical routine for the evaluation of known or suspected CAD. MR protocol included cine imaging, adenosine stress perfusion and late gadolinium enhancement. Pacemaker indications were sinus node dysfunction (n = 18) and second or third degree AV block (n = 6). Under a pacing protocol intended to avoid competitive pacing on the one hand and bradycardia due to AV block on the other no arrhythmia occurred. Pacemaker stimulation was paused to prevent competitive pacing in sinus node dysfunction with resting heart rate >45 bpm. Sympatho-excitatory effect of adenosine led to a significant acceleration of heart rate by 12.3 ± 8.3 bpm (p < 0.001), no bradycardia occurred. On the contrary in AV block heart rate remained constant; asynchronous pacing above resting heart rate did not interfere with intrinsic rhythm. Adenosine stress CMR appears to be feasible and safe in patients with MR conditional pacemakers. Heart rate response to adenosine

Nonalcoholic Fatty Liver Disease: Diagnostic and Fat-Grading Accuracy of Low-Flip-Angle Multiecho Gradient-Recalled-Echo MR Imaging at 1.5 T

PubMed Central

Yokoo, Takeshi; Bydder, Mark; Hamilton, Gavin; Middleton, Michael S.; Gamst, Anthony C.; Wolfson, Tanya; Hassanein, Tarek; Patton, Heather M.; Lavine, Joel E.; Schwimmer, Jeffrey B.; Sirlin, Claude B.

2009-01-01

Purpose: To assess the accuracy of four fat quantification methods at low-flip-angle multiecho gradient-recalled-echo (GRE) magnetic resonance (MR) imaging in nonalcoholic fatty liver disease (NAFLD) by using MR spectroscopy as the reference standard. Materials and Methods: In this institutional review board–approved, HIPAA-compliant prospective study, 110 subjects (29 with biopsy-confirmed NAFLD, 50 overweight and at risk for NAFLD, and 31 healthy volunteers) (mean age, 32.6 years ± 15.6 [standard deviation]; range, 8–66 years) gave informed consent and underwent MR spectroscopy and GRE MR imaging of the liver. Spectroscopy involved a long repetition time (to suppress T1 effects) and multiple echo times (to estimate T2 effects); the reference fat fraction (FF) was calculated from T2-corrected fat and water spectral peak areas. Imaging involved a low flip angle (to suppress T1 effects) and multiple echo times (to estimate T2* effects); imaging FF was calculated by using four analysis methods of progressive complexity: dual echo, triple echo, multiecho, and multiinterference. All methods except dual echo corrected for T2* effects. The multiinterference method corrected for multiple spectral interference effects of fat. For each method, the accuracy for diagnosis of fatty liver, as defined with a spectroscopic threshold, was assessed by estimating sensitivity and specificity; fat-grading accuracy was assessed by comparing imaging and spectroscopic FF values by using linear regression. Results: Dual-echo, triple-echo, multiecho, and multiinterference methods had a sensitivity of 0.817, 0.967, 0.950, and 0.983 and a specificity of 1.000, 0.880, 1.000, and 0.880, respectively. On the basis of regression slope and intercept, the multiinterference (slope, 0.98; intercept, 0.91%) method had high fat-grading accuracy without statistically significant error (P > .05). Dual-echo (slope, 0.98; intercept, −2.90%), triple-echo (slope, 0.94; intercept, 1.42%), and

Evaluation of PET and MR datasets in integrated 18F-FDG PET/MRI: A comparison of different MR sequences for whole-body restaging of breast cancer patients.